Martin Karplus (2016) - Motion: Hallmark of Life. From Marsupials to Molecules

In this lecture what I shall try to do is to trace an intellectual pass from motion in animals to a molecule which makes this motion possible. Let me begin by showing you a marsupial which was in the title. This is the opossum, it’s the only North American marsupial. It’s an animal that carries its young in a pouch, like kangaroos, unlike placental mammals like us, or at least a fraction of us. And on the right is shown the molecule ATP synthase which makes what’s already been mentioned before, the molecule ATP which is called the currency of life. Now why do I start with the opossum? Because it can, where the word comes from, "play possum", in other words it can look as if it’s dead. This is a fear reflex. It has an involuntary comatose state induced by extreme fear. Predators find “the kill”, namely to kill their prey an important part of being excited to go after their prey. So if the opossum is already dead they’ll just hopefully go away. And when the opossum wakes up after a while it will be safe. The opossum does something in addition to this. It also is able to emit a putrid smell, which I won’t show here, which makes it even more likely that the predator will say, I don’t want this. Now, when one first thinks about it, if you think that, well, playing possum is something that’s very rare. But in fact it’s very common. It was given the name tonic immobility which didn’t mean we understood anything about it at all but people liked to give a name and they’re very important in making big papers appear in “Nature” and such. But actually it was found that it’s very general. It exists from insects to mammals and it was discovered in about 1646 by a Jesuit priest named Kircher. He saw that chickens would every so often fall down, and his interpretation was that they were communicating with God, they had made their peace with the world and when they woke up they were ready to be slaughtered. (Laughter) So it didn’t actually, didn’t have survival value in this particular case. I show the hognose snake which is very common in New England, it probably doesn’t mean anything to you. But again it’s very, it looks as dead as can be. Now, how does this actually happen? Well it’s now known that the hypothalamus is the source of these reflexes and that it works by neurotransmitters. This gives me the opportunity to actually talk about my grandfather, Johann Paul Karplus, who was a neurologist in Vienna and he actually discovered how the hypothalamus worked. And for a part of the brain it is very interesting. But what he did was to anesthetise cats and then he took all the nerves from the hypothalamus and cut them away, stimulated the hypothalamus and noticed that the cats had this fear reflex where their eyes opened wide. And so he reasoned that actually this particular part of the brain was not working by nervous impulses but rather by producing hormones. And it’s a relatively restricted part of the brain that does use hormones. Interestingly, Otto Loewi, a scientist, did something similar about 25 years later in which he took a frog heart, isolated it, stimulated the vagus nerve, which makes the heart beat faster, had this frog heart in solution and then took the solution and put another frog heart into it and discovered it also moved faster as if it was excited. For this he got the Nobel Prize in 1938. My grandfather who discovered this in 1900 didn’t get a Nobel Prize. But that’s the way Nobel Prizes actually work. Let me now go on and begin to talk, something that is related to what the Nobel Prize was given for. And let me just read this. was that a classical mechanical description of the atomic motions is adequate in most cases.” Particularly at room temperature where most of us live. And as far as I’m concerned I realise this, I studied a very simple reaction in the 1960s which is the H+H2 exchange reaction, a hydrogen atom and a hydrogen molecule collides to give you a new hydrogen molecule, an atom. And what we found was that if we use a potential which was calculated by approximate quantum mechanics and just solve Newton’s law step by step, F=ma, we were able to obtain the reaction cross sections in very good agreement with experiments. They were limited and then 10 years later with complete quantum mechanical calculations. So given this, if hydrogen atoms, the lightest atoms, which you’d expect to be most quantum mechanical, can be treated by classical mechanics and proteins or DNA. Others are made up of carbon, nitrogen, oxygen which are heavier, though about half of the proteins are still hydrogen atoms. You should be able to do what we did on a computer for H+H2 for a system which has 1,500 degrees of freedom like myoglobin. And indeed that’s what we started to do. Now, my chemistry colleagues said, well, you know we can’t really work very well with these small molecules. You’re crazy to think that you can get interesting results for big molecules like proteins. And the biologists said, well, even if you get these results we wouldn’t be very interested. One of the important points I want to make is that students, if you have a good idea, you should stick to that good idea and not let somebody argue you out of it. So let me now go on and ask the question, what makes molecules and biological systems special? Now, using F=ma, solving Newton’s equation, we have on the left a man-made polymer which is 153 units. The side chain is a methyl group. On the right we have a nature-made polymer, myoglobin, which also has 153 units. And R are the side chains, which you certainly knew and also have heard over and over again in some of these lectures, determine the structure of the molecule, the sequence of amino acids. And if we now look at their motions, there really isn’t anything particularly different. You wouldn’t be able to distinguish the man-made molecule from the nature-made molecule. So what is it that’s special about the molecules in biological systems? And one key to thinking about this comes from Richard Feynman's famous lectures. Feynman has already appeared when people were discussing quantum electrodynamics. But he was interested in everything. And he wrote, “... everything that living things do can be understood in terms of the jigglings and wigglings of atoms.” Now interestingly when I was sort of doing research on this, not chemical research but just trying to understand better what can go on, I came across the writings of Titus Lucretius who was a Roman poet. He wrote one poem as far as we know called “The Nature of Things”. And he wrote, “The atoms are eternal and always moving. Everything comes into existence simply because of the random movement of atoms, which, given enough time, will form and reform, constantly experimenting with different configurations of matter from which will eventually emerge everything we know." Which is very similar in some sense, maybe more poetic. Feynman never was really poetic, he just got to the point of what he was trying to say. But it has the similar idea. And then if you look further into history you find that the Greeks actually, Democritus and other philosophers, had rather detailed ideas about atoms. They knew that atoms in solids were strongly bound together, that atoms in liquids could move past each other. And that was, you know, in about 300 BC. And then this information was completely lost. And it was only John Dalton with his atomic theory in the 1800s that he introduced the idea, obviously with more factual data. He didn’t know anything about what the Greeks did. And again, that’s something to remember, that if somebody makes a great discovery and it has no effect on the future of science, is it useful or is it not? The individual may think, ah, I really discovered something great. But it actually doesn’t move science forward. So let me now go actually to look at a couple of specific molecules you all know and we saw this in this example. Each atom at room temperature has 3 kt of kinetic energy. We have heard about Brownian motion, they move sort of randomly. So how does nature take this random motion of the individual atoms and make it to do something useful? And the answer is that it has evolved structures which make it easiest, requiring the lowest free energy, for example, to do what they’re supposed to do. And here I show you an enzyme. On the left is the enzyme open structure, on the right it has a closed structure. And let’s just think about enzyme, it doesn’t matter exactly what it’s doing, but the following: Nature wants to be able to bring the substrates into the catalytic site where the action takes place, and you’ve heard much about enzymes in the earlier talks. And then it wants to isolate this region from solution so that a side reaction induced by water doesn’t happen. And then after the reaction has taken place it has to open up again and release the products. Well, let me show you this as a cartoon of an enzyme that transfers a phosphate group from 2 adenosine diphosphates between them. Let me just show you the cartoon. On the left you see the substrate coming in, the 2 substrates and when they’re in there the lid closes over them and gives you this catalytic reactor that the system needs. After the reaction has taken place, and if you look carefully on the right, you will be able to see one of the phosphate groups moving over, and once this has happened the system opens up again and the products move out. Now, how has nature done this? Remember that we are dealing with random motions. And if we look here, what I have illustrated here with green lines, evolution has introduced these hinges, so that it’s very easy, it takes less free energy, for the lid to close over the core. And other motions, the jigglings of Feynman rather than these wigglings, if you like, play a role in making this possible. But the overall closing is directed by the fact that that’s the easiest motion to occur. Let me now talk about another system which is kinesin, which is a motor that walks on microtubules, although you may have seen pictures of cells which look like a big mess, they have a large number of different molecules in them. But nevertheless they are organised and in particular cells have rails which go from one end of the cell to the other. And kinesin is a molecule which has 2 globular catalytic units or feet which walk on the microtubules. And then they come together to form a coiled-coil and at the top is a vesicle whose structure isn’t actually known. So it isn’t shown here. And it’s in that part of the molecule that it carries things from one part of the cell to another. So let’s look at what the system does. And one thing, I have talked about ATP and you will see when ATP binds right now, the other foot is thrown forward, the left foot, and then if we look again - again the mechanism is more complicated – ATP comes in and the right foot is thrown forward and so on. And if we look here there’s a micrograph. It’s actually real-time but enlarged about 10 million times. And you see the rails and you see kinesin molecules walking on these, moving on these rails, you obviously can’t see that they’re walking. They move in both directions which means there are different kinds of kinesins because some move in one direction and some move in the other. And if we now go back and look a little bit more, if we watch there goes the left foot forward and then the right foot forward and so on. And to me I used to describe this, it’s like the walking of a man with artificial legs. But thanks to Boston Dynamics which you have already heard a lot about - Google bought it because they’re very clever. And somebody said about the dogs, well, walking on 4 feet is difficult. But here we have somebody who walks on 2 feet, and he certainly walks very much like kinesin walks on the microtubules. Of course, the people at Boston Dynamics, I have talked to them, didn’t know anything about kinesin and that nature had invented it first. But nevertheless we have it here. Now, of course, the importance of having motors like this is that they do something. And in particular when cells divide they pull the genetic part of the daughter cells apart. If you inhibit kinesins you may be able to prevent the reproduction, the faster reproduction of cancer cells. And so it’s being used for that. It’s also, and I think this may have been mentioned, important in the brain and other parts of the system. You know that the nerve usually has a cell body. And then it has often a long axon, very long in the giant squid axon, and then meets the next body to transmit information. And the nerve has to get food down this axon and a kinesin carries it down. And one other thing I just want to mention is you know viruses are very clever. We’ve heard about how they evade the antibiotics and such. And they’ve actually learned that if they jump on top of a kinesin molecule, they can get from one part of a cell to the other in about 10 minutes instead of 10 hours which it would take by Brownian motion. Well, myoglobin, as I have already mentioned, is a very important molecule. In particular you have large amounts in the muscles of diving mammals because it stores the oxygen which is necessary for aerobic metabolism, an efficient way to generate the ATP, which they need to make their muscles work. And so this gives me the excuse of showing some of these dolphins because specifically somebody noted that dolphins require 20% more oxygen than they can store in myoglobin to dive 350 meters by continuous swimming. And they photograph the dolphins under water. And they noticed rather than they are swimming continuously, basically they take a stroke with their tail fins and then glide and take another stroke. And buy doing this, by sort of gliding silently, they were able to dive as deep as they do. Here you hear them talking to each other. They are in pairs. You can see the tail fins moving. And they really are a lot of fun. And obviously people try to study dolphins. I will show you another picture which has absolutely nothing to do in detail with my talk but it’s really spectacular. These are spinning dolphins. And now if you watch – here he comes – he spins around. Now, we don’t really know why they do this, whether it’s for the fun of it, whether they’re demonstrating in front of a female. But as we all know dolphins have been subject to a lot of study and many people think they communicate almost like human beings. But getting back to oxygen. (Laughter) We’ve already talked about it. And oxygen is used to make ATP. Now, we have seen how it’s used in the walking of the kinesin molecules, it’s also used in synthesis reactions. And maybe I should say this, that what you can see from this slide, which was in French where I first gave this talk, in France, that ATP plus water molecules hydrolysed to ADP plus PI plus a hydrogen atom. And this liberates about 7.3 kilocalories under standard conditions. Now, if this just happened in water all it would do is raise the temperature, you know 1 kilocalorie raises the temperature of a litre of water by 1 degree. And that would be a very inefficient way of using it. So we use it to make motors work and we also use it to shift the equilibrium of synthesis reactions that we need to make amino acid and lipids and so on. Let’s look a little at the ATP metabolism. That’s already come up, I’ve forgotten in whose talk. But the sedentary adult uses about 40 kilograms a day, sedentary adults like us. A runner uses about that much in a race or something like that. And so the interesting thing is that in our body we only store a very small amount, 250 grams, which, given this arithmetic, tells you in about 10 minutes all the ATP we would have would have been used up, it would have been hydrolysed overall. And so something has to make it go backwards. So ATP is being synthesised continuously from ADP and PI. And each ATP molecule is used about 500 times a day. Now, where does this happen? It happens in the mitochondria. They are about the size of bacteria and some people think that they were actually bacteria which were incorporated into the cells. And this is a low resolution micrograph. If you make an artist drawing of it you can see that it has convoluted inner membrane on which are little sticks with balls on them. And these are the ATP synthase molecules. Here’s a photomicrograph enlarged which actually shows them. And basically, the oxygen, which I have mentioned repeatedly, and energy from glucose in aerobic production produces 38 molecules of ATP for 6 molecules of oxygen. And again the numbers are, there are thousands of mitochondria per cell, each one has 15,000 ATP syntheses. So there are 30 million ATP syntheses per cell. So we go back now to what I showed at the beginning, this ATP synthase motor, which has 3 Beta subunits which are the active ones, 3 Alpha subunits which contribute something and has a Gamma subunit which goes through the inner part of it. And now if you give it ATP and PI and it’s connected to the F zero ATP synthase which is in the membrane, which has a hydrogen gradient, which has already been talked about - which Peter Mitchell received the Nobel Prize for his hypothesis about the hydrogen gradients being important – this turns the subunit in the membrane, which then turns the Gamma subunit, which causes conformational changes of the Beta subunits in particular to synthesise ATP. Now, one can run this motor in reverse. Namely you can give the motor ATP, usually you separate it from the membrane part and then observe that it works as a motor rotating the Gamma subunit which is in here. And this was actually first demonstrated by Kinoshita and his group in Japan. This whole group in Japan has done beautiful single-molecule work. That really has been important in understanding molecular motors like the ATP synthase. And what they did, if we now turn this whole thing upside down, and they attached an acting filament. That has nothing to do with myosin walking on actin but it just is a big molecule so it’s easy to see, and over here you actually see the rotation. Now, obviously with the big molecule like this there’s a large frictional drag. If you use a small gold particle under ideal conditions this can, this little motor can rotate about 1,000 times a second. Now, something that was learned very recently, and that ties in a little bit with Ada Yonath’s talk about the ribosome, Weissman and his co-workers published a paper in 2014 where they were able to determine the absolute protein synthesis rate of different compounds. There was an E.coli and in particular the ATP synthase. And what they found was that the ribosome, well, maybe I’ll say a little bit this way, the ATP synthase has 10 e subunits which are in the membrane and has 3 Alpha and 3 Beta subunits. And the ribosome makes exactly the ratio that’s required for making the whole molecule. In other words, it doesn’t make extra Alpha subunits or something like that. Partly it saves energy and partly it avoids having these isolated subunits which might form these organised globules rather than the regular proteins. So that’s really some new knowledge that just came very recently. Now, let me go finally to talk as far as the main talk is concerned. The question is I said that when ATPase as it’s called, if it doesn’t have the membrane part, acts as a motor. It makes the, if you feed it ATP, it makes the Gamma subunit rotate. And so we did some simulations of this where we took the - I just show you the Beta subunits, the active ones, and made them open and close in the way that they do and observed the rotation that occurs. And you see again the little wiggling before anything happens of Feynman’s and then the jiggling, the larger motion, and it’s stepwise in 35 degrees and 85 degrees. And 3 of these rotations give you 360 degrees. But what you saw was that the opening and closing of the subunits are the factor that leads to rotation. And so you ask how does an in and out motion like this give you a rotation? And the answer is, what you might think, we’re now looking down on the molecule. This is the Gamma subunit, the red is the methionine which is known to be very important, if you mutate it, it doesn’t work. And if we watch what happens, you can see that - we’re repeating now – one of the Beta subunits basically kicks the Gamma subunit off centre. And if it’s sort of held in this cone here, if you kick it off centre, it will rotate. And that’s how nature has figured out to do this. And actually in a Stirling engine, which I will not show, it uses the same principle. So these are all the people that contributed. Many of these things were taken down from articles. Some of them with permission, some of them, one assumes that they’re freely available on the web, if you give credit it’s alright. These are some of the students that worked on this. And now I want to go to the last slide that I showed in my Nobel Lecture which said that as time goes on applications of simulations will be used for ever more complex systems - viruses, ribosomes, cells. Some of this is actually happening in the brain and I just want to show you one example of the brain that we’re actually looking at. And this is this little worm. Now, this little worm is very special because in our case, if you have identical twins, they will not have identical brains because of a certain randomness in the brain. But in this little worm everything is determined by genetics, as Sydney Brenner showed long, long ago, in 1986, in which he made sections to look at this. And he showed that there were 302 neurons, every little worm had 302 neurons and 6,400 synapses approximately. So if you have a population of worms and they have the same genetic makeup, they will really be identical. And so looking at the PNAS I saw a paper of Aravinthan Samuel’s group which studied these worms. And what they did was they took plates, 10 centimetres by 10 centimetres. They were very close together so the worms moved only in 2 dimensions which made it easier to analyse the motion. And then they found, or thought that they found, that if they raised the worm at 15 degrees – maybe I can show you some of the trajectory – if they raised the worms at 15 degrees and had a thermal gradient along the x-axis and no gradient along the y-axis, the worms would stay in this region where they were raised. What I recognise is that they were just looking at these trajectories trying to do a little bit of statistics. But I knew that from studying protein folding we had analysed trajectories, protein folding trajectories, and whether they were made by the worms moving or by us, by proteins, we could analyse them in the same way. And the essential idea is that we can take all of these trajectories together and get statistically meaningful results. And I won’t go through the details of what we found. But what we found was in the converged results we have to use a Markov state model which gave a certain amount of time between the recording of the results, and we expressed it in free energy which is just probability. And along the x-direction where there was the gradient you see that the free energy is high, meaning that the worms don’t like it. But along the low temperature it’s high but along the high temperature you don’t really see that the worms don’t like it. It was a great surprise to the people who were doing the analysis and it basically destroyed many dogma. If you look in the y-direction where there was no gradient you get uniform converged results. Following up on this we’re now working on a paper to describe these results. But the interesting thing for you is that we took something from a completely different field, protein folding, and were able to use it to analyse how these worms move. Now, two other things I want to mention. One is that Jean-Pierre Changeux, who is a famous neuroscientist, said that every scientist should have a secret garden. We know that many scientists are musicians. I’m not musical at all. But my secret garden is shown here, it’s photography. And I’ll just run through very quickly, through a number of photographs. This is actually from Germany, in Mosel Valley. You can see all the vineyards climbing up on the hills. This is Hong Kong before, when Hong Kong looked like a little village instead of what you see when you look at Hong Kong which is all sky scrapers. And I’ll just run through this, just to show you. This is Israel. And this is a self-portrait of me with my Leica. And now, finally, what I would like to do is to read a quotation. This is from an interview, the last interview of a good friend of mine who has passed away, Alex Rich, a famous scientist. He actually appeared in Ada Yonath’s slide as a thank-you for being part of the commission of the Weizman institute or something like that. But let me just read this to you. What often happens when they go to school is that they are taught what is known in such a way as to stifle their curiosity. Scientists are the grown-ups who remain as curious about the world as they were when they were little children.” Thank you very much.

Martin Karplus (2016)

Motion: Hallmark of Life. From Marsupials to Molecules

Martin Karplus (2016)

Motion: Hallmark of Life. From Marsupials to Molecules

Abstract

The lecture will present an intellectual path from the role of motion in animals to the molecules that make the motion possible. Motion is usually a way of distinguishing live animals from those that are not, but not always. Just as for the whole animal, motion is an essential part of the function of the cellular components. What about the molecules themselves? Does motion distinguish animate from inanimate molecules? For animals to move, they require energy, which is obtained primarily by using oxygen. So how are whales and dolphins able to use their muscles to dive to great depths, where oxygen is not available? The immediate energy source for muscle function is the molecule ATP. Nature, by evolution, has developed a marvelous rotary nanomotor for the generation of this molecule. Experiments and simulations, particularly those with supercomputers, are now revealing the mechanism of this nanomotor and other cellular machines.

Content User Level

Beginner  Intermediate  Advanced 

Cite


Specify width: px

Share

COPYRIGHT

Content User Level

Beginner  Intermediate  Advanced 

Cite


Specify width: px

Share

COPYRIGHT


Related Content