1 00:00:03,919 --> 00:00:05,430 all right today we're going to talk about protein folding and its relation to linkage folding we're going to look at sort of a mechanical model of proteins this is an example of a protein from lecture one there's a ton out there in this place called the protein data bank all freely available it's really hard to get pictures like this but you get some idea that there's a linkage embedded in here you see various little uh spheres and edges that's of course not reality those spheres are actually atoms and they're the kind of amorphous blobs the edges are chemical bonds and those are connections we don't know whether they're it's not really matter but it's a force this is a rather messy picture this is what a protein folds into some 3d shape most proteins fold consistently into one shape we don't really know how that happens we can't watch it happen so we the big challenge is to know how proteins fold given a protein what does it fold into that's the protein folding problem major unsolved problem in biology biochemistry the protein design problem is i want to make a particular 3d shape so that it docks into something binds to a virus whatever what protein should i synthesize in order for it to fold into that shape that is potentially an easier question algorithmically it's the really useful one from a drug design standpoint you come up some some new virus comes along you design a drug to attack it and only it you build it usually you would manufacture some synthetic dna you feed it into a cell dna goes to the rna goes to the mrna goes to the protein you all remember biology 101 hopefully we don't need to know much about it if you look at what's called the backbone of the protein protein is basically a chain and attached to the chain are various amino acids today i'm going to ignore the amino acids which is a little crazy and just think about the backbone chain backbone chain looks something like this um one of the challenges of video recording a class is i can only use copyright free or creative commons images this one i couldn't get one so i had to draw it there's various measurements here certain numbers of angstroms those are the chemical bonds various uh atoms here nitrogen carbon so on hydrogen but basically it's a chain zigzags back and forth you can also see the angles here they're not quite all the same but they're very similar all the lengths and the angles are close so uh it zigzags this is really in three dimensions and try to draw the sphere so you can see the three dimensionality but it's a little tricky and then attached on the sides are the amino acids i'm going to focus just on the backbone the way this thing is allowed to fold these lengths as far as we know are are pretty static they probably jiggle a little bit but you can think of them as edges so you can think of this as a linkage the catch is also the angles are fixed because the way this atom wants to bind to other things has very fixed angle patterns if you ever played with a chemistry construction set that's that's how they work to have holes at just particular angles so if you think of like a robotic arm normally uh like here i have a two edge robotic arm let's say normally you have two degrees of freedom in three dimensions you can change the angle and you can spin around this edge now i'm saying the angle is fixed for example here it's say at 90 degrees all i can do is spin i'm not allowed to flex my muscle in this way okay so that is the model all of in this case we have a tree all of the angles here are fixed but you can still for example take this entire sub chain and spin it around this edge that'll preserve all the angles and all the lengths that's all you're allowed to do you take an edge you spin it spin once half of the edge relative to the other half these are called fixed angle linkages and they've been studied quite a lot because of their connection to protein folding so embedded in the term linkage we assume that the edge lengths are fixed and then we add the constraint that the angles are fixed and the motivation is the backbone is something like put the background of a protein is something like a fixed angle tree of course it's not much of a tree most of it is a chain there's just small objects hanging off and if you add the amino acids there are bigger things hanging off but still constant size they'll have some cycles they're not trees but it's slightly more approximately maybe i should draw wavier lines uh it's a chain usually an open chain although occasionally closed chain so we think a lot about fixed angle chains and sometimes about fixed angle trees now fixed angle linkages are harder to think about than universal joints that's the usual kind of linkage um so and we know 3d linkages are kind of tough nonetheless we found lots of really interesting mathematical problems to solve here and that is the topic of today at some level we are thinking about the mechanics of protein folding we're throwing away energy we're throwing away the the actuators in real life that make proteins fold we're just imagining given this mechanical model of how a protein might fold what's possible so it's some sense it's broader than reality and the hope is you find an interesting algorithm for how to fold these protein chains maybe that's the algorithm that nature is implementing that's the kind of general picture we're not constrained by reality and by how nature actually folds things so i'm going to talk today about four main problems here first one's called span second one's called flattening third one is flat state connectivity and the fourth one is locked our good friend locked chains and of course there are lock chains because we're constraining linkages even more than before so if you take knitting needles it'll still be locked because you add extra constraints makes it harder to fold but there are actually some interesting positive results we can give of chains that are not locked in some sense and flat state connectivity is about the same kind of thing instead of worrying about getting from anywhere to anywhere we just worry about getting from one flat state to another flat state flat means lying in a plane flattening is about is there such a configuration and span is about given robotic arm like a more complicated one like with multiple edges how far apart can the endpoints get and how close can the endpoints get the universal chain is not very exciting the farthest thing is when it's straight and the least far they can get is when it's closed and you can always do that i think well no i guess you can't always close it up that's a little non-trivial but for fixed angle linkages you can't straighten out because you have to preserve the angles so it's kind of what is the straightest like configuration given that the angles are fixed so let's start with span so the span of a configuration is the distance between the endpoints and in general you'll find the max span and the min span this search was begun by a guy named mike sauce who was a phd student at mcgill and he proved that if you want to find for example flat state that lives in two dimensions with the minimum or the maximum span this is np hard this is in his phd thesis question oh here i'm assuming open chain i should say that which most proteins are yeah i've been talking about trees and stuff i hear i mean chain otherwise there aren't two end points to think about good uh so here are his np hardness proofs in fact the problems are mp complete they're pretty simple the problem here we're reducing from is partition i give you a bunch of integers i want to divide them into two halves of equal sum and the top example is minimum flat span problem so you have you make an orthogonal chain where the horizontal edges are long and they're proportional to the integers you're given and the vertical edges are really tiny and so what you'd like to do what all you can do is sort of flip in the because you have to stay in the plane you can flip one of the vertical edges say and make any of these edges go left or right you get that freedom but so each integer you get to choose do i go right by that amount and go or do i go left by that amount and if the amount you go left is equal to the amount you go right in other words there's a partition into two equal sums then those endpoints will be aligned and then their distance will be very tiny otherwise it will be quite large because the horizontal distances are all big so that's kind of an e very easy np hardness proof to maximize your flat span instead of mapping your integers onto lengths you map them onto angles or turn angles i won't specify that too precisely but again if you if you make your total counterclockwise turn equal to your total clockwise turn then the two end edges which are super super long will be parallel and to maximize the distance between the endpoints you want them to be parallel if you make them go some other angle they're closer now both of these proofs rely on the requirement that you want a flat configuration with minimum and maximum span now there's a claim that flat configurations matter for proteins so it's a natural constraint but what about the general problem what about i have something in three dimensions i want to maximize i have a fixed angle chain in 3d maximize or minimize the span both of those problems are open can you solve them in polynomial time for 3d max span so the non-flat version just for maximization there's been a lot of work and there are two papers on the subject one of them is by nadia and joe o'rourke another one is by borsea and stranu and i just want to quickly summarize that because there's a lot of stuff there but essentially they find what the structure of those spans look like i have an early figure that's in our book before all this work was done of a simple chain this black guy one two three four bars open chain and in that black three-dimensional state it maximizes the span the the green span there and if you look from above which is this picture of course the endpoints look much closer in in projection and the red configuration is the max span if you restrict to flat configurations so here of course 3d buys you something in general it always will an interesting thing is that this max span the green line passes through another vertex that seems kind of weird and in fact there's a general theorem there sort of characterizing the structure of these chains it's still not known whether we can solve this problem in polynomial time but for orthogonal chains where all the angles are 90 degrees uh we can solve that in linear time i guess and here's what it looks like suppose you have some orthogonal chain orthogonal chains are nice because you can draw them in a plane as a staircase so there's a nice canonical configuration what one way to think about how to find the maxspan configuration i'm just going to give a high level overview here this won't be a complete algorithm is you triangulate that staircase in this sort of obvious way of connecting every endpoint to the one to a head this you can think about this is like a body that's hinging around here because i can spin if i spin the left part of this chain around this edge it's like hinging that triangle around that hinge same thing you can think of these triangles as just being hinged together like in rigid origami it's the same class of motions and now you can uh what i'm going to do is compute a shortest path in this surface from here to here confusingly this is called a geodesic shortest path although it's not really related to geodesics from polyhedral surfaces but if i compute a shortest path it's going to go like to this vertex and then probably to that vertex but i'm constrained to say stay inside the unit of those triangles i want to go from one endpoint to another then i claim that okay the these two edges will stay planar of course they form a triangle uh i claim these four edges will stay planar and in the orthogonal case they'll stay zigzag and then also these two guys will stay in their own plane and then uh i claim that actually this wiggly line which is not straight because it bends here and it bends here the total length of that wiggly line is the max span and you achieve that by folding this planar part with respect to this planar part with respect to this planar part so that the wiggly lines become aligned and straight and that's very hard to draw but it can be done and that's what you do in the orthogonal case and that gives you the answer in linear time with enough work for non-orthogonal though it's open whether you can do this in polynomial time maybe it's np hard actually i don't know all right that's all i want to say about span next we go to flattening i guess the first question about flattening and and the main one we'll we'll talk about here until we get to flat state connectivity is does a fixed angle chain have a flat state at all can you even draw it in the plane without crossings so we're restricted here to have no no self intersections we want a flat state no self intersection then there would be a question of given some configuration can actually continuously get to a flat state but sort of the simplest question is ignore about getting ignore getting there just is there a flat state and this problem is np-hard again mike sauce and his advisor godfrey toussaint it's a little more complicated but it's basically the same idea as that very simple proof which was just to map integers to a little zigzag staircase here so the goal is to force x to end up being the two endpoints of the green curve to be aligned with each other that will exist if and only if there is a partition of the given integers and there's all this infrastructure this sort of uh there's a little lock here and a key and and some structure on the left basically forces the picture to look like that um so the first claim is that the black stuff is basically unique i think there's one global reflection you can do that doesn't affect anything but you try any of the other flips again we're restricted to flat states here so there's only sort of a bounded number of things you can do finite number of things you can do you try all of them they self-intersect so the black thing is basically forced and it forces the end point this endpoint x from the black side to be aligned with this very narrow spike and because the angles are preserved that red guy is going to be vertical it can't go down so it must go up and so only if this thing is aligned in the center aligned with x in other words this problem has a partition will this have a flat state so it's not the most exciting example this is only a weak np hardness proof lots of interesting questions still open here like if all the lengths are the same if they're all equal then we don't know or if all the lengths are even polynomially bounded this needs really really long lengths versus really really tiny lengths exponentially exponential and ratio all these problems are open and that's flattening so we're going very quick uh because there isn't uh well partly because i'm more excited about this but there's more work in these two parts so i'm gonna focus on that next topic is flat state connectivity so the idea is to think about the configuration space of these fixed angle chains let's say and we kind of know that it's going to be disconnected because there are knitting needles there are nasty things so there's maybe various connected components but let's say that we really care about flat states and the question is are they connected to each other so in other words do all the flat states mark them with x's do they all appear there's only finitely many so configurations there's it's this continuum and there are these messy blobs semi-algebraic sets but flat states those are discrete things because we have fixed angles you can flip or not flip every edge so most exponentially many of them so finite are they all in one component so i can get for if i pick two of my favorite flat states there's a path between them or are some of them in multiple components so in this case we call it flat state disconnected and if they're all like this we call it flat state connected and we just like to know which chains which fixed angle trees whatever are flat state connected versus flat state disconnected i would say the big the big open problem here is our is every flat as every fixed angle chain open chain flat state connected that is still open we have lots of results in in that direction so the top four results are about open chains but they have an extra constraint example open chains that have a monotone configuration like the staircase those are flat state connected and so in fact whenever the angles between the edges are either orthogonal or obtuse then their flats stay connected when the angles are acute we're not really sure if all the angles are equal and acute then we can do it but if they're different and acute we don't know unless the edges are all unit length and the angles are in this funny range then we can do it so there's all these special cases we can solve the most relevant to proteins is actually obtuse chains so we've solved sort of the main problem with this second result but there's a natural theoretical question here is are all open chains flat state connected or do we get disconnectivity i will show you that i'll show you the orthogonal case in a little bit we can do some stuff we have multiple chains that are attached to some blob like a cell closed chains is a little bit for disconnected uh we don't have very interesting examples i would say this is funny because locked examples are easy to come by but flat state disconnected examples are a little trickier because flat is so constrained so let me just show you these examples this is what we call a partially rigid fixed angle tree so not only are the angles fixed but also the black edges are not in fact only the blue edges here are allowed to spin everything else is held rigid so these arms are somehow forced to be in exactly that geometry i can spin it around this edge just spin it up into 3d for example these are two different flat states of the same linkage right all i all the only difference between these two i haven't rotated or anything is i've taken each of these arms and flipped it around a blue axis if i do all four of them i would get this picture but the claim is you cannot do that without self-intersection the intuition is when there aren't very oh one other thing this makes this slightly more interesting it's weird to say well why did you force some of the edges to be rigid and not others one way to force that is to use a general graph if you add some extra edges to sort of brace this and all these angles are fixed then this linkage will behave exactly like that one so that at least is somewhat more natural although what we really care about are chains maybe trees but we don't know whether there's a we also don't know whether all true fixed angle trees are flat state connected these are the the worst examples we know let me give you an idea of why that it doesn't work this is a little animation of just a couple of moves attempted it's just going to cycle through that and these are some static images of same kind of thing so the intuition is the following you have four arms you have two sides to the plane there's up and down for four arms and two sides at least two of them are going to have to go to the same side the best you can do is two and two or three and one but in either case you have two sides go to the two arms to go on the same side now it could be like in this image that they're opposite arms so there's this arm here and there's this arm here so they're connected by 180 degree angle and those guys when they fold up actually these edges will just hit each other dead on so that's uh kind of obvious from a geometric standpoint maybe you call it cheating for them to hit dead on you can twiddle the edge length so that they will properly intersect without dead-on collision without being degenerate basically the alternative is the and this is a little harder to see geometrically and that's why we drew that animation is that you have you have one arm and you have an adjacent arm connected by a 90 degree angle now here there's clearly some collision going on and if you happen to fold it up 90 degrees like that and then fold the other guy obviously you get stuck but maybe you fold it a little bit and the other guy goes a little bit more and there could be some dance between those two degrees of freedom those two arms that somehow gets them both to pass over to the other side it's obviously not possible how do you prove it well you can prove it with topology not not theory or link theory so it's very cute proof uh you start with so here's the the full example but i've highlighted the two arms in red that are going to move and i imagine connecting the endpoints of each arm with these little blue ropes underneath the plane so all right they they're both going on the same side let's say that somehow pass through each other on the top side then i'm free to connect stuff on the bottom and i shouldn't collide with that so if somehow both of these guys flip over so the arm on the left a3 flips over a3 stays where it is but now the arm is on the top the north side instead of the south side and the other guy from b to b3 used to go like this and now it goes like this if that happened somehow then these ropes could remain intact during that whole motion and on the top you have two closed loops that are not interlocked on the bottom you have two closed loops that are interlocked so there's no way to get from there to there without colliding somewhere the blue stuff didn't move so the red stuff must have collided so even just topologically you are screwed that is our only negative example lots of interesting open questions here on the positive side let me show you for orthogonal chains and the same algorithm works for obtuse chains all the angles are obtuse uh how they are flat state connected so in order to show its flat stay connected i take i want to think about two flat states and show that i can fold from one to the other via some intermediate 3d stuff let's start with one of the flat states so it's orthogonal so in two dimensions they really all the edges will be horizontal or vertical in 3d they can kind of be in many many different angles many different dihedral angles in 2d it's pretty simple and all i need to do is sort of pick up that chain and i'm going to try to pick it up into a staircase because there's only one staircase if i can make it a staircase i make configuration flat configuration a staircase flat configuration b staircase i just fed x in the middle right once they're both staircases i play one motion and the other one backwards get from anywhere to anywhere so here's all you do you take the first edge and you just rotate it up to the red line a uh and then you take the next edge and you take both of those edges and you just rotate them like this so you get that little two-step staircase now i'd really like to pick up this edge but i want to first get these two edges in a plane with that edge so i rotate this flag over to the left i get those two guys and now they're in a plane with this and i just lift that up then i'm going to flip then rotate up flip rotate flip rotate here's some more examples so if at this point i have this staircase um sorry i guess originally i have from v3 to d up there i it's not in plane with this guy so i just rotate it like that i'm spinning around this edge so now i have from v3 to e and then i rotate it up along that green arc and i get a bigger staircase above the chain and because everything's staying above it will never penetrate the plane it'll never hit anybody else and i'm building a staircase by design i always rotate this there's actually two ways i could be in plane but i always rotate it so that when i pick some an edge up it'll be in a staircase so this is actually really easy and slight generalization is to obtuse chains then instead of making a staircase we make a monotone get this right yeah some z monotone state so it goes monotone and z out of the plane and that's enough to avoid collision and you get a canonical configuration also if you have acute angles but all the angles are equal then there's a natural canonical state which is just like a compressed staircase and that will work here too although that takes more effort that was in a separate paper but big open question is chains with arbitrary angles we have no idea it seems very hard to do an operation like this wow we are burning through this is fun so the next topic is about locked chains now as i said you can take a knitting needles example which has five edges and that will still be locked if you force the angles to be fixed because it was locked without the angles being fixed now it required a length ratio of uh three to one i think yeah this edge had to be longer than the sum of those three uh so let me put down uh some open problems so you may recall in the case of universal chains universal joints i should say the big open question was can you lock a universal joint 3d chain with unit edge lengths so equilateral every edge is the same length is there a lock chain like the knitting needles where all the edge lengths are the same and one of the motivations for that is in proteins the edge lengths are all within like 50 of each other so it's pretty natural of course we don't have universal joints with proteins we have fixed angle joints so the big open problem for fixed angle joints i guess we'll do this in parts is there a locked 3d fixed angle chain that's equilateral okay i'm going to add some conditions here so that's first natural question knitting needles doesn't suffice we need a three to one length ratio as far as we know uh yeah turns out that question is not very interesting i need to do slightly non-linear editing here so you take a knitting needles example and you just subdivide the edges into lots of little tiny bars it doesn't have to be this extreme you could not subdivide these edges at all and make these guys subdivide them into like three or four parts because the angles are fixed these guys act as a single bar there's really no difference maybe you make slight curve there and then they can wiggle they can bend a little bit but really not much so if you just say oh i want it to be unit length i don't constrain what the angles are but i fix them then it's trivial to come up with locked examples so that's not very interesting what if i make it not only equilateral the lengths are the same if i make it equally angular because again in proteins all the angles are similar they're around 110 108 something like that they're all pretty close within if i think within 10 20 of each other well here there's also a locked example and just to show you how research was done back at the turn of the century this is pre web 2.0 pre-ajax and all that fancy stuff we used ascii art this was email was the tool of choice i know it's hard to imagine a time 2002 so long ago and i i tracked this down this is the original claim where it looks we call this the crossed legs example because it's like two legs crossed around each other and uh this is the the first time we thought oh maybe it can be done unit length this is stefan langerman and uh and here for the first time ever this is not the first model but this is the first photograph of any model i'm aware of this is the cross legs example um this is made with a construction toy that used to be sold around here but is no longer in production it's hard to so they're pretty hard to get is straws nicely colored straws and the cool part are these uh these connectors so the connectors force particular angles in this case every angle is 45 degrees so this is equiangular and equilateral because all the straws i'm told are the same length that's how they're sold and you can do edge spins so whoops that's called cheating it's not totally obvious that this is locked the problem with the model is that the edges can bend but if you treat it properly and only spin around edges then you're you're stuck now there is one thing you can do let me see if i uh yeah like this so here i'm almost in a plane i've got the purple edge right against the pink one is it easier to see from that angle i don't know so here this guy can come out and this guy can barely go along the edge so actually this doesn't quite work for equilateral it works for one plus epsilon that's why i added these little nubs at the ends so if it if they're all exactly equal length and you allow just a abrasion of the endpoint then this could go around like that and then you'd be unlocked if you just add slightly either you change the angles to be not quite equal so ben make this a little smaller or you make the lengths a little bit longer at the ends then the claim is it's locked we don't actually have a formal proof of this we're just remembering hey we should probably write this up i was talking to stefan last night and uh yeah so someday we will prove that this is locked but certainly looks like it so this isn't open yet i mean modulo the details of that proof equilateral and equiangular seems easy to lock with fixed angle chains in fact even easier that this example only has four edges so even less than the knitting needles fixed angles make for complicated motions i guess make it hard to unlock things so i need to add one more constraint and the constraint is obtuse so again all of these properties are enjoyed by proteins protein protein backbones have all these properties even if you looked at fixed angle trees is there something like this that's locked and now we don't know and this seems quite tricky i guess the intuition is that obtuse or and usually we think about orthogonal just because it's easier to draw the pictures but reality is more like 108 degrees uh conjectures of two chains obtuse fixed angle chains behave kind of like universal joints and with universal joints we don't know whether equal equilateral is enough so it's tricky what if you instead had like made your ribbon lengths basically like a bunch of little unit obtuse angle connectors and then when you hit the the big turns it's just you know up to yeah you can definitely you can make this example be entirely obtuse you can make every angle obtuse here you could arc a little bit here you could arc some more but not too sharp and because here we actually know that this part can be made a string we don't really care what it looks like so you can make it fairly obtuse it's just that these guys should not bend much they have to be long no matter how you fold them so if you want equilateral and obtuse that's also easy but to make all the angles actually be equal as far as we know you cannot take that knitting needle subdivided make all the lengths equal and all the angles equal and make them obtuse that's open but any two out of the three it's easy uh of course in reality they're not quite equilateral they're not quite equal angular but it's still open for the if you have like a small range for the lengths and a small range for the angles this is open we pose it this way because it's the cleanest geometrically but the the real question you care about is when these are fuzzy constraints obtuse is real but these guys are fuzzier so uh if you think about proteins uh which fold very well in nature there are a couple of reasons they might fold well we know as far as fixed angle chains go it's actually quite easy to find locked examples and this is somewhat intuitive but bear with me because there are locked examples in this configuration space we believe these configuration spaces are really ugly nasty so it would be very hard even if you know oh i only need to fold something in my component if these guys are highly disconnected and flat states are all over the place it's probably even within this connected component it looks really ugly and so it's very hard to find a path from one state to another probably p-space complete although we don't know that for sure but that's the intuition locked equals messy when there are no locked configurations like carpenter's roles we get really nice algorithms it's super easy to get from state a to state b now if you're nature or you're designing nature let's say or you're building your own virtual world second life and you want to design proteins you would like to design them in such a way that they fold easily because it happens all the time every thing that is being acted on by our body every living thing that we know has tons of little proteins that are doing all the work they are fold into their shape and they do something that's proteins plus rna but mostly proteins so uh to understand life we should understand proteins now how do proteins fold so well when we know there are all these locked configurations one possible answer is that proteins have extra structure namely these three things which somehow make it very easy to algorithmically go from a to b notice i'm not even i'm not assuming anything about how proteins fold in terms of what is the mechanism that drives them because we don't really understand those mechanisms there's hydrophobia which we don't really know how it works it's all these little forces um that we don't fully understand lots of we understand lots of parts of the story but not the whole story and what's convenient about these kinds of problems is you don't need to assume anything about how it actually happens all we're assuming is the mechanical behavior of proteins and how they could possibly fold and the the idea is if there's a lot configurations that's probably the wrong model because then everything's messy now there's also evolution coming into play and maybe some proteins are easy to fold some proteins are hard to fold that's an interesting question which should be experimented with but let's hope that there's a model things are mutating randomly you really like everything to fold nicely maybe it's because you have all three of these properties approximately in real proteins so the general idea is that nature has some extra constraints that make protein folding easy we just have to figure out what they are and why it makes them easy unfortunately this is still an open problem if this had an algorithm that would be a natural candidate for what nature is doing using its mechanical or using its for energies and forces and so on this would be a rather unsatisfactory ending if this was if the climax was an open problem we have a theorem too and this is what i'll cover in most detail and it's paper called producible protein chains protein chains just means fixed angle chains open chains and the idea is well yeah there are these constraints uh or there are these extra features we don't know how to exploit them so let's not even worry about them suppose they don't even exist maybe i'm going to assume obtuse but none of the others there's another constraint in how proteins fold or really how proteins are created they're created by a machine a molecular machine made up of a whole bunch of proteins and rna called the ribosome you may have heard of it translates messenger rna into proteins so there's some mrna around here maybe don't know exactly how this machine works but there are actually very accurate three-dimensional reconstructions of the ribosome with no copyright free images you're going to have to there's a link on this slide that goes to the cool amp 3d models of the ribosome with a slice away so you can see this there's a tunnel down here and the prot the protein gets sort of created here the backbone gets created here and starts going through this tunnel there's a bend in the tunnel around here where it's conjectured an amino acid gets attached and then that it goes out the tunnel and the protein starts spewing out here and presumably folding at the same time we don't really know so this is how proteins are created um the birds and bees i guess of proteins so what's interesting about this is it's not like a protein exists and then folds which is how a lot of people might think about it at first glance that's natural way to model protein folding you start with a protein say in just zigzag configuration if it's obtuse there's a nice zigzag monotone configuration then you see what is the best configuration i could fold into for some notion of best and that's sort of what this configuration space picture is about it's if i already have a protein what configurations can i reach by motions and that is interesting that's important because you're still going to have to reach by emotion but it's actually more flexible than that because protein could just be partially built the the rest of the protein hasn't been built and it could start folding already and it might be easier to fold when you don't have the obstacles of your existing protein so that's both a worry but it's also a convenient structure because this ribosome is a giant obstacle it's bigger than most proteins there if your protein is really long maybe it could go over here but most of the time it's going to stay on one side of this plane because locally this thing is basically flat if you look at the real 3d pictures not the schematic now this is good news for a geometer because there's this giant obstacle think of it as a half space which the protein cannot penetrate while it's being produced over here that's it that half half space constraint is enough to get really good algorithms for folding your chain it's weird because we've made our problem both harder because the protein is only partially produced at any time and it can fold which is part of it but we've also made our life easier because there's this big obstacle yeah right we're out of this we're going to get that the angles in the protein are constrained and in particular for this angle uh it depends i mean you could in this picture because it's perpendicular here yeah uh you can the the sharpest angle you can make is 90 degrees more or less that's a good point so it's a convenient match between the chemistry which also forces the angles to be obtuse i guess i don't know a ton of chemistry but also the ribosome just geometrically forces we're going to use a property like that our model is going to be a little bit more both more general and simpler we're going to imagine that the ribosome is a cone it's part of the upper cone here this is like a mirror image and in reality that cone is actually a plane and everything above the plane but to be more general we're going to allow some angle alpha here it's also just easier to think about when alpha is smaller than 90 but it's work everything i say will work when alpha equals 90 and that is sort of the reality case so so the model is so the ribosome is a cone who we call this the half angle of the cone from the vertical axis to the edge of the cone is alpha so if you're going from one axis to the other would be two alpha the the model is you start with one link of your chain which is inside the cone it spews out uh through the apex okay that's that's the exit of the tunnel here we're allowing the tunnel to be actually quite free it doesn't have to be perpendicular to the to the apex or the plane of the apex so the edge comes out and as soon as the vert the end point of the chain reaches here then a new link is created this is like a very simple model for how a chain can come out of a cone without worrying about what's happening inside the cone imagine everything's totally free this is like you can allow self-intersection the cone who knows what but once you come outside the cone you're not allowed to self-intersect and you're not allowed to intersect the cone once you come out you can't go back in so that is a model of producing protein chains and if you have a cone of angle alpha we call this an alpha producible chain for whatever reason we often call it a beta producible chain just change the variables so if you think of the ribosome as a cone with half angle beta you can produce it like this that is beta producible now this is a pretty powerful model because you only have to worry about it link by link you don't have to worry about the rest of the chain until it gets spews outside of the cone but it's restrictive in that you cannot penetrate the [ __ ] all right one thing we can talk about is angles so i'm gonna write call a chain a less than or equal to alpha chain if all the turn angles are less than or equal to alpha i don't know if i've used turn angles in this class probably if i have two edges the angle would be this the turn angle would be this supplement yeah i guess we use trit angles way back in origami land kawasaki's theorem and so on it's just if you're going straight how much do you have to turn to get to the next edge so we'd like uh fairly obtuse things so alpha's going to be small there isn't a ton of turn but in general less than or equal to alpha chain for some alpha now there's a relation as jason was mentioning there's a relation between alpha and beta in the ribosome because you always exited orthogonally to the the plane that was your cone the sharpest angle you could get was 90 degree turn angle here we're a little freer because this edge can wiggle around as long as it touches the apex so if you're up against the cone you have to slide out into the complementary cone that was the previous picture and as soon as you get there you could create a new edge which is like this so the sharpest angle you can get is actually twice beta in general we're going to have alpha over 2 is less than or equal to beta that is you can get up to beta equals 2 alpha get that right and also in the obtuse case this is not too exciting but it's true uh there's actually some open problems here when you have that full flexibility and you set um sorry alpha to two beta not the other way around uh i'm going to assume here that alpha equals beta this will be convenient and it's the interesting case because in reality the cone has a half angle of 90 degrees so beta is 90. and the sharpest angle we're going to make is always obtuse so saying that you have a less than or equal to 90 chain is just fine but in on the mathematical side i think we solve the case when alpha is less than or equal to beta um but not when alpha over 2 is less than or equal to beta that's a weaker constraint so there is a range where it's not so easy all right now what do i claim about these chains other than their angles are not so sharp i claim they're good algorithms for folding them what could i possibly mean there are still locked configurations is that true well yeah i mean presumably this is acute but you take the obtuse versions of this guy because i didn't constrain the edge links or anything i just said that they're that the angles are obtuse so i could just sort of round these corners make it obtuse you know add lots of dots just at the corners that will be obtuse and a chain like this will be producible a chain with these angles and these edge links can be produced from a cone but this configuration of this chain cannot be produced i claim i claim anything that can be produced is in one connected component so while i can make a linkage that is locked in that there are bad configurations you can't get out of the things you can actually make you can always get out of so there's going to be the space of producible configurations uh maybe there's some stuff that's unproducible but still connected to it i don't i don't know doesn't matter too much i won't worry about this stuff there's other bad locked configurations that you cannot cannot reach here but everything that's producible is in one connected component of the configuration space that's property one that's kind of nice also all the flat states are going to be in here this is actually pretty easy i just need to prove that flat states are producible which we'll worry about later so in particular these guys are flat state connected all the producible protein chains are flat state connected that's interesting because we don't even know that all chains are flat state connected but here i guess we know that obtuse chains are flat stay connected so maybe it's not so surprising but what's important is not only are the flat states connected to each other and the producible states are connected to each other but producibles connected to flat flat states everything is together here i might have more properties but that's already some good news and there's algorithms to do all of this how do we prove it well as usual we use the fedex method and some since one of the challenges is what is the natural canonical state for protein chains in fact we're just going to assume that our chain is in reality we're going to assume that it's an orthogonal chain an obtuse chain i should say but in general for any lesser equal to alpha chain for whatever alpha you like and it will be the half angle of the cone so alpha equals beta we will define a canonical configuration i think we called it the alpha ccc so it's going to be kind of like a helix i think i have an example an actual computed example that's not the best picture because you can't see everything that's going on but this will this is an actual canonical configuration of a particular chain let me tell you how it works in general so in general we have some chain v1 v2 sorry starting at v0 v1 v2 um i want to define a canonic and there's defined lengths between the two and there's defined angles between every triple in sequence so i'm going to start with v0 somewhere it doesn't really matter by translation say the origin of space and what i'm going to do is draw a cone whose apex is at v0 and the half angle here is going to be alpha over 2 not alpha this is a smaller cone than by a factor of 2 than the ribosome that's important so there's this uh vertical line and to pick v1 i'm just going to use this the right edge which is let's say this is the x direction this is the z direction maximum x coordinate it's going to lie on the cone maximum export it that's v1 okay now v1 let me redraw this picture a little lower so there was v0 v1 now i want to draw v2 i want to draw it above so what i'll do is draw a vertical cone whose half angle here is alpha over two and i want to draw v2 on the cone here of course the the height of the cone is the length of the edge not the height but you know this you can think of the cone as infinite and then i just clip this to when it has the right length so again i'm at this might be a different height cone i clip it to whatever the length v1 v2 is i want it to be somewhere on this cone but now i'm constrained to have the correct angle at v1 i can't just put it over here because then the angle here would be 180 presumably i don't want to make 180 degree angle so in reality what happens is that there's a cone which is um who's whose axis is the edge v0v1 so i extend v0v1 out here which in this case happens to lie here and i make a cone like that let me draw it slightly more accurately okay in this case the center axis of the cone would go right here whatever the extension of v0v1 was and to be to have the right angle at v1 v2 must be on that cone conveniently there are two intersection points between those two cones i can choose either one of them to be v2 and i will choose the counterclockwise most one which is this one this is going to be v2 so draw that edge now i repeat so from v2 i'm going to draw a vertical cone whose half angle here the half angle was always alpha over 2. if angle is alpha over 2. this cone had angle or half angle whatever the angle v0 v1 v2 was is that the half angle or the angle the half angle so i think this is right okay and then i take the intersection of those two cones and that will give me where v3 is so i do the same thing for v2 for v3 and so on this i have a unique choice at every moment yeah basically and the only exception was at the beginning here when i had a vertical line these cones two cones could actually be equal and then the intersection is the entire cone in that case i guess i choose the maximum x-coordinate one again and then i'll i have a canonical choice of everything along the way it will always go up and it sort of spirals around because of the counterclockwise most choice and the result is a picture like this anything else i need to say here all right i claim this canonical configuration lies in an alpha over two half angle cone that's true by construction the challenge is does the construction really work so i start obviously with one cone and i can think of this as actually an infinite cone that goes out to infinity here and i claim the entire construction will lie inside that cone and it's kind of obvious because v2 v1 i chose v2 to lie in in this co the same cone just translated up to start at v1 instead of starting at v0 of course this cone is contained in this bigger one and by induction in fact the entire rest of the chain will lie in this smaller cone therefore it lies in the big one also okay fine so by construction it will lie in alpha over two cone the worry is that these two cones don't intersect here we have an angle the half angle of the cone is whatever angle the angle is at v1 sorry this should not be the angle this should be the turn angle that that angle is how much you turn from v0 v1 now we know that we're assuming that the turn angles are all at most alpha this cone so this the the turn angle cone could actually be twice as big as the vertical cone that we were always using we always use a vertical cone half angle alpha over two but because it's okay because we always keep these edges like v0 v1 was on the edge of the cone uh and so if when we extend it it lies on the edge of this vertical cone so its angle in in the most extreme case its half angle is alpha which would look like this would go all the way over from the right side of the cone to the left side of the cone in general it's not going to be right and left but it's going to be some side and the antipodal point and because the double angle of the cone is alpha it's still okay you will intersect somewhere on the cone this is a subtle detail but it's really crucial because we start with a chain that has relatively large angles alpha and we get it into we squeeze it into a cone that still has double twice its angle is alpha but we kind of compress it into something of half angle alpha over two you might think oh i'm just changing the definition calling a half angle therefore i could stand alpha over two but it's a little tricky to actually get it to fit in a vertical alpha over two cone once we have this it's really easy to canonicalize a chain a producible chain so let me tell you how to do that so we're going to use the fedex method of taking some configuration and canonicalizing it and then uncanonicalizing to something else we're also going to use a new method which i just came up with the term it's called the momento method which is you play the movie in reverse so i guess also the merlin method uh that's more complicated so we have a movie here in mind which is how was the chain produced so what i want to show is that if i want to start with a producible configuration and chain somehow it got produced so uh you had your cone and the thing starts spewing out and folding and doing whatever uh that's that's an animation in some sense of of one edge coming out and stuff is folding at the same time then an edge is created then another edge comes out and so on what i want to do is play that movie backwards this is pretty intuitive idea i just want to start feeding the edges back into the cone and just keep stuffing them in now what happens out here is easy because we know it doesn't penetrate the cone that's the assumption and we know whatever was created here could be uncreated as long as you can't afford to erase edges one by one that's the tricky part how do i erase an edge usually i can't but it's not i don't have to erase any edge like if i had to erase this one that would be hard because some motion here might penetrate where that edge ought to have been and erasing the edge will not will make it adding the edge makes it harder to fold so i can't erase it but the edges i have to erase are the ones that have been fully inserted into the cone so if i can somehow do something inside the cone i would be okay all this work of defining a canonical configuration was about forcing a chain to stay inside a cone and not only an alpha cone which is what we're going to have as the ribosome but an alpha over two cone this is smaller than my ribosome cone by a factor of two and i need that why do i need that because this thing i have no control over the outside chain so the way that it approaches the cone could be as sharp as like this where i have it the first edge that is or the the current edge that is inside the cone as far as the movie is concerned there's only one edge there's nothing up here i want to put something up here in a cone naturally but i don't get to control the first angle because that is controlled by this motion maybe it really needed to go sharp like that so they could make a sharper angle or whatever so you know you might say well of course i can put it inside an alpha cone which is the same as as this alpha sorry bad picture this is alpha this would be a problem because i have this weird angle coming in and now suddenly i have to bend back like that maybe the turn angle here is not so sharp as alpha maybe it's one degree so i really can't force the rest of my chain to lie in this cone ah but i claim i can force it to lie in this cone with half angle alpha over two this is a little more subtle oh right i wanted to mention that helices appear in nature they appear in proteins but they also appear in this crazy climber plant marty have you seen this in costa rica yes yeah there's some really incredible wildlife in costa rica i've never been there but i've seen lots of pictures and this is uh spirals in practice also um proteins tend to form these things they call them alpha helices because they spin like an alpha i guess so this it's kind of neat that the canonical configuration which is totally geometrically motivated also appears in biology not that kind of biology though so here is the picture i have the big cone that is my ribosome and here i'm going to write beta for the beta for big i guess and then we know that we can canonicalize a chain or there at least exists a canonical configuration of the chain where everything lies inside a cone of half angle alpha over two now the problem is that cone we want it to be at a funny angle let me draw a real picture here's a ribosome has a big angle here called alpha now i'm going to do the not extreme case try to be a little more general there's some edge that is currently entering and we have no control over that edge or the rest of the chain that's plate that's determined by the movie which we're trying to play backwards what we what we have to control and what we're free to control is the rest of the chain because as far as the movie is concerned that hasn't been created yet or it hasn't been just it's already been destroyed depending on where you're playing forwards or backwards uh we need to say what happens to it and i what i want to happen is so that by the time this edge is inside that edge plus the rest is in the canonical configuration if i can achieve that then as edges come in they become canonicalized and then everything will be canonical and inside the cone we're done that's our goal canonicalization so uh what's the deal well in reality there's some cone uh yeah it can penetrate like that could penetrate the outside cone and this is getting messy so if i extend this line there's a cone of half angle here which is equal to whatever the turn angle is at that vertex which is again specified we're not free to set it to whatever we want we know the next edge must lie on this cone what i do uh for the now i have on the other hand off to the side i have in mind a vertical cone whose half angle is alpha over two so it's quite small and i know um how do we do it initially the first edge was along the maximum x direction and then it you know it spirals up from there okay here's what i'm going to do there are sort of two situations i what i'd like to do is put a cone here that is vertical something like that just like i have here the trouble is the right side of this cone does not intersect the boundary of this cone and i need it to in order to form the right angle here it's going to it might go through the middle of the cone like it does here so then what i do is i take this canonical configuration and i rotate it so that this is hard to draw it'll be something like this i think there's no hope of seeing this so it's on the surface of this cone it's not on the far right edge it's going to be some some intermediate point and that's that's exactly where it intersects this cone it's just like the previous picture just harder to see i'm taking the intersection of these two cones if i just rotate the picture then it will lie on the intersection if they intersect but they might not intersect so let me go here try it again so the easy case is when i can draw a vertical cone and it intersects the the cone that i need to intersect the harder case is maybe it's more extreme maybe it's a very tight angle here so there's a very small turn angle i have to intersect this cone because my the cone that i'm working with is actually smaller it might it's half half of this angle it might not intersect this cone in that case i'm going to rotate the cone to fall over a little bit so instead of being like that it's going to be like this okay so i want the intersection of these two cones which i've conveniently made this this edge here so the first edge will be lie along here and then it's going to spiral it from there so i still have the canonical configuration i've just tilted it tilting is going to be necessary because i have this angle to match up the convenient thing about the canonical this the alpha ccc canonical configuration is that i have this half angle of alpha over two so i can afford to tilt it by up to alpha over two it will still stay within the ribosome which is of half angle alpha and all i need to show here and sort of once you think about it for a while it's obvious that you ideally i don't tilt it at all got tons of rooms huge amount of room here but sometimes i'll have to tilt it but by at most alpha over two so i will stay inside the ribosome because this apex was inside the cone and this smaller cone even if i tilt it all the way to meet this edge it will stay inside the cone in fact it'll stay inside the big cone in fact this cone that i tilt the one that contains the rest of the canonical configuration will always contain the up direction that's how to see it if it always contains the up direction then at most it's that big and that will uh because that is ha that's an angle of alpha because that was the half angle of the big cone and so that would be a half angle of alpha over two as long as you contain the up direction at all times you will not fall outside the big cone so the rest is just memento so you play this movie backwards as things come in here uh you this cone is going to wiggle back and forth depending on how this angle changes once the edge gets all the way in you absorb it into the canonical configuration it's a little bit of work there but you just sort of twist the cone around until that algorithm that we described for producing canonical configuration would actually produce what's inside the cone then the next edge comes in the cone wiggles around until the edge gets all the way in then you canonicalize what's inside the cone and repeat so if you had a way to get it out you can put it back in and keep track of all the stuff that happens on the inside that's what this theorem says and then there's just slightly more to say if you have a flat state we want to prove these things are flat state connected so take some flat state i ideally should have only obtuse angles i claim this flat state can be produced using a cone of the appropriate angle this is the sharpest turn angle here is alpha then you need an alpha cone and the way to think about that is to think of the cone moving instead of as the chain moving it's a lot easier so you want the chain to lie around here so you start by moving the cone i guess like this so that it just barely touches the plane and this edge spews out is that the right way to think about it no no no it should be like this so you you take the cone this this is like putting frosting on a cake okay so you move your cone like here you squirt out some this this edge okay then uh you do it so that when you're here and the new edge is created uh it's still in the plane and then you just sort of move around there i'm just going to leave it as a sketch like that once you know that you can produce any flat state of course you can reorient yourself by relativity so that the chain is moving instead of the cone so you can produce this thing with a ribosome once you know all flat states can be produced and you know all producible configurations can be canonicalized then you know it's flat stay connected and you know all canonical things are flattenable and vice versa by continuous motions without self-intersection and all of this is algorithmic can tell you how to go from one place to another and so this is a candidate algorithm i would say for how nature folds proteins just thinking about the mechanics not worrying about how it's implemented maybe you take this model and then you try to make it physical physical forces and you get a way to fold proteins that of course remains a mystery but next time we will talk about uh some very simple models that are motivated more closely by biology of how proteins might actually fold and talk about the complexities that you get there 2 00:00:05,430 --> 00:00:06,789 all right today we're going to talk about protein folding and its relation to linkage folding we're going to look at sort of a mechanical model of proteins this is an example of a protein from lecture one there's a ton out there in this place called the protein data bank all freely available it's really hard to get pictures like this but you get some idea that there's a linkage embedded in here you see various little uh spheres and edges that's of course not reality those spheres are actually atoms and they're the kind of amorphous blobs the edges are chemical bonds and those are connections we don't know whether they're it's not really matter but it's a force this is a rather messy picture this is what a protein folds into some 3d shape most proteins fold consistently into one shape we don't really know how that happens we can't watch it happen so we the big challenge is to know how proteins fold given a protein what does it fold into that's the protein folding problem major unsolved problem in biology biochemistry the protein design problem is i want to make a particular 3d shape so that it docks into something binds to a virus whatever what protein should i synthesize in order for it to fold into that shape that is potentially an easier question algorithmically it's the really useful one from a drug design standpoint you come up some some new virus comes along you design a drug to attack it and only it you build it usually you would manufacture some synthetic dna you feed it into a cell dna goes to the rna goes to the mrna goes to the protein you all remember biology 101 hopefully we don't need to know much about it if you look at what's called the backbone of the protein protein is basically a chain and attached to the chain are various amino acids today i'm going to ignore the amino acids which is a little crazy and just think about the backbone chain backbone chain looks something like this um one of the challenges of video recording a class is i can only use copyright free or creative commons images this one i couldn't get one so i had to draw it there's various measurements here certain numbers of angstroms those are the chemical bonds various uh atoms here nitrogen carbon so on hydrogen but basically it's a chain zigzags back and forth you can also see the angles here they're not quite all the same but they're very similar all the lengths and the angles are close so uh it zigzags this is really in three dimensions and try to draw the sphere so you can see the three dimensionality but it's a little tricky and then attached on the sides are the amino acids i'm going to focus just on the backbone the way this thing is allowed to fold these lengths as far as we know are are pretty static they probably jiggle a little bit but you can think of them as edges so you can think of this as a linkage the catch is also the angles are fixed because the way this atom wants to bind to other things has very fixed angle patterns if you ever played with a chemistry construction set that's that's how they work to have holes at just particular angles so if you think of like a robotic arm normally uh like here i have a two edge robotic arm let's say normally you have two degrees of freedom in three dimensions you can change the angle and you can spin around this edge now i'm saying the angle is fixed for example here it's say at 90 degrees all i can do is spin i'm not allowed to flex my muscle in this way okay so that is the model all of in this case we have a tree all of the angles here are fixed but you can still for example take this entire sub chain and spin it around this edge that'll preserve all the angles and all the lengths that's all you're allowed to do you take an edge you spin it spin once half of the edge relative to the other half these are called fixed angle linkages and they've been studied quite a lot because of their connection to protein folding so embedded in the term linkage we assume that the edge lengths are fixed and then we add the constraint that the angles are fixed and the motivation is the backbone is something like put the background of a protein is something like a fixed angle tree of course it's not much of a tree most of it is a chain there's just small objects hanging off and if you add the amino acids there are bigger things hanging off but still constant size they'll have some cycles they're not trees but it's slightly more approximately maybe i should draw wavier lines uh it's a chain usually an open chain although occasionally closed chain so we think a lot about fixed angle chains and sometimes about fixed angle trees now fixed angle linkages are harder to think about than universal joints that's the usual kind of linkage um so and we know 3d linkages are kind of tough nonetheless we found lots of really interesting mathematical problems to solve here and that is the topic of today at some level we are thinking about the mechanics of protein folding we're throwing away energy we're throwing away the the actuators in real life that make proteins fold we're just imagining given this mechanical model of how a protein might fold what's possible so it's some sense it's broader than reality and the hope is you find an interesting algorithm for how to fold these protein chains maybe that's the algorithm that nature is implementing that's the kind of general picture we're not constrained by reality and by how nature actually folds things so i'm going to talk today about four main problems here first one's called span second one's called flattening third one is flat state connectivity and the fourth one is locked our good friend locked chains and of course there are lock chains because we're constraining linkages even more than before so if you take knitting needles it'll still be locked because you add extra constraints makes it harder to fold but there are actually some interesting positive results we can give of chains that are not locked in some sense and flat state connectivity is about the same kind of thing instead of worrying about getting from anywhere to anywhere we just worry about getting from one flat state to another flat state flat means lying in a plane flattening is about is there such a configuration and span is about given robotic arm like a more complicated one like with multiple edges how far apart can the endpoints get and how close can the endpoints get the universal chain is not very exciting the farthest thing is when it's straight and the least far they can get is when it's closed and you can always do that i think well no i guess you can't always close it up that's a little non-trivial but for fixed angle linkages you can't straighten out because you have to preserve the angles so it's kind of what is the straightest like configuration given that the angles are fixed so let's start with span so the span of a configuration is the distance between the endpoints and in general you'll find the max span and the min span this search was begun by a guy named mike sauce who was a phd student at mcgill and he proved that if you want to find for example flat state that lives in two dimensions with the minimum or the maximum span this is np hard this is in his phd thesis question oh here i'm assuming open chain i should say that which most proteins are yeah i've been talking about trees and stuff i hear i mean chain otherwise there aren't two end points to think about good uh so here are his np hardness proofs in fact the problems are mp complete they're pretty simple the problem here we're reducing from is partition i give you a bunch of integers i want to divide them into two halves of equal sum and the top example is minimum flat span problem so you have you make an orthogonal chain where the horizontal edges are long and they're proportional to the integers you're given and the vertical edges are really tiny and so what you'd like to do what all you can do is sort of flip in the because you have to stay in the plane you can flip one of the vertical edges say and make any of these edges go left or right you get that freedom but so each integer you get to choose do i go right by that amount and go or do i go left by that amount and if the amount you go left is equal to the amount you go right in other words there's a partition into two equal sums then those endpoints will be aligned and then their distance will be very tiny otherwise it will be quite large because the horizontal distances are all big so that's kind of an e very easy np hardness proof to maximize your flat span instead of mapping your integers onto lengths you map them onto angles or turn angles i won't specify that too precisely but again if you if you make your total counterclockwise turn equal to your total clockwise turn then the two end edges which are super super long will be parallel and to maximize the distance between the endpoints you want them to be parallel if you make them go some other angle they're closer now both of these proofs rely on the requirement that you want a flat configuration with minimum and maximum span now there's a claim that flat configurations matter for proteins so it's a natural constraint but what about the general problem what about i have something in three dimensions i want to maximize i have a fixed angle chain in 3d maximize or minimize the span both of those problems are open can you solve them in polynomial time for 3d max span so the non-flat version just for maximization there's been a lot of work and there are two papers on the subject one of them is by nadia and joe o'rourke another one is by borsea and stranu and i just want to quickly summarize that because there's a lot of stuff there but essentially they find what the structure of those spans look like i have an early figure that's in our book before all this work was done of a simple chain this black guy one two three four bars open chain and in that black three-dimensional state it maximizes the span the the green span there and if you look from above which is this picture of course the endpoints look much closer in in projection and the red configuration is the max span if you restrict to flat configurations so here of course 3d buys you something in general it always will an interesting thing is that this max span the green line passes through another vertex that seems kind of weird and in fact there's a general theorem there sort of characterizing the structure of these chains it's still not known whether we can solve this problem in polynomial time but for orthogonal chains where all the angles are 90 degrees uh we can solve that in linear time i guess and here's what it looks like suppose you have some orthogonal chain orthogonal chains are nice because you can draw them in a plane as a staircase so there's a nice canonical configuration what one way to think about how to find the maxspan configuration i'm just going to give a high level overview here this won't be a complete algorithm is you triangulate that staircase in this sort of obvious way of connecting every endpoint to the one to a head this you can think about this is like a body that's hinging around here because i can spin if i spin the left part of this chain around this edge it's like hinging that triangle around that hinge same thing you can think of these triangles as just being hinged together like in rigid origami it's the same class of motions and now you can uh what i'm going to do is compute a shortest path in this surface from here to here confusingly this is called a geodesic shortest path although it's not really related to geodesics from polyhedral surfaces but if i compute a shortest path it's going to go like to this vertex and then probably to that vertex but i'm constrained to say stay inside the unit of those triangles i want to go from one endpoint to another then i claim that okay the these two edges will stay planar of course they form a triangle uh i claim these four edges will stay planar and in the orthogonal case they'll stay zigzag and then also these two guys will stay in their own plane and then uh i claim that actually this wiggly line which is not straight because it bends here and it bends here the total length of that wiggly line is the max span and you achieve that by folding this planar part with respect to this planar part with respect to this planar part so that the wiggly lines become aligned and straight and that's very hard to draw but it can be done and that's what you do in the orthogonal case and that gives you the answer in linear time with enough work for non-orthogonal though it's open whether you can do this in polynomial time maybe it's np hard actually i don't know all right that's all i want to say about span next we go to flattening i guess the first question about flattening and and the main one we'll we'll talk about here until we get to flat state connectivity is does a fixed angle chain have a flat state at all can you even draw it in the plane without crossings so we're restricted here to have no no self intersections we want a flat state no self intersection then there would be a question of given some configuration can actually continuously get to a flat state but sort of the simplest question is ignore about getting ignore getting there just is there a flat state and this problem is np-hard again mike sauce and his advisor godfrey toussaint it's a little more complicated but it's basically the same idea as that very simple proof which was just to map integers to a little zigzag staircase here so the goal is to force x to end up being the two endpoints of the green curve to be aligned with each other that will exist if and only if there is a partition of the given integers and there's all this infrastructure this sort of uh there's a little lock here and a key and and some structure on the left basically forces the picture to look like that um so the first claim is that the black stuff is basically unique i think there's one global reflection you can do that doesn't affect anything but you try any of the other flips again we're restricted to flat states here so there's only sort of a bounded number of things you can do finite number of things you can do you try all of them they self-intersect so the black thing is basically forced and it forces the end point this endpoint x from the black side to be aligned with this very narrow spike and because the angles are preserved that red guy is going to be vertical it can't go down so it must go up and so only if this thing is aligned in the center aligned with x in other words this problem has a partition will this have a flat state so it's not the most exciting example this is only a weak np hardness proof lots of interesting questions still open here like if all the lengths are the same if they're all equal then we don't know or if all the lengths are even polynomially bounded this needs really really long lengths versus really really tiny lengths exponentially exponential and ratio all these problems are open and that's flattening so we're going very quick uh because there isn't uh well partly because i'm more excited about this but there's more work in these two parts so i'm gonna focus on that next topic is flat state connectivity so the idea is to think about the configuration space of these fixed angle chains let's say and we kind of know that it's going to be disconnected because there are knitting needles there are nasty things so there's maybe various connected components but let's say that we really care about flat states and the question is are they connected to each other so in other words do all the flat states mark them with x's do they all appear there's only finitely many so configurations there's it's this continuum and there are these messy blobs semi-algebraic sets but flat states those are discrete things because we have fixed angles you can flip or not flip every edge so most exponentially many of them so finite are they all in one component so i can get for if i pick two of my favorite flat states there's a path between them or are some of them in multiple components so in this case we call it flat state disconnected and if they're all like this we call it flat state connected and we just like to know which chains which fixed angle trees whatever are flat state connected versus flat state disconnected i would say the big the big open problem here is our is every flat as every fixed angle chain open chain flat state connected that is still open we have lots of results in in that direction so the top four results are about open chains but they have an extra constraint example open chains that have a monotone configuration like the staircase those are flat state connected and so in fact whenever the angles between the edges are either orthogonal or obtuse then their flats stay connected when the angles are acute we're not really sure if all the angles are equal and acute then we can do it but if they're different and acute we don't know unless the edges are all unit length and the angles are in this funny range then we can do it so there's all these special cases we can solve the most relevant to proteins is actually obtuse chains so we've solved sort of the main problem with this second result but there's a natural theoretical question here is are all open chains flat state connected or do we get disconnectivity i will show you that i'll show you the orthogonal case in a little bit we can do some stuff we have multiple chains that are attached to some blob like a cell closed chains is a little bit for disconnected uh we don't have very interesting examples i would say this is funny because locked examples are easy to come by but flat state disconnected examples are a little trickier because flat is so constrained so let me just show you these examples this is what we call a partially rigid fixed angle tree so not only are the angles fixed but also the black edges are not in fact only the blue edges here are allowed to spin everything else is held rigid so these arms are somehow forced to be in exactly that geometry i can spin it around this edge just spin it up into 3d for example these are two different flat states of the same linkage right all i all the only difference between these two i haven't rotated or anything is i've taken each of these arms and flipped it around a blue axis if i do all four of them i would get this picture but the claim is you cannot do that without self-intersection the intuition is when there aren't very oh one other thing this makes this slightly more interesting it's weird to say well why did you force some of the edges to be rigid and not others one way to force that is to use a general graph if you add some extra edges to sort of brace this and all these angles are fixed then this linkage will behave exactly like that one so that at least is somewhat more natural although what we really care about are chains maybe trees but we don't know whether there's a we also don't know whether all true fixed angle trees are flat state connected these are the the worst examples we know let me give you an idea of why that it doesn't work this is a little animation of just a couple of moves attempted it's just going to cycle through that and these are some static images of same kind of thing so the intuition is the following you have four arms you have two sides to the plane there's up and down for four arms and two sides at least two of them are going to have to go to the same side the best you can do is two and two or three and one but in either case you have two sides go to the two arms to go on the same side now it could be like in this image that they're opposite arms so there's this arm here and there's this arm here so they're connected by 180 degree angle and those guys when they fold up actually these edges will just hit each other dead on so that's uh kind of obvious from a geometric standpoint maybe you call it cheating for them to hit dead on you can twiddle the edge length so that they will properly intersect without dead-on collision without being degenerate basically the alternative is the and this is a little harder to see geometrically and that's why we drew that animation is that you have you have one arm and you have an adjacent arm connected by a 90 degree angle now here there's clearly some collision going on and if you happen to fold it up 90 degrees like that and then fold the other guy obviously you get stuck but maybe you fold it a little bit and the other guy goes a little bit more and there could be some dance between those two degrees of freedom those two arms that somehow gets them both to pass over to the other side it's obviously not possible how do you prove it well you can prove it with topology not not theory or link theory so it's very cute proof uh you start with so here's the the full example but i've highlighted the two arms in red that are going to move and i imagine connecting the endpoints of each arm with these little blue ropes underneath the plane so all right they they're both going on the same side let's say that somehow pass through each other on the top side then i'm free to connect stuff on the bottom and i shouldn't collide with that so if somehow both of these guys flip over so the arm on the left a3 flips over a3 stays where it is but now the arm is on the top the north side instead of the south side and the other guy from b to b3 used to go like this and now it goes like this if that happened somehow then these ropes could remain intact during that whole motion and on the top you have two closed loops that are not interlocked on the bottom you have two closed loops that are interlocked so there's no way to get from there to there without colliding somewhere the blue stuff didn't move so the red stuff must have collided so even just topologically you are screwed that is our only negative example lots of interesting open questions here on the positive side let me show you for orthogonal chains and the same algorithm works for obtuse chains all the angles are obtuse uh how they are flat state connected so in order to show its flat stay connected i take i want to think about two flat states and show that i can fold from one to the other via some intermediate 3d stuff let's start with one of the flat states so it's orthogonal so in two dimensions they really all the edges will be horizontal or vertical in 3d they can kind of be in many many different angles many different dihedral angles in 2d it's pretty simple and all i need to do is sort of pick up that chain and i'm going to try to pick it up into a staircase because there's only one staircase if i can make it a staircase i make configuration flat configuration a staircase flat configuration b staircase i just fed x in the middle right once they're both staircases i play one motion and the other one backwards get from anywhere to anywhere so here's all you do you take the first edge and you just rotate it up to the red line a uh and then you take the next edge and you take both of those edges and you just rotate them like this so you get that little two-step staircase now i'd really like to pick up this edge but i want to first get these two edges in a plane with that edge so i rotate this flag over to the left i get those two guys and now they're in a plane with this and i just lift that up then i'm going to flip then rotate up flip rotate flip rotate here's some more examples so if at this point i have this staircase um sorry i guess originally i have from v3 to d up there i it's not in plane with this guy so i just rotate it like that i'm spinning around this edge so now i have from v3 to e and then i rotate it up along that green arc and i get a bigger staircase above the chain and because everything's staying above it will never penetrate the plane it'll never hit anybody else and i'm building a staircase by design i always rotate this there's actually two ways i could be in plane but i always rotate it so that when i pick some an edge up it'll be in a staircase so this is actually really easy and slight generalization is to obtuse chains then instead of making a staircase we make a monotone get this right yeah some z monotone state so it goes monotone and z out of the plane and that's enough to avoid collision and you get a canonical configuration also if you have acute angles but all the angles are equal then there's a natural canonical state which is just like a compressed staircase and that will work here too although that takes more effort that was in a separate paper but big open question is chains with arbitrary angles we have no idea it seems very hard to do an operation like this wow we are burning through this is fun so the next topic is about locked chains now as i said you can take a knitting needles example which has five edges and that will still be locked if you force the angles to be fixed because it was locked without the angles being fixed now it required a length ratio of uh three to one i think yeah this edge had to be longer than the sum of those three uh so let me put down uh some open problems so you may recall in the case of universal chains universal joints i should say the big open question was can you lock a universal joint 3d chain with unit edge lengths so equilateral every edge is the same length is there a lock chain like the knitting needles where all the edge lengths are the same and one of the motivations for that is in proteins the edge lengths are all within like 50 of each other so it's pretty natural of course we don't have universal joints with proteins we have fixed angle joints so the big open problem for fixed angle joints i guess we'll do this in parts is there a locked 3d fixed angle chain that's equilateral okay i'm going to add some conditions here so that's first natural question knitting needles doesn't suffice we need a three to one length ratio as far as we know uh yeah turns out that question is not very interesting i need to do slightly non-linear editing here so you take a knitting needles example and you just subdivide the edges into lots of little tiny bars it doesn't have to be this extreme you could not subdivide these edges at all and make these guys subdivide them into like three or four parts because the angles are fixed these guys act as a single bar there's really no difference maybe you make slight curve there and then they can wiggle they can bend a little bit but really not much so if you just say oh i want it to be unit length i don't constrain what the angles are but i fix them then it's trivial to come up with locked examples so that's not very interesting what if i make it not only equilateral the lengths are the same if i make it equally angular because again in proteins all the angles are similar they're around 110 108 something like that they're all pretty close within if i think within 10 20 of each other well here there's also a locked example and just to show you how research was done back at the turn of the century this is pre web 2.0 pre-ajax and all that fancy stuff we used ascii art this was email was the tool of choice i know it's hard to imagine a time 2002 so long ago and i i tracked this down this is the original claim where it looks we call this the crossed legs example because it's like two legs crossed around each other and uh this is the the first time we thought oh maybe it can be done unit length this is stefan langerman and uh and here for the first time ever this is not the first model but this is the first photograph of any model i'm aware of this is the cross legs example um this is made with a construction toy that used to be sold around here but is no longer in production it's hard to so they're pretty hard to get is straws nicely colored straws and the cool part are these uh these connectors so the connectors force particular angles in this case every angle is 45 degrees so this is equiangular and equilateral because all the straws i'm told are the same length that's how they're sold and you can do edge spins so whoops that's called cheating it's not totally obvious that this is locked the problem with the model is that the edges can bend but if you treat it properly and only spin around edges then you're you're stuck now there is one thing you can do let me see if i uh yeah like this so here i'm almost in a plane i've got the purple edge right against the pink one is it easier to see from that angle i don't know so here this guy can come out and this guy can barely go along the edge so actually this doesn't quite work for equilateral it works for one plus epsilon that's why i added these little nubs at the ends so if it if they're all exactly equal length and you allow just a abrasion of the endpoint then this could go around like that and then you'd be unlocked if you just add slightly either you change the angles to be not quite equal so ben make this a little smaller or you make the lengths a little bit longer at the ends then the claim is it's locked we don't actually have a formal proof of this we're just remembering hey we should probably write this up i was talking to stefan last night and uh yeah so someday we will prove that this is locked but certainly looks like it so this isn't open yet i mean modulo the details of that proof equilateral and equiangular seems easy to lock with fixed angle chains in fact even easier that this example only has four edges so even less than the knitting needles fixed angles make for complicated motions i guess make it hard to unlock things so i need to add one more constraint and the constraint is obtuse so again all of these properties are enjoyed by proteins protein protein backbones have all these properties even if you looked at fixed angle trees is there something like this that's locked and now we don't know and this seems quite tricky i guess the intuition is that obtuse or and usually we think about orthogonal just because it's easier to draw the pictures but reality is more like 108 degrees uh conjectures of two chains obtuse fixed angle chains behave kind of like universal joints and with universal joints we don't know whether equal equilateral is enough so it's tricky what if you instead had like made your ribbon lengths basically like a bunch of little unit obtuse angle connectors and then when you hit the the big turns it's just you know up to yeah you can definitely you can make this example be entirely obtuse you can make every angle obtuse here you could arc a little bit here you could arc some more but not too sharp and because here we actually know that this part can be made a string we don't really care what it looks like so you can make it fairly obtuse it's just that these guys should not bend much they have to be long no matter how you fold them so if you want equilateral and obtuse that's also easy but to make all the angles actually be equal as far as we know you cannot take that knitting needle subdivided make all the lengths equal and all the angles equal and make them obtuse that's open but any two out of the three it's easy uh of course in reality they're not quite equilateral they're not quite equal angular but it's still open for the if you have like a small range for the lengths and a small range for the angles this is open we pose it this way because it's the cleanest geometrically but the the real question you care about is when these are fuzzy constraints obtuse is real but these guys are fuzzier so uh if you think about proteins uh which fold very well in nature there are a couple of reasons they might fold well we know as far as fixed angle chains go it's actually quite easy to find locked examples and this is somewhat intuitive but bear with me because there are locked examples in this configuration space we believe these configuration spaces are really ugly nasty so it would be very hard even if you know oh i only need to fold something in my component if these guys are highly disconnected and flat states are all over the place it's probably even within this connected component it looks really ugly and so it's very hard to find a path from one state to another probably p-space complete although we don't know that for sure but that's the intuition locked equals messy when there are no locked configurations like carpenter's roles we get really nice algorithms it's super easy to get from state a to state b now if you're nature or you're designing nature let's say or you're building your own virtual world second life and you want to design proteins you would like to design them in such a way that they fold easily because it happens all the time every thing that is being acted on by our body every living thing that we know has tons of little proteins that are doing all the work they are fold into their shape and they do something that's proteins plus rna but mostly proteins so uh to understand life we should understand proteins now how do proteins fold so well when we know there are all these locked configurations one possible answer is that proteins have extra structure namely these three things which somehow make it very easy to algorithmically go from a to b notice i'm not even i'm not assuming anything about how proteins fold in terms of what is the mechanism that drives them because we don't really understand those mechanisms there's hydrophobia which we don't really know how it works it's all these little forces um that we don't fully understand lots of we understand lots of parts of the story but not the whole story and what's convenient about these kinds of problems is you don't need to assume anything about how it actually happens all we're assuming is the mechanical behavior of proteins and how they could possibly fold and the the idea is if there's a lot configurations that's probably the wrong model because then everything's messy now there's also evolution coming into play and maybe some proteins are easy to fold some proteins are hard to fold that's an interesting question which should be experimented with but let's hope that there's a model things are mutating randomly you really like everything to fold nicely maybe it's because you have all three of these properties approximately in real proteins so the general idea is that nature has some extra constraints that make protein folding easy we just have to figure out what they are and why it makes them easy unfortunately this is still an open problem if this had an algorithm that would be a natural candidate for what nature is doing using its mechanical or using its for energies and forces and so on this would be a rather unsatisfactory ending if this was if the climax was an open problem we have a theorem too and this is what i'll cover in most detail and it's paper called producible protein chains protein chains just means fixed angle chains open chains and the idea is well yeah there are these constraints uh or there are these extra features we don't know how to exploit them so let's not even worry about them suppose they don't even exist maybe i'm going to assume obtuse but none of the others there's another constraint in how proteins fold or really how proteins are created they're created by a machine a molecular machine made up of a whole bunch of proteins and rna called the ribosome you may have heard of it translates messenger rna into proteins so there's some mrna around here maybe don't know exactly how this machine works but there are actually very accurate three-dimensional reconstructions of the ribosome with no copyright free images you're going to have to there's a link on this slide that goes to the cool amp 3d models of the ribosome with a slice away so you can see this there's a tunnel down here and the prot the protein gets sort of created here the backbone gets created here and starts going through this tunnel there's a bend in the tunnel around here where it's conjectured an amino acid gets attached and then that it goes out the tunnel and the protein starts spewing out here and presumably folding at the same time we don't really know so this is how proteins are created um the birds and bees i guess of proteins so what's interesting about this is it's not like a protein exists and then folds which is how a lot of people might think about it at first glance that's natural way to model protein folding you start with a protein say in just zigzag configuration if it's obtuse there's a nice zigzag monotone configuration then you see what is the best configuration i could fold into for some notion of best and that's sort of what this configuration space picture is about it's if i already have a protein what configurations can i reach by motions and that is interesting that's important because you're still going to have to reach by emotion but it's actually more flexible than that because protein could just be partially built the the rest of the protein hasn't been built and it could start folding already and it might be easier to fold when you don't have the obstacles of your existing protein so that's both a worry but it's also a convenient structure because this ribosome is a giant obstacle it's bigger than most proteins there if your protein is really long maybe it could go over here but most of the time it's going to stay on one side of this plane because locally this thing is basically flat if you look at the real 3d pictures not the schematic now this is good news for a geometer because there's this giant obstacle think of it as a half space which the protein cannot penetrate while it's being produced over here that's it that half half space constraint is enough to get really good algorithms for folding your chain it's weird because we've made our problem both harder because the protein is only partially produced at any time and it can fold which is part of it but we've also made our life easier because there's this big obstacle yeah right we're out of this we're going to get that the angles in the protein are constrained and in particular for this angle uh it depends i mean you could in this picture because it's perpendicular here yeah uh you can the the sharpest angle you can make is 90 degrees more or less that's a good point so it's a convenient match between the chemistry which also forces the angles to be obtuse i guess i don't know a ton of chemistry but also the ribosome just geometrically forces we're going to use a property like that our model is going to be a little bit more both more general and simpler we're going to imagine that the ribosome is a cone it's part of the upper cone here this is like a mirror image and in reality that cone is actually a plane and everything above the plane but to be more general we're going to allow some angle alpha here it's also just easier to think about when alpha is smaller than 90 but it's work everything i say will work when alpha equals 90 and that is sort of the reality case so so the model is so the ribosome is a cone who we call this the half angle of the cone from the vertical axis to the edge of the cone is alpha so if you're going from one axis to the other would be two alpha the the model is you start with one link of your chain which is inside the cone it spews out uh through the apex okay that's that's the exit of the tunnel here we're allowing the tunnel to be actually quite free it doesn't have to be perpendicular to the to the apex or the plane of the apex so the edge comes out and as soon as the vert the end point of the chain reaches here then a new link is created this is like a very simple model for how a chain can come out of a cone without worrying about what's happening inside the cone imagine everything's totally free this is like you can allow self-intersection the cone who knows what but once you come outside the cone you're not allowed to self-intersect and you're not allowed to intersect the cone once you come out you can't go back in so that is a model of producing protein chains and if you have a cone of angle alpha we call this an alpha producible chain for whatever reason we often call it a beta producible chain just change the variables so if you think of the ribosome as a cone with half angle beta you can produce it like this that is beta producible now this is a pretty powerful model because you only have to worry about it link by link you don't have to worry about the rest of the chain until it gets spews outside of the cone but it's restrictive in that you cannot penetrate the [ __ ] all right one thing we can talk about is angles so i'm gonna write call a chain a less than or equal to alpha chain if all the turn angles are less than or equal to alpha i don't know if i've used turn angles in this class probably if i have two edges the angle would be this the turn angle would be this supplement yeah i guess we use trit angles way back in origami land kawasaki's theorem and so on it's just if you're going straight how much do you have to turn to get to the next edge so we'd like uh fairly obtuse things so alpha's going to be small there isn't a ton of turn but in general less than or equal to alpha chain for some alpha now there's a relation as jason was mentioning there's a relation between alpha and beta in the ribosome because you always exited orthogonally to the the plane that was your cone the sharpest angle you could get was 90 degree turn angle here we're a little freer because this edge can wiggle around as long as it touches the apex so if you're up against the cone you have to slide out into the complementary cone that was the previous picture and as soon as you get there you could create a new edge which is like this so the sharpest angle you can get is actually twice beta in general we're going to have alpha over 2 is less than or equal to beta that is you can get up to beta equals 2 alpha get that right and also in the obtuse case this is not too exciting but it's true uh there's actually some open problems here when you have that full flexibility and you set um sorry alpha to two beta not the other way around uh i'm going to assume here that alpha equals beta this will be convenient and it's the interesting case because in reality the cone has a half angle of 90 degrees so beta is 90. and the sharpest angle we're going to make is always obtuse so saying that you have a less than or equal to 90 chain is just fine but in on the mathematical side i think we solve the case when alpha is less than or equal to beta um but not when alpha over 2 is less than or equal to beta that's a weaker constraint so there is a range where it's not so easy all right now what do i claim about these chains other than their angles are not so sharp i claim they're good algorithms for folding them what could i possibly mean there are still locked configurations is that true well yeah i mean presumably this is acute but you take the obtuse versions of this guy because i didn't constrain the edge links or anything i just said that they're that the angles are obtuse so i could just sort of round these corners make it obtuse you know add lots of dots just at the corners that will be obtuse and a chain like this will be producible a chain with these angles and these edge links can be produced from a cone but this configuration of this chain cannot be produced i claim i claim anything that can be produced is in one connected component so while i can make a linkage that is locked in that there are bad configurations you can't get out of the things you can actually make you can always get out of so there's going to be the space of producible configurations uh maybe there's some stuff that's unproducible but still connected to it i don't i don't know doesn't matter too much i won't worry about this stuff there's other bad locked configurations that you cannot cannot reach here but everything that's producible is in one connected component of the configuration space that's property one that's kind of nice also all the flat states are going to be in here this is actually pretty easy i just need to prove that flat states are producible which we'll worry about later so in particular these guys are flat state connected all the producible protein chains are flat state connected that's interesting because we don't even know that all chains are flat state connected but here i guess we know that obtuse chains are flat stay connected so maybe it's not so surprising but what's important is not only are the flat states connected to each other and the producible states are connected to each other but producibles connected to flat flat states everything is together here i might have more properties but that's already some good news and there's algorithms to do all of this how do we prove it well as usual we use the fedex method and some since one of the challenges is what is the natural canonical state for protein chains in fact we're just going to assume that our chain is in reality we're going to assume that it's an orthogonal chain an obtuse chain i should say but in general for any lesser equal to alpha chain for whatever alpha you like and it will be the half angle of the cone so alpha equals beta we will define a canonical configuration i think we called it the alpha ccc so it's going to be kind of like a helix i think i have an example an actual computed example that's not the best picture because you can't see everything that's going on but this will this is an actual canonical configuration of a particular chain let me tell you how it works in general so in general we have some chain v1 v2 sorry starting at v0 v1 v2 um i want to define a canonic and there's defined lengths between the two and there's defined angles between every triple in sequence so i'm going to start with v0 somewhere it doesn't really matter by translation say the origin of space and what i'm going to do is draw a cone whose apex is at v0 and the half angle here is going to be alpha over 2 not alpha this is a smaller cone than by a factor of 2 than the ribosome that's important so there's this uh vertical line and to pick v1 i'm just going to use this the right edge which is let's say this is the x direction this is the z direction maximum x coordinate it's going to lie on the cone maximum export it that's v1 okay now v1 let me redraw this picture a little lower so there was v0 v1 now i want to draw v2 i want to draw it above so what i'll do is draw a vertical cone whose half angle here is alpha over two and i want to draw v2 on the cone here of course the the height of the cone is the length of the edge not the height but you know this you can think of the cone as infinite and then i just clip this to when it has the right length so again i'm at this might be a different height cone i clip it to whatever the length v1 v2 is i want it to be somewhere on this cone but now i'm constrained to have the correct angle at v1 i can't just put it over here because then the angle here would be 180 presumably i don't want to make 180 degree angle so in reality what happens is that there's a cone which is um who's whose axis is the edge v0v1 so i extend v0v1 out here which in this case happens to lie here and i make a cone like that let me draw it slightly more accurately okay in this case the center axis of the cone would go right here whatever the extension of v0v1 was and to be to have the right angle at v1 v2 must be on that cone conveniently there are two intersection points between those two cones i can choose either one of them to be v2 and i will choose the counterclockwise most one which is this one this is going to be v2 so draw that edge now i repeat so from v2 i'm going to draw a vertical cone whose half angle here the half angle was always alpha over 2. if angle is alpha over 2. this cone had angle or half angle whatever the angle v0 v1 v2 was is that the half angle or the angle the half angle so i think this is right okay and then i take the intersection of those two cones and that will give me where v3 is so i do the same thing for v2 for v3 and so on this i have a unique choice at every moment yeah basically and the only exception was at the beginning here when i had a vertical line these cones two cones could actually be equal and then the intersection is the entire cone in that case i guess i choose the maximum x-coordinate one again and then i'll i have a canonical choice of everything along the way it will always go up and it sort of spirals around because of the counterclockwise most choice and the result is a picture like this anything else i need to say here all right i claim this canonical configuration lies in an alpha over two half angle cone that's true by construction the challenge is does the construction really work so i start obviously with one cone and i can think of this as actually an infinite cone that goes out to infinity here and i claim the entire construction will lie inside that cone and it's kind of obvious because v2 v1 i chose v2 to lie in in this co the same cone just translated up to start at v1 instead of starting at v0 of course this cone is contained in this bigger one and by induction in fact the entire rest of the chain will lie in this smaller cone therefore it lies in the big one also okay fine so by construction it will lie in alpha over two cone the worry is that these two cones don't intersect here we have an angle the half angle of the cone is whatever angle the angle is at v1 sorry this should not be the angle this should be the turn angle that that angle is how much you turn from v0 v1 now we know that we're assuming that the turn angles are all at most alpha this cone so this the the turn angle cone could actually be twice as big as the vertical cone that we were always using we always use a vertical cone half angle alpha over two but because it's okay because we always keep these edges like v0 v1 was on the edge of the cone uh and so if when we extend it it lies on the edge of this vertical cone so its angle in in the most extreme case its half angle is alpha which would look like this would go all the way over from the right side of the cone to the left side of the cone in general it's not going to be right and left but it's going to be some side and the antipodal point and because the double angle of the cone is alpha it's still okay you will intersect somewhere on the cone this is a subtle detail but it's really crucial because we start with a chain that has relatively large angles alpha and we get it into we squeeze it into a cone that still has double twice its angle is alpha but we kind of compress it into something of half angle alpha over two you might think oh i'm just changing the definition calling a half angle therefore i could stand alpha over two but it's a little tricky to actually get it to fit in a vertical alpha over two cone once we have this it's really easy to canonicalize a chain a producible chain so let me tell you how to do that so we're going to use the fedex method of taking some configuration and canonicalizing it and then uncanonicalizing to something else we're also going to use a new method which i just came up with the term it's called the momento method which is you play the movie in reverse so i guess also the merlin method uh that's more complicated so we have a movie here in mind which is how was the chain produced so what i want to show is that if i want to start with a producible configuration and chain somehow it got produced so uh you had your cone and the thing starts spewing out and folding and doing whatever uh that's that's an animation in some sense of of one edge coming out and stuff is folding at the same time then an edge is created then another edge comes out and so on what i want to do is play that movie backwards this is pretty intuitive idea i just want to start feeding the edges back into the cone and just keep stuffing them in now what happens out here is easy because we know it doesn't penetrate the cone that's the assumption and we know whatever was created here could be uncreated as long as you can't afford to erase edges one by one that's the tricky part how do i erase an edge usually i can't but it's not i don't have to erase any edge like if i had to erase this one that would be hard because some motion here might penetrate where that edge ought to have been and erasing the edge will not will make it adding the edge makes it harder to fold so i can't erase it but the edges i have to erase are the ones that have been fully inserted into the cone so if i can somehow do something inside the cone i would be okay all this work of defining a canonical configuration was about forcing a chain to stay inside a cone and not only an alpha cone which is what we're going to have as the ribosome but an alpha over two cone this is smaller than my ribosome cone by a factor of two and i need that why do i need that because this thing i have no control over the outside chain so the way that it approaches the cone could be as sharp as like this where i have it the first edge that is or the the current edge that is inside the cone as far as the movie is concerned there's only one edge there's nothing up here i want to put something up here in a cone naturally but i don't get to control the first angle because that is controlled by this motion maybe it really needed to go sharp like that so they could make a sharper angle or whatever so you know you might say well of course i can put it inside an alpha cone which is the same as as this alpha sorry bad picture this is alpha this would be a problem because i have this weird angle coming in and now suddenly i have to bend back like that maybe the turn angle here is not so sharp as alpha maybe it's one degree so i really can't force the rest of my chain to lie in this cone ah but i claim i can force it to lie in this cone with half angle alpha over two this is a little more subtle oh right i wanted to mention that helices appear in nature they appear in proteins but they also appear in this crazy climber plant marty have you seen this in costa rica yes yeah there's some really incredible wildlife in costa rica i've never been there but i've seen lots of pictures and this is uh spirals in practice also um proteins tend to form these things they call them alpha helices because they spin like an alpha i guess so this it's kind of neat that the canonical configuration which is totally geometrically motivated also appears in biology not that kind of biology though so here is the picture i have the big cone that is my ribosome and here i'm going to write beta for the beta for big i guess and then we know that we can canonicalize a chain or there at least exists a canonical configuration of the chain where everything lies inside a cone of half angle alpha over two now the problem is that cone we want it to be at a funny angle let me draw a real picture here's a ribosome has a big angle here called alpha now i'm going to do the not extreme case try to be a little more general there's some edge that is currently entering and we have no control over that edge or the rest of the chain that's plate that's determined by the movie which we're trying to play backwards what we what we have to control and what we're free to control is the rest of the chain because as far as the movie is concerned that hasn't been created yet or it hasn't been just it's already been destroyed depending on where you're playing forwards or backwards uh we need to say what happens to it and i what i want to happen is so that by the time this edge is inside that edge plus the rest is in the canonical configuration if i can achieve that then as edges come in they become canonicalized and then everything will be canonical and inside the cone we're done that's our goal canonicalization so uh what's the deal well in reality there's some cone uh yeah it can penetrate like that could penetrate the outside cone and this is getting messy so if i extend this line there's a cone of half angle here which is equal to whatever the turn angle is at that vertex which is again specified we're not free to set it to whatever we want we know the next edge must lie on this cone what i do uh for the now i have on the other hand off to the side i have in mind a vertical cone whose half angle is alpha over two so it's quite small and i know um how do we do it initially the first edge was along the maximum x direction and then it you know it spirals up from there okay here's what i'm going to do there are sort of two situations i what i'd like to do is put a cone here that is vertical something like that just like i have here the trouble is the right side of this cone does not intersect the boundary of this cone and i need it to in order to form the right angle here it's going to it might go through the middle of the cone like it does here so then what i do is i take this canonical configuration and i rotate it so that this is hard to draw it'll be something like this i think there's no hope of seeing this so it's on the surface of this cone it's not on the far right edge it's going to be some some intermediate point and that's that's exactly where it intersects this cone it's just like the previous picture just harder to see i'm taking the intersection of these two cones if i just rotate the picture then it will lie on the intersection if they intersect but they might not intersect so let me go here try it again so the easy case is when i can draw a vertical cone and it intersects the the cone that i need to intersect the harder case is maybe it's more extreme maybe it's a very tight angle here so there's a very small turn angle i have to intersect this cone because my the cone that i'm working with is actually smaller it might it's half half of this angle it might not intersect this cone in that case i'm going to rotate the cone to fall over a little bit so instead of being like that it's going to be like this okay so i want the intersection of these two cones which i've conveniently made this this edge here so the first edge will be lie along here and then it's going to spiral it from there so i still have the canonical configuration i've just tilted it tilting is going to be necessary because i have this angle to match up the convenient thing about the canonical this the alpha ccc canonical configuration is that i have this half angle of alpha over two so i can afford to tilt it by up to alpha over two it will still stay within the ribosome which is of half angle alpha and all i need to show here and sort of once you think about it for a while it's obvious that you ideally i don't tilt it at all got tons of rooms huge amount of room here but sometimes i'll have to tilt it but by at most alpha over two so i will stay inside the ribosome because this apex was inside the cone and this smaller cone even if i tilt it all the way to meet this edge it will stay inside the cone in fact it'll stay inside the big cone in fact this cone that i tilt the one that contains the rest of the canonical configuration will always contain the up direction that's how to see it if it always contains the up direction then at most it's that big and that will uh because that is ha that's an angle of alpha because that was the half angle of the big cone and so that would be a half angle of alpha over two as long as you contain the up direction at all times you will not fall outside the big cone so the rest is just memento so you play this movie backwards as things come in here uh you this cone is going to wiggle back and forth depending on how this angle changes once the edge gets all the way in you absorb it into the canonical configuration it's a little bit of work there but you just sort of twist the cone around until that algorithm that we described for producing canonical configuration would actually produce what's inside the cone then the next edge comes in the cone wiggles around until the edge gets all the way in then you canonicalize what's inside the cone and repeat so if you had a way to get it out you can put it back in and keep track of all the stuff that happens on the inside that's what this theorem says and then there's just slightly more to say if you have a flat state we want to prove these things are flat state connected so take some flat state i ideally should have only obtuse angles i claim this flat state can be produced using a cone of the appropriate angle this is the sharpest turn angle here is alpha then you need an alpha cone and the way to think about that is to think of the cone moving instead of as the chain moving it's a lot easier so you want the chain to lie around here so you start by moving the cone i guess like this so that it just barely touches the plane and this edge spews out is that the right way to think about it no no no it should be like this so you you take the cone this this is like putting frosting on a cake okay so you move your cone like here you squirt out some this this edge okay then uh you do it so that when you're here and the new edge is created uh it's still in the plane and then you just sort of move around there i'm just going to leave it as a sketch like that once you know that you can produce any flat state of course you can reorient yourself by relativity so that the chain is moving instead of the cone so you can produce this thing with a ribosome once you know all flat states can be produced and you know all producible configurations can be canonicalized then you know it's flat stay connected and you know all canonical things are flattenable and vice versa by continuous motions without self-intersection and all of this is algorithmic can tell you how to go from one place to another and so this is a candidate algorithm i would say for how nature folds proteins just thinking about the mechanics not worrying about how it's implemented maybe you take this model and then you try to make it physical physical forces and you get a way to fold proteins that of course remains a mystery but next time we will talk about uh some very simple models that are motivated more closely by biology of how proteins might actually fold and talk about the complexities that you get there 3 00:00:06,789 --> 00:00:08,950 4 00:00:08,950 --> 00:00:09,990 5 00:00:09,990 --> 00:00:10,000 6 00:00:10,000 --> 00:00:10,790 7 00:00:10,790 --> 00:00:14,310 8 00:00:14,310 --> 00:00:16,070 9 00:00:16,070 --> 00:00:17,830 10 00:00:17,830 --> 00:00:19,590 11 00:00:19,590 --> 00:00:21,830 12 00:00:21,830 --> 00:00:22,790 13 00:00:22,790 --> 00:00:24,790 14 00:00:24,790 --> 00:00:26,310 15 00:00:26,310 --> 00:00:29,509 16 00:00:29,509 --> 00:00:31,509 17 00:00:31,509 --> 00:00:33,270 18 00:00:33,270 --> 00:00:35,030 19 00:00:35,030 --> 00:00:35,040 20 00:00:35,040 --> 00:00:35,750 21 00:00:35,750 --> 00:00:38,709 22 00:00:38,709 --> 00:00:38,719 23 00:00:38,719 --> 00:00:39,030 24 00:00:39,030 --> 00:00:40,150 25 00:00:40,150 --> 00:00:42,229 26 00:00:42,229 --> 00:00:42,239 27 00:00:42,239 --> 00:00:43,110 28 00:00:43,110 --> 00:00:47,430 29 00:00:47,430 --> 00:00:49,670 30 00:00:49,670 --> 00:00:52,069 31 00:00:52,069 --> 00:00:55,029 32 00:00:55,029 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327 00:11:15,269 --> 00:11:16,630 328 00:11:16,630 --> 00:11:20,230 329 00:11:20,230 --> 00:11:22,550 330 00:11:22,550 --> 00:11:24,389 331 00:11:24,389 --> 00:11:25,910 332 00:11:25,910 --> 00:11:27,670 333 00:11:27,670 --> 00:11:28,949 334 00:11:28,949 --> 00:11:34,389 335 00:11:34,389 --> 00:11:36,470 336 00:11:36,470 --> 00:11:39,110 337 00:11:39,110 --> 00:11:42,550 338 00:11:42,550 --> 00:11:49,030 339 00:11:49,030 --> 00:11:51,350 340 00:11:51,350 --> 00:11:51,360 341 00:11:51,360 --> 00:11:52,550 342 00:11:52,550 --> 00:11:54,230 343 00:11:54,230 --> 00:11:56,629 344 00:11:56,629 --> 00:11:57,670 345 00:11:57,670 --> 00:12:00,310 346 00:12:00,310 --> 00:12:02,790 347 00:12:02,790 --> 00:12:06,310 348 00:12:06,310 --> 00:12:07,110 349 00:12:07,110 --> 00:12:08,949 350 00:12:08,949 --> 00:12:11,269 351 00:12:11,269 --> 00:12:13,590 352 00:12:13,590 --> 00:12:14,949 353 00:12:14,949 --> 00:12:17,590 354 00:12:17,590 --> 00:12:19,509 355 00:12:19,509 --> 00:12:22,790 356 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--> 00:13:12,639 386 00:13:12,639 --> 00:13:15,509 387 00:13:15,509 --> 00:13:23,430 388 00:13:23,430 --> 00:13:27,190 389 00:13:27,190 --> 00:13:27,200 390 00:13:27,200 --> 00:13:31,430 391 00:13:31,430 --> 00:13:39,430 392 00:13:39,430 --> 00:13:40,870 393 00:13:40,870 --> 00:13:42,389 394 00:13:42,389 --> 00:13:43,509 395 00:13:43,509 --> 00:13:45,750 396 00:13:45,750 --> 00:13:48,790 397 00:13:48,790 --> 00:13:51,829 398 00:13:51,829 --> 00:13:56,150 399 00:13:56,150 --> 00:13:59,189 400 00:13:59,189 --> 00:14:00,629 401 00:14:00,629 --> 00:14:02,310 402 00:14:02,310 --> 00:14:05,110 403 00:14:05,110 --> 00:14:06,949 404 00:14:06,949 --> 00:14:10,150 405 00:14:10,150 --> 00:14:13,430 406 00:14:13,430 --> 00:14:15,590 407 00:14:15,590 --> 00:14:17,030 408 00:14:17,030 --> 00:14:19,110 409 00:14:19,110 --> 00:14:20,870 410 00:14:20,870 --> 00:14:22,710 411 00:14:22,710 --> 00:14:24,389 412 00:14:24,389 --> 00:14:26,069 413 00:14:26,069 --> 00:14:26,079 414 00:14:26,079 --> 00:14:26,470 415 00:14:26,470 --> 00:14:30,710 416 00:14:30,710 --> 00:14:33,750 417 00:14:33,750 --> 00:14:36,150 418 00:14:36,150 --> 00:14:36,790 419 00:14:36,790 --> 00:14:40,310 420 00:14:40,310 --> 00:14:42,069 421 00:14:42,069 --> 00:14:43,750 422 00:14:43,750 --> 00:14:43,760 423 00:14:43,760 --> 00:14:44,069 424 00:14:44,069 --> 00:14:46,710 425 00:14:46,710 --> 00:14:46,720 426 00:14:46,720 --> 00:14:47,670 427 00:14:47,670 --> 00:14:49,590 428 00:14:49,590 --> 00:14:51,590 429 00:14:51,590 --> 00:14:53,829 430 00:14:53,829 --> 00:14:54,790 431 00:14:54,790 --> 00:14:56,710 432 00:14:56,710 --> 00:14:57,990 433 00:14:57,990 --> 00:14:58,000 434 00:14:58,000 --> 00:14:59,269 435 00:14:59,269 --> 00:15:02,790 436 00:15:02,790 --> 00:15:04,389 437 00:15:04,389 --> 00:15:06,389 438 00:15:06,389 --> 00:15:09,590 439 00:15:09,590 --> 00:15:09,600 440 00:15:09,600 --> 00:15:10,150 441 00:15:10,150 --> 00:15:11,509 442 00:15:11,509 --> 00:15:14,550 443 00:15:14,550 --> 00:15:16,310 444 00:15:16,310 --> 00:15:18,790 445 00:15:18,790 --> 00:15:20,870 446 00:15:20,870 --> 00:15:23,110 447 00:15:23,110 --> 00:15:24,710 448 00:15:24,710 --> 00:15:26,069 449 00:15:26,069 --> 00:15:28,310 450 00:15:28,310 --> 00:15:30,069 451 00:15:30,069 --> 00:15:32,150 452 00:15:32,150 --> 00:15:35,030 453 00:15:35,030 --> 00:15:36,470 454 00:15:36,470 --> 00:15:38,389 455 00:15:38,389 --> 00:15:39,990 456 00:15:39,990 --> 00:15:41,990 457 00:15:41,990 --> 00:15:45,269 458 00:15:45,269 --> 00:15:45,279 459 00:15:45,279 --> 00:15:48,230 460 00:15:48,230 --> 00:15:50,629 461 00:15:50,629 --> 00:15:51,990 462 00:15:51,990 --> 00:15:52,000 463 00:15:52,000 --> 00:15:52,710 464 00:15:52,710 --> 00:15:58,389 465 00:15:58,389 --> 00:16:05,670 466 00:16:05,670 --> 00:16:08,710 467 00:16:08,710 --> 00:16:09,189 468 00:16:09,189 --> 00:16:20,150 469 00:16:20,150 --> 00:16:21,749 470 00:16:21,749 --> 00:16:23,749 471 00:16:23,749 --> 00:16:25,430 472 00:16:25,430 --> 00:16:27,269 473 00:16:27,269 --> 00:16:30,870 474 00:16:30,870 --> 00:16:32,470 475 00:16:32,470 --> 00:16:34,870 476 00:16:34,870 --> 00:16:35,990 477 00:16:35,990 --> 00:16:39,110 478 00:16:39,110 --> 00:16:40,310 479 00:16:40,310 --> 00:16:46,310 480 00:16:46,310 --> 00:16:50,870 481 00:16:50,870 --> 00:16:52,389 482 00:16:52,389 --> 00:16:53,829 483 00:16:53,829 --> 00:16:55,430 484 00:16:55,430 --> 00:16:56,870 485 00:16:56,870 --> 00:16:57,749 486 00:16:57,749 --> 00:16:59,590 487 00:16:59,590 --> 00:17:01,030 488 00:17:01,030 --> 00:17:04,150 489 00:17:04,150 --> 00:17:06,390 490 00:17:06,390 --> 00:17:06,400 491 00:17:06,400 --> 00:17:09,829 492 00:17:09,829 --> 00:17:11,270 493 00:17:11,270 --> 00:17:12,870 494 00:17:12,870 --> 00:17:14,470 495 00:17:14,470 --> 00:17:17,350 496 00:17:17,350 --> 00:17:18,470 497 00:17:18,470 --> 00:17:22,390 498 00:17:22,390 --> 00:17:24,630 499 00:17:24,630 --> 00:17:26,230 500 00:17:26,230 --> 00:17:27,669 501 00:17:27,669 --> 00:17:29,270 502 00:17:29,270 --> 00:17:29,280 503 00:17:29,280 --> 00:17:30,789 504 00:17:30,789 --> 00:17:32,950 505 00:17:32,950 --> 00:17:33,830 506 00:17:33,830 --> 00:17:37,029 507 00:17:37,029 --> 00:17:39,430 508 00:17:39,430 --> 00:17:41,190 509 00:17:41,190 --> 00:17:44,549 510 00:17:44,549 --> 00:17:46,150 511 00:17:46,150 --> 00:17:48,150 512 00:17:48,150 --> 00:17:49,750 513 00:17:49,750 --> 00:17:51,590 514 00:17:51,590 --> 00:17:53,590 515 00:17:53,590 --> 00:17:55,190 516 00:17:55,190 --> 00:17:56,549 517 00:17:56,549 --> 00:17:57,830 518 00:17:57,830 --> 00:17:59,590 519 00:17:59,590 --> 00:18:01,750 520 00:18:01,750 --> 00:18:03,909 521 00:18:03,909 --> 00:18:05,590 522 00:18:05,590 --> 00:18:07,510 523 00:18:07,510 --> 00:18:09,510 524 00:18:09,510 --> 00:18:09,520 525 00:18:09,520 --> 00:18:10,870 526 00:18:10,870 --> 00:18:12,630 527 00:18:12,630 --> 00:18:14,150 528 00:18:14,150 --> 00:18:16,230 529 00:18:16,230 --> 00:18:18,549 530 00:18:18,549 --> 00:18:20,470 531 00:18:20,470 --> 00:18:22,070 532 00:18:22,070 --> 00:18:22,080 533 00:18:22,080 --> 00:18:23,590 534 00:18:23,590 --> 00:18:27,669 535 00:18:27,669 --> 00:18:29,270 536 00:18:29,270 --> 00:18:31,510 537 00:18:31,510 --> 00:18:33,590 538 00:18:33,590 --> 00:18:36,630 539 00:18:36,630 --> 00:18:39,669 540 00:18:39,669 --> 00:18:41,909 541 00:18:41,909 --> 00:18:44,150 542 00:18:44,150 --> 00:18:45,990 543 00:18:45,990 --> 00:18:48,549 544 00:18:48,549 --> 00:18:51,190 545 00:18:51,190 --> 00:18:52,870 546 00:18:52,870 --> 00:18:55,029 547 00:18:55,029 --> 00:18:56,630 548 00:18:56,630 --> 00:18:59,669 549 00:18:59,669 --> 00:19:01,110 550 00:19:01,110 --> 00:19:02,150 551 00:19:02,150 --> 00:19:05,350 552 00:19:05,350 --> 00:19:05,360 553 00:19:05,360 --> 00:19:05,909 554 00:19:05,909 --> 00:19:21,590 555 00:19:21,590 --> 00:19:24,070 556 00:19:24,070 --> 00:19:26,390 557 00:19:26,390 --> 00:19:29,190 558 00:19:29,190 --> 00:19:30,470 559 00:19:30,470 --> 00:19:31,830 560 00:19:31,830 --> 00:19:33,270 561 00:19:33,270 --> 00:19:36,830 562 00:19:36,830 --> 00:19:36,840 563 00:19:36,840 --> 00:19:40,310 564 00:19:40,310 --> 00:19:43,669 565 00:19:43,669 --> 00:19:47,430 566 00:19:47,430 --> 00:19:49,990 567 00:19:49,990 --> 00:19:50,870 568 00:19:50,870 --> 00:19:53,190 569 00:19:53,190 --> 00:19:54,630 570 00:19:54,630 --> 00:19:56,710 571 00:19:56,710 --> 00:19:58,549 572 00:19:58,549 --> 00:19:59,990 573 00:19:59,990 --> 00:20:02,230 574 00:20:02,230 --> 00:20:04,149 575 00:20:04,149 --> 00:20:05,750 576 00:20:05,750 --> 00:20:07,350 577 00:20:07,350 --> 00:20:09,750 578 00:20:09,750 --> 00:20:12,789 579 00:20:12,789 --> 00:20:14,870 580 00:20:14,870 --> 00:20:14,880 581 00:20:14,880 --> 00:20:15,669 582 00:20:15,669 --> 00:20:17,990 583 00:20:17,990 --> 00:20:19,350 584 00:20:19,350 --> 00:20:22,230 585 00:20:22,230 --> 00:20:27,669 586 00:20:27,669 --> 00:20:29,590 587 00:20:29,590 --> 00:20:32,310 588 00:20:32,310 --> 00:20:35,029 589 00:20:35,029 --> 00:20:35,039 590 00:20:35,039 --> 00:20:35,350 591 00:20:35,350 --> 00:20:37,990 592 00:20:37,990 --> 00:20:38,870 593 00:20:38,870 --> 00:20:41,590 594 00:20:41,590 --> 00:20:41,600 595 00:20:41,600 --> 00:20:42,710 596 00:20:42,710 --> 00:20:45,990 597 00:20:45,990 --> 00:20:49,510 598 00:20:49,510 --> 00:20:53,430 599 00:20:53,430 --> 00:20:55,590 600 00:20:55,590 --> 00:20:59,350 601 00:20:59,350 --> 00:21:02,070 602 00:21:02,070 --> 00:21:03,750 603 00:21:03,750 --> 00:21:05,669 604 00:21:05,669 --> 00:21:07,990 605 00:21:07,990 --> 00:21:10,390 606 00:21:10,390 --> 00:21:14,310 607 00:21:14,310 --> 00:21:16,630 608 00:21:16,630 --> 00:21:17,830 609 00:21:17,830 --> 00:21:21,909 610 00:21:21,909 --> 00:21:24,149 611 00:21:24,149 --> 00:21:25,110 612 00:21:25,110 --> 00:21:27,029 613 00:21:27,029 --> 00:21:28,470 614 00:21:28,470 --> 00:21:29,990 615 00:21:29,990 --> 00:21:33,029 616 00:21:33,029 --> 00:21:36,149 617 00:21:36,149 --> 00:21:38,230 618 00:21:38,230 --> 00:21:39,669 619 00:21:39,669 --> 00:21:41,990 620 00:21:41,990 --> 00:21:43,669 621 00:21:43,669 --> 00:21:45,029 622 00:21:45,029 --> 00:21:47,270 623 00:21:47,270 --> 00:21:47,280 624 00:21:47,280 --> 00:21:48,310 625 00:21:48,310 --> 00:21:51,190 626 00:21:51,190 --> 00:21:51,200 627 00:21:51,200 --> 00:21:51,750 628 00:21:51,750 --> 00:21:53,830 629 00:21:53,830 --> 00:21:55,909 630 00:21:55,909 --> 00:21:57,909 631 00:21:57,909 --> 00:21:59,750 632 00:21:59,750 --> 00:22:01,830 633 00:22:01,830 --> 00:22:03,270 634 00:22:03,270 --> 00:22:05,110 635 00:22:05,110 --> 00:22:07,990 636 00:22:07,990 --> 00:22:10,789 637 00:22:10,789 --> 00:22:15,029 638 00:22:15,029 --> 00:22:16,870 639 00:22:16,870 --> 00:22:18,710 640 00:22:18,710 --> 00:22:20,310 641 00:22:20,310 --> 00:22:22,230 642 00:22:22,230 --> 00:22:23,750 643 00:22:23,750 --> 00:22:23,760 644 00:22:23,760 --> 00:22:25,430 645 00:22:25,430 --> 00:22:29,270 646 00:22:29,270 --> 00:22:32,630 647 00:22:32,630 --> 00:22:34,710 648 00:22:34,710 --> 00:22:36,390 649 00:22:36,390 --> 00:22:40,070 650 00:22:40,070 --> 00:22:42,310 651 00:22:42,310 --> 00:22:43,510 652 00:22:43,510 --> 00:22:45,909 653 00:22:45,909 --> 00:22:47,990 654 00:22:47,990 --> 00:22:49,110 655 00:22:49,110 --> 00:22:52,149 656 00:22:52,149 --> 00:22:54,789 657 00:22:54,789 --> 00:22:56,470 658 00:22:56,470 --> 00:22:56,480 659 00:22:56,480 --> 00:22:58,230 660 00:22:58,230 --> 00:22:59,990 661 00:22:59,990 --> 00:23:02,149 662 00:23:02,149 --> 00:23:04,070 663 00:23:04,070 --> 00:23:04,080 664 00:23:04,080 --> 00:23:05,029 665 00:23:05,029 --> 00:23:08,549 666 00:23:08,549 --> 00:23:10,230 667 00:23:10,230 --> 00:23:11,909 668 00:23:11,909 --> 00:23:14,390 669 00:23:14,390 --> 00:23:16,630 670 00:23:16,630 --> 00:23:18,710 671 00:23:18,710 --> 00:23:19,830 672 00:23:19,830 --> 00:23:21,270 673 00:23:21,270 --> 00:23:22,710 674 00:23:22,710 --> 00:23:24,870 675 00:23:24,870 --> 00:23:26,789 676 00:23:26,789 --> 00:23:27,990 677 00:23:27,990 --> 00:23:29,750 678 00:23:29,750 --> 00:23:31,190 679 00:23:31,190 --> 00:23:31,200 680 00:23:31,200 --> 00:23:31,830 681 00:23:31,830 --> 00:23:33,669 682 00:23:33,669 --> 00:23:35,110 683 00:23:35,110 --> 00:23:38,070 684 00:23:38,070 --> 00:23:39,510 685 00:23:39,510 --> 00:23:39,520 686 00:23:39,520 --> 00:23:39,909 687 00:23:39,909 --> 00:23:43,590 688 00:23:43,590 --> 00:23:45,590 689 00:23:45,590 --> 00:23:46,789 690 00:23:46,789 --> 00:23:49,430 691 00:23:49,430 --> 00:23:49,440 692 00:23:49,440 --> 00:23:50,310 693 00:23:50,310 --> 00:23:53,909 694 00:23:53,909 --> 00:23:57,029 695 00:23:57,029 --> 00:23:58,310 696 00:23:58,310 --> 00:24:00,310 697 00:24:00,310 --> 00:24:02,470 698 00:24:02,470 --> 00:24:03,750 699 00:24:03,750 --> 00:24:09,269 700 00:24:09,269 --> 00:24:12,710 701 00:24:12,710 --> 00:24:14,310 702 00:24:14,310 --> 00:24:16,310 703 00:24:16,310 --> 00:24:19,110 704 00:24:19,110 --> 00:24:19,669 705 00:24:19,669 --> 00:24:22,870 706 00:24:22,870 --> 00:24:24,710 707 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--> 00:25:08,950 737 00:25:08,950 --> 00:25:13,029 738 00:25:13,029 --> 00:25:14,310 739 00:25:14,310 --> 00:25:16,310 740 00:25:16,310 --> 00:25:16,320 741 00:25:16,320 --> 00:25:17,190 742 00:25:17,190 --> 00:25:18,789 743 00:25:18,789 --> 00:25:20,789 744 00:25:20,789 --> 00:25:22,310 745 00:25:22,310 --> 00:25:23,990 746 00:25:23,990 --> 00:25:25,590 747 00:25:25,590 --> 00:25:27,350 748 00:25:27,350 --> 00:25:29,110 749 00:25:29,110 --> 00:25:31,510 750 00:25:31,510 --> 00:25:34,310 751 00:25:34,310 --> 00:25:35,590 752 00:25:35,590 --> 00:25:35,600 753 00:25:35,600 --> 00:25:36,230 754 00:25:36,230 --> 00:25:38,950 755 00:25:38,950 --> 00:25:40,230 756 00:25:40,230 --> 00:25:43,269 757 00:25:43,269 --> 00:25:45,990 758 00:25:45,990 --> 00:25:46,000 759 00:25:46,000 --> 00:25:47,110 760 00:25:47,110 --> 00:25:48,789 761 00:25:48,789 --> 00:25:50,870 762 00:25:50,870 --> 00:25:53,669 763 00:25:53,669 --> 00:25:55,590 764 00:25:55,590 --> 00:25:59,669 765 00:25:59,669 --> 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795 00:26:52,240 --> 00:26:56,230 796 00:26:56,230 --> 00:26:59,269 797 00:26:59,269 --> 00:27:02,390 798 00:27:02,390 --> 00:27:06,710 799 00:27:06,710 --> 00:27:08,710 800 00:27:08,710 --> 00:27:10,710 801 00:27:10,710 --> 00:27:13,430 802 00:27:13,430 --> 00:27:15,190 803 00:27:15,190 --> 00:27:16,390 804 00:27:16,390 --> 00:27:18,549 805 00:27:18,549 --> 00:27:20,149 806 00:27:20,149 --> 00:27:22,710 807 00:27:22,710 --> 00:27:22,720 808 00:27:22,720 --> 00:27:23,510 809 00:27:23,510 --> 00:27:27,510 810 00:27:27,510 --> 00:27:30,549 811 00:27:30,549 --> 00:27:33,590 812 00:27:33,590 --> 00:27:34,310 813 00:27:34,310 --> 00:27:35,750 814 00:27:35,750 --> 00:27:37,510 815 00:27:37,510 --> 00:27:37,520 816 00:27:37,520 --> 00:27:38,470 817 00:27:38,470 --> 00:27:40,549 818 00:27:40,549 --> 00:27:43,510 819 00:27:43,510 --> 00:27:45,269 820 00:27:45,269 --> 00:27:46,870 821 00:27:46,870 --> 00:27:47,990 822 00:27:47,990 --> 00:27:49,830 823 00:27:49,830 --> 00:27:51,350 824 00:27:51,350 --> 00:27:53,350 825 00:27:53,350 --> 00:27:55,029 826 00:27:55,029 --> 00:27:57,750 827 00:27:57,750 --> 00:27:57,760 828 00:27:57,760 --> 00:27:58,070 829 00:27:58,070 --> 00:27:59,909 830 00:27:59,909 --> 00:28:01,990 831 00:28:01,990 --> 00:28:03,669 832 00:28:03,669 --> 00:28:05,510 833 00:28:05,510 --> 00:28:07,350 834 00:28:07,350 --> 00:28:09,830 835 00:28:09,830 --> 00:28:13,029 836 00:28:13,029 --> 00:28:14,630 837 00:28:14,630 --> 00:28:16,070 838 00:28:16,070 --> 00:28:18,389 839 00:28:18,389 --> 00:28:18,399 840 00:28:18,399 --> 00:28:19,110 841 00:28:19,110 --> 00:28:22,230 842 00:28:22,230 --> 00:28:23,110 843 00:28:23,110 --> 00:28:25,350 844 00:28:25,350 --> 00:28:26,710 845 00:28:26,710 --> 00:28:30,070 846 00:28:30,070 --> 00:28:30,080 847 00:28:30,080 --> 00:28:30,549 848 00:28:30,549 --> 00:28:33,269 849 00:28:33,269 --> 00:28:35,510 850 00:28:35,510 --> 00:28:38,070 851 00:28:38,070 --> 00:28:40,470 852 00:28:40,470 --> 00:28:43,510 853 00:28:43,510 --> 00:28:43,520 854 00:28:43,520 --> 00:28:44,149 855 00:28:44,149 --> 00:28:47,909 856 00:28:47,909 --> 00:28:50,470 857 00:28:50,470 --> 00:28:51,110 858 00:28:51,110 --> 00:28:53,830 859 00:28:53,830 --> 00:28:53,840 860 00:28:53,840 --> 00:28:54,389 861 00:28:54,389 --> 00:28:56,310 862 00:28:56,310 --> 00:28:58,389 863 00:28:58,389 --> 00:29:01,669 864 00:29:01,669 --> 00:29:04,389 865 00:29:04,389 --> 00:29:07,510 866 00:29:07,510 --> 00:29:08,789 867 00:29:08,789 --> 00:29:10,470 868 00:29:10,470 --> 00:29:12,549 869 00:29:12,549 --> 00:29:14,789 870 00:29:14,789 --> 00:29:15,990 871 00:29:15,990 --> 00:29:17,350 872 00:29:17,350 --> 00:29:19,029 873 00:29:19,029 --> 00:29:20,789 874 00:29:20,789 --> 00:29:22,149 875 00:29:22,149 --> 00:29:24,070 876 00:29:24,070 --> 00:29:26,310 877 00:29:26,310 --> 00:29:29,669 878 00:29:29,669 --> 00:29:32,070 879 00:29:32,070 --> 00:29:38,549 880 00:29:38,549 --> 00:29:40,710 881 00:29:40,710 --> 00:29:41,909 882 00:29:41,909 --> 00:29:43,830 883 00:29:43,830 --> 00:29:44,950 884 00:29:44,950 --> 00:29:47,029 885 00:29:47,029 --> 00:29:49,269 886 00:29:49,269 --> 00:29:51,590 887 00:29:51,590 --> 00:29:53,269 888 00:29:53,269 --> 00:29:54,789 889 00:29:54,789 --> 00:29:56,950 890 00:29:56,950 --> 00:29:58,710 891 00:29:58,710 --> 00:30:02,789 892 00:30:02,789 --> 00:30:05,110 893 00:30:05,110 --> 00:30:07,350 894 00:30:07,350 --> 00:30:10,230 895 00:30:10,230 --> 00:30:11,190 896 00:30:11,190 --> 00:30:15,669 897 00:30:15,669 --> 00:30:19,110 898 00:30:19,110 --> 00:30:23,110 899 00:30:23,110 --> 00:30:24,470 900 00:30:24,470 --> 00:30:26,789 901 00:30:26,789 --> 00:30:34,070 902 00:30:34,070 --> 00:30:35,430 903 00:30:35,430 --> 00:30:37,269 904 00:30:37,269 --> 00:30:38,630 905 00:30:38,630 --> 00:30:38,640 906 00:30:38,640 --> 00:30:39,750 907 00:30:39,750 --> 00:30:42,950 908 00:30:42,950 --> 00:30:45,110 909 00:30:45,110 --> 00:30:49,269 910 00:30:49,269 --> 00:30:52,310 911 00:30:52,310 --> 00:30:55,990 912 00:30:55,990 --> 00:31:00,070 913 00:31:00,070 --> 00:31:10,070 914 00:31:10,070 --> 00:31:13,830 915 00:31:13,830 --> 00:31:16,870 916 00:31:16,870 --> 00:31:21,590 917 00:31:21,590 --> 00:31:24,789 918 00:31:24,789 --> 00:31:26,310 919 00:31:26,310 --> 00:31:27,909 920 00:31:27,909 --> 00:31:29,430 921 00:31:29,430 --> 00:31:31,190 922 00:31:31,190 --> 00:31:33,669 923 00:31:33,669 --> 00:31:35,350 924 00:31:35,350 --> 00:31:38,870 925 00:31:38,870 --> 00:31:42,950 926 00:31:42,950 --> 00:31:45,110 927 00:31:45,110 --> 00:31:45,120 928 00:31:45,120 --> 00:31:48,470 929 00:31:48,470 --> 00:31:50,310 930 00:31:50,310 --> 00:31:50,320 931 00:31:50,320 --> 00:31:52,389 932 00:31:52,389 --> 00:31:55,669 933 00:31:55,669 --> 00:31:59,990 934 00:31:59,990 --> 00:32:03,350 935 00:32:03,350 --> 00:32:23,029 936 00:32:23,029 --> 00:32:25,190 937 00:32:25,190 --> 00:32:30,870 938 00:32:30,870 --> 00:32:32,470 939 00:32:32,470 --> 00:32:34,870 940 00:32:34,870 --> 00:32:36,549 941 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--> 00:33:30,549 971 00:33:30,549 --> 00:33:37,750 972 00:33:37,750 --> 00:33:40,230 973 00:33:40,230 --> 00:33:40,240 974 00:33:40,240 --> 00:33:41,110 975 00:33:41,110 --> 00:33:44,310 976 00:33:44,310 --> 00:33:45,830 977 00:33:45,830 --> 00:33:47,830 978 00:33:47,830 --> 00:33:51,029 979 00:33:51,029 --> 00:33:52,470 980 00:33:52,470 --> 00:33:55,350 981 00:33:55,350 --> 00:33:55,360 982 00:33:55,360 --> 00:33:55,750 983 00:33:55,750 --> 00:33:57,990 984 00:33:57,990 --> 00:33:58,000 985 00:33:58,000 --> 00:33:58,789 986 00:33:58,789 --> 00:34:01,669 987 00:34:01,669 --> 00:34:01,679 988 00:34:01,679 --> 00:34:02,310 989 00:34:02,310 --> 00:34:05,590 990 00:34:05,590 --> 00:34:06,789 991 00:34:06,789 --> 00:34:10,149 992 00:34:10,149 --> 00:34:13,990 993 00:34:13,990 --> 00:34:15,669 994 00:34:15,669 --> 00:34:17,349 995 00:34:17,349 --> 00:34:19,190 996 00:34:19,190 --> 00:34:21,270 997 00:34:21,270 --> 00:34:22,470 998 00:34:22,470 --> 00:34:24,310 999 00:34:24,310 --> 00:34:25,510 1000 00:34:25,510 --> 00:34:28,550 1001 00:34:28,550 --> 00:34:32,710 1002 00:34:32,710 --> 00:34:34,230 1003 00:34:34,230 --> 00:34:35,829 1004 00:34:35,829 --> 00:34:36,629 1005 00:34:36,629 --> 00:34:39,589 1006 00:34:39,589 --> 00:34:40,629 1007 00:34:40,629 --> 00:34:42,230 1008 00:34:42,230 --> 00:34:43,349 1009 00:34:43,349 --> 00:34:44,710 1010 00:34:44,710 --> 00:34:47,829 1011 00:34:47,829 --> 00:34:49,190 1012 00:34:49,190 --> 00:34:51,349 1013 00:34:51,349 --> 00:34:51,359 1014 00:34:51,359 --> 00:34:52,710 1015 00:34:52,710 --> 00:34:54,790 1016 00:34:54,790 --> 00:34:56,790 1017 00:34:56,790 --> 00:34:56,800 1018 00:34:56,800 --> 00:34:57,510 1019 00:34:57,510 --> 00:35:00,150 1020 00:35:00,150 --> 00:35:01,190 1021 00:35:01,190 --> 00:35:03,190 1022 00:35:03,190 --> 00:35:04,310 1023 00:35:04,310 --> 00:35:07,670 1024 00:35:07,670 --> 00:35:11,510 1025 00:35:11,510 --> 00:35:13,109 1026 00:35:13,109 --> 00:35:13,119 1027 00:35:13,119 --> 00:35:15,349 1028 00:35:15,349 --> 00:35:16,710 1029 00:35:16,710 --> 00:35:18,550 1030 00:35:18,550 --> 00:35:21,750 1031 00:35:21,750 --> 00:35:25,829 1032 00:35:25,829 --> 00:35:29,990 1033 00:35:29,990 --> 00:35:32,470 1034 00:35:32,470 --> 00:35:34,390 1035 00:35:34,390 --> 00:35:34,400 1036 00:35:34,400 --> 00:35:37,430 1037 00:35:37,430 --> 00:35:40,470 1038 00:35:40,470 --> 00:35:42,310 1039 00:35:42,310 --> 00:35:43,910 1040 00:35:43,910 --> 00:35:45,750 1041 00:35:45,750 --> 00:35:47,190 1042 00:35:47,190 --> 00:35:50,230 1043 00:35:50,230 --> 00:35:53,910 1044 00:35:53,910 --> 00:35:55,270 1045 00:35:55,270 --> 00:35:56,710 1046 00:35:56,710 --> 00:35:58,310 1047 00:35:58,310 --> 00:35:59,270 1048 00:35:59,270 --> 00:36:02,390 1049 00:36:02,390 --> 00:36:04,310 1050 00:36:04,310 --> 00:36:05,910 1051 00:36:05,910 --> 00:36:08,310 1052 00:36:08,310 --> 00:36:09,030 1053 00:36:09,030 --> 00:36:12,069 1054 00:36:12,069 --> 00:36:13,670 1055 00:36:13,670 --> 00:36:15,430 1056 00:36:15,430 --> 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