Protein Folding and Disease

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00:00:08.00 Hi there. I'm Susan Lindquist.
00:00:10.29 I'm at the Whitehead Institute in the Department of Biology at MIT,
00:00:14.19 and I'm here to tell you about protein folding.
00:00:18.10 Protein folding is a universal problem
00:00:21.19 of biological systems,
00:00:23.09 and it winds up influencing
00:00:25.29 every aspect of biology that you can imagine.
00:00:30.23 So, these are very simple organisms
00:00:33.19 called the yeast, Saccharomyces cerevisiae.
00:00:35.18 It's a microorganism.
00:00:37.16 This is obviously a very, very large magnification of these organisms.
00:00:41.06 That organism is responsible for beer, bread, wine --
00:00:44.29 all kinds of things that make life worth living.
00:00:48.12 Anyway, that organism is also
00:00:52.04 a wonderful experimental system
00:00:53.26 that has the same types of problems with protein folding
00:00:56.08 that those organisms over there have.
00:00:59.22 This is a universal aspect of life.
00:01:03.05 And we're used to thinking about life
00:01:05.27 in terms of all the very different things
00:01:07.22 that make up different individuals,
00:01:09.18 but there's a unifying principle of life
00:01:12.15 that relates to protein folding
00:01:14.24 and that plays out from this organism to that organism,
00:01:18.28 in ways that allow us to deeply understand
00:01:22.17 some the worst problems in human biology
00:01:24.08 and try to find clever solutions to fix them.
00:01:31.10 So, proteins are us.
00:01:34.09 Many people think about proteins as being food,
00:01:38.01 but the reason why we think of them as being food
00:01:40.21 is because we need to take some of those elements
00:01:43.15 of proteins into ourselves,
00:01:45.06 chop them up into little pieces,
00:01:48.02 and reassemble them into our own proteins.
00:01:50.29 Because proteins do just about everything
00:01:52.20 that you can think of in our bodies.
00:01:54.12 Proteins are the muscle that powers our arms and legs.
00:01:59.12 Proteins are carrying pigments in our eyes,
00:02:03.05 and it's when light strikes those pigments
00:02:06.11 -- that causes the protein to change shape --
00:02:08.04 that sends a signal to our brain,
00:02:10.00 and that's how we see.
00:02:11.19 Proteins are parked in our stomachs
00:02:13.22 and ready to receive the food we eat and...
00:02:16.14 and tear it apart into little component parts
00:02:19.12 that we can use to build up new proteins,
00:02:21.18 that, as I mentioned,
00:02:24.17 do just about everything in our biology
00:02:27.11 that we think about as a living system.
00:02:31.07 Now, the problem with protein folding
00:02:34.11 is that these things look kinda complicated, right?
00:02:37.19 And they are very complicated.
00:02:39.12 But they start out very simply.
00:02:42.08 So, the code of life
00:02:45.03 is often called the double helix.
00:02:46.18 And it's a very long, linear string of information.
00:02:51.09 It itself doesn't look too interesting.
00:02:53.24 But along different parts of this,
00:02:57.13 it codes for the essential elements of proteins
00:03:00.14 that make up living systems.
00:03:02.27 And a good analogy for the way
00:03:05.18 in which this information is encoded
00:03:08.06 in this long, linear molecule
00:03:11.02 is to think about cassette tapes.
00:03:14.02 Now, cassette tapes were something
00:03:16.20 I played all the time when I was young.
00:03:18.24 I know that you're mostly playing CDs
00:03:21.22 and other digital forms of music.
00:03:24.05 But the cassette tape provides a really great analogy
00:03:26.10 for the way in which very complex information
00:03:30.04 can be encoded by a simple, long thread.
00:03:34.15 So, here we go.
00:03:37.04 Here's a cassette tape.
00:03:38.28 You look at the tape that's wound around those two spools,
00:03:42.10 and it doesn't look the least bit interesting.
00:03:44.12 But when you put it into this machine
00:03:47.05 that decodes the information
00:03:48.20 -- just like DNA is decoded in the machinery of the cell --
00:03:53.18 out comes the most amazing and complex
00:03:57.07 and beautiful sounds.
00:04:11.06 And you can play another piece of the tape
00:04:13.02 and get completely different sounds.
00:04:23.14 And another piece of the tape.
00:04:33.24 So, how does that complexity
00:04:36.10 get encoded in that simple, linear molecule?
00:04:40.19 Well, that's a problem biologists have worked on for a long time,
00:04:44.02 and we understand how the code
00:04:46.23 gets decoded into particular elements.
00:04:48.08 So, there's one particular part of it
00:04:50.06 we still don't perfectly understand,
00:04:52.06 and that we need to understand
00:04:54.24 because it impinges on all aspects of human biology and medicine.
00:04:58.15 These proteins need to fold up into
00:05:01.10 very precise shapes
00:05:03.19 in order to do anything interesting in the cell.
00:05:05.22 And those shapes are incredibly complicated.
00:05:07.18 So, let's look at some real protein structures.
00:05:12.29 You can see each of these different parts of the code
00:05:16.06 has been decoded into a long, linear string,
00:05:18.00 but that folds up and folds up
00:05:20.25 and moves back and forth and back and forth
00:05:23.26 on top of itself.
00:05:26.02 And it's the complexity of this fold
00:05:27.29 that can actually do something powerful.
00:05:30.20 Now, the difficulty in terms of how this plays out in living systems
00:05:35.10 is we don't really understand the forces
00:05:37.18 that allow the protein to fold so precisely
00:05:39.22 into exactly the right shape.
00:05:42.06 What we are understanding, however,
00:05:44.16 is that when they don't fold into exactly that right shape,
00:05:46.29 disaster occurs.
00:05:50.07 And a way of thinking about this...
00:05:52.12 again, to kind of...
00:05:54.04 to illustrate this process,
00:05:57.00 is to think again about that music...
00:05:59.03 that long, linear piece of information in the cassette tape
00:06:02.10 that encodes extraordinary music...
00:06:04.16 well, it's played by instruments, right?
00:06:07.10 And the instruments are together,
00:06:09.14 playing together, and they make great music,
00:06:12.01 just like the proteins are together in a cell
00:06:14.05 and they make wonderful, wonderful biology.
00:06:16.20 And we have different proteins
00:06:18.17 making different types of biology
00:06:20.02 in your digestive system,
00:06:21.25 in your brain, in your heart.
00:06:24.26 The problem is that making these complex folds
00:06:27.14 is very much like taking a lon... lot...
00:06:32.14 long sheet or square sheet of metal
00:06:34.12 and moving it into forming a musical instrument.
00:06:42.17 So, if you get the fold exactly right,
00:06:46.11 it can play some beautiful music.
00:06:53.09 But if there's some very small element of the fold that's...
00:06:57.06 you get almost right, but you don't get it quite right...
00:07:04.10 it can be a disaster.
00:07:07.15 Here's another example.
00:07:10.26 A different piece of metal,
00:07:12.24 folding up into a different shape,
00:07:14.22 making and doing different things in the cell.
00:07:19.19 But if you don't get it just right,
00:07:21.16 the fold isn't quite right...
00:07:24.04 it's a disaster.
00:07:25.23 So, now you've got this orchestra of proteins
00:07:29.00 that make up the living system,
00:07:31.22 and they need to play together exactly right.
00:07:33.19 They need to fold properly,
00:07:35.00 and then they need to play together exactly right
00:07:37.13 if you want the living system to be disease-free.
00:07:41.00 So, let's take a look at how these protein instruments
00:07:43.21 are actually functioning together inside of a living cell.
00:07:47.29 You'll... you're gonna see pictures of proteins serving as architecture --
00:07:51.25 the structural integrity of the cell.
00:07:54.04 You'll see proteins talking to each other between cells.
00:07:58.09 You'll see proteins cutting proteins,
00:08:00.12 assembling into various structures,
00:08:03.19 disassembling.
00:08:05.01 And all of these are part of the orchestration of life
00:08:07.17 inside the living cell.
00:09:21.19 That's a very special kind of protein
00:09:23.20 that's moving along the information highway
00:09:26.08 of the cell
00:09:28.24 and bringing packets of goodies from one end of the cell
00:09:31.15 to the other end of the cell.
00:09:33.03 Anyway, you can see, I think,
00:09:36.05 the extraordinary complexity of living systems and the proteins
00:09:38.10 that are operating in it to keep us
00:09:41.03 biologically active and doing all the amazing things
00:09:42.12 that we can do.
00:09:44.07 I urge you, by the way, to get on the web
00:09:46.22 and plug in that reference
00:09:49.01 and take a look longer look at the...
00:09:50.28 at the movie,
00:09:52.16 and there's also an animation that will tell you exactly what you're looking at all...
00:09:54.28 all... in various parts of it.
00:09:56.26 It's... I've just shown you a very small snippet.
00:10:00.28 But this incredibly complicated biology
00:10:06.16 that's represented by this beautiful movie
00:10:08.28 is misrepresented in just one particular way.
00:10:11.15 And that is that in order to illustrate
00:10:13.25 how these proteins are moving about and doing their things
00:10:16.28 and interacting with other proteins in the cell,
00:10:18.27 they've taken most of the proteins
00:10:21.13 out of that system so that you can see them.
00:10:25.00 In reality, the cell is
00:10:27.17 much, much, much more crowded.
00:10:29.22 So, if you think about this complicated protein fold
00:10:33.28 and the fact that different proteins have different folds,
00:10:38.04 they have to go from a long, linear string of amino acids
00:10:41.02 into those complicated folds
00:10:43.08 so that they can interact with themselves properly.
00:10:47.10 And they have to do that in a really crazy environment.
00:10:50.16 They have to do this in an environment
00:10:52.23 that's this packed with proteins.
00:10:55.15 So, each one of these colors
00:10:57.10 actually represents a different protein
00:10:59.10 in its complex, beautiful shape
00:11:02.11 that can change and move around
00:11:05.21 and do various things.
00:11:07.08 But this image, although it represents the crowding of a cell,
00:11:11.08 is missing one other piece.
00:11:13.18 By the way, this is a beautiful movie by Adrian Elcock.
00:11:16.01 And again, it's... it's...
00:11:18.09 you can find it on the web.
00:11:20.24 The thing that this particular image does not convey
00:11:24.22 is how energetic the system is.
00:11:27.22 Proteins are actually moving about like crazy all the time,
00:11:30.04 and it's this aspect of proteins being able
00:11:33.27 to move and signal and...
00:11:35.08 from one end of the cell to the other end of the cell,
00:11:38.13 help us to interpret what we see...
00:11:40.00 one moment, I'm looking here at you,
00:11:42.04 or looking over here at the screen...
00:11:43.24 I completely change everything I understand about
00:11:46.10 what I'm looking at because the proteins
00:11:48.11 are changing shape so fast.
00:11:50.12 So, living systems have proteins that work
00:11:53.26 at incredible speed.
00:11:55.13 And here's an example of the way they move about
00:11:57.22 and how the crowding is...
00:11:59.16 is jostling and banging into each other all the time.
00:12:03.01 The one way in which this animation
00:12:05.14 doesn't quite convey what's happening in the cell
00:12:07.22 is that it too, for the...
00:12:09.21 for the purposes of clarity,
00:12:11.24 has been modified in a certain way.
00:12:14.04 And that is it's been slowed down.
00:12:17.10 So, just as the other movie I showed you
00:12:21.13 was not very crowded,
00:12:23.09 and things were moving around rather slowly,
00:12:25.28 in this movie, which shows the crowding,
00:12:28.07 things are actually not moving at real speed,
00:12:33.00 so you can illustrate and understand and look
00:12:35.22 at how they these proteins are interacting with each other
00:12:38.16 and moving around.
00:12:40.06 In order to get a realistic idea of how fast these proteins
00:12:42.01 are moving around in the cell,
00:12:43.16 you'd have to speed that movie up
00:12:45.16 not ten times, not a hundred times,
00:12:47.23 not a thousand times,
00:12:49.23 not a hundred thousand times,
00:12:51.22 but 1 million times.
00:12:54.15 So, that movie is real slow motion
00:12:57.02 compared to what's happening in the biology of a living system.
00:13:01.13 And there you have the heart of the protein folding problem.
00:13:04.21 Because if these long, linear strings of amino acids
00:13:07.12 have to fold up into these very, very precise shapes,
00:13:10.12 without getting into trouble with other proteins
00:13:13.28 while they're doing it,
00:13:15.13 under such incredibly kinetic, energetic conditions,
00:13:19.11 you can imagine that sometimes
00:13:21.14 they get that fold wrong.
00:13:22.26 Just like those musical instruments,
00:13:24.29 if you don't... don't fold...
00:13:26.09 wouldn't fold the metal exactly right,
00:13:28.01 it could ruin an orchestra.
00:13:29.17 The same thing can happen in living systems.
00:13:33.27 So, I want to give you one more illustration,
00:13:36.22 one more analogy.
00:13:38.07 What happens when proteins start to misfold,
00:13:41.13 and bang into each other in inappropriate ways,
00:13:43.19 and stick to each other,
00:13:45.25 and... it's something...
00:13:48.05 a process we call protein aggregation.
00:13:50.04 And you know exactly what protein aggregation is like.
00:13:54.00 I know that you've seen it many times.
00:13:56.08 The egg white in this little photograph
00:14:01.28 is actually a solution of protein.
00:14:03.28 And the proteins are all folded properly,
00:14:06.01 and so they're clear and beautiful,
00:14:08.12 and they're not in any trouble.
00:14:10.23 But when you apply heat to that system,
00:14:13.20 the proteins start to move around a little faster.
00:14:16.06 They start banging into each other.
00:14:18.05 They start unfolding a little bit.
00:14:19.29 And what happens is the properties of the biological system
00:14:23.03 change completely.
00:14:24.26 And that is, in fact, what you get.
00:14:28.05 So, those are aggregated proteins.
00:14:29.22 And it's just a nice visual illustration
00:14:34.19 of the problem that can occur
00:14:37.16 when proteins don't fall properly in our living systems.
00:14:41.02 So, we want to understand
00:14:43.18 how we can keep the proteins looking more like this,
00:14:46.24 and how, if they start to go off pathway
00:14:50.07 and start to form little bitty aggregates,
00:14:53.04 we can bring them back to life.
00:14:55.04 Because just a little bit of that aggregation state
00:14:58.16 causes disaster for a living system.
00:15:02.27 So, what are the solutions that life has found?
00:15:05.21 Well, the first way we started to discover and learn something
00:15:09.02 about the solutions to that problem
00:15:11.01 actually involved heat.
00:15:13.23 So, here we have a very simple experiment
00:15:16.27 that was done with yeast cells.
00:15:19.04 We're growing yeast cells in a culture,
00:15:21.04 in a shaking Erlenmeyer flask.
00:15:24.00 And we took some of those cells out.
00:15:28.01 We took two identical aliquots of cells out.
00:15:31.04 What I mean by an aliquot
00:15:33.03 is just a little portion of the culture.
00:15:34.17 So, we took two identical portions of the culture out,
00:15:36.29 and that one on the top there
00:15:41.01 was exposed directly to a high temperature,
00:15:43.10 and the proteins denatured and killed the cell.
00:15:47.00 This one on the bottom was first exposed
00:15:50.08 to an intermediate temperature,
00:15:51.26 to allow it to kind of condition.
00:15:54.02 Basically, it was exposed for half an hour to 39 degrees
00:15:59.04 instead of being shifted directly to 50 degrees.
00:16:01.19 And as you can see, that short, half-hour pretreatment
00:16:05.24 provided tremendous increased capacity of the cells
00:16:09.11 to survive that second, higher heat treatment.
00:16:13.05 Now, this is a universal property of life.
00:16:18.01 And so, it is not only true for yeast cells.
00:16:20.08 It's true for Arabidopsis seedlings.
00:16:23.13 This is basically the same experiment.
00:16:24.27 Arabidopsis seedlings were planted in these little dishes,
00:16:27.00 one treated directly at high temperatures,
00:16:30.08 the other one given this intermediate treatment
00:16:32.19 that allowed it to condition itself
00:16:34.15 and then to withstand the rigors of that more intense condition.
00:16:39.03 And these are human cells in culture.
00:16:41.26 Basically the same experiment.
00:16:44.21 You can do this experiment with all living organisms on Earth,
00:16:48.03 because all living organisms face this same problem
00:16:50.28 of protein folding,
00:16:52.10 and they all prepare for problems in protein folding
00:16:55.26 the same way,
00:16:57.12 by making other proteins that help the proteins
00:17:01.12 to stay in their normal shapes and sizes.
00:17:05.03 So, how do we find out
00:17:07.24 what they're doing during those conditioning pretreatments?
00:17:09.20 What we do is we, again,
00:17:11.17 take out a small portion of the cells
00:17:13.25 and label them with radioactive amino acids
00:17:16.09 so that, as the ce...
00:17:18.06 as the cell is making its own proteins,
00:17:21.06 each of those proteins will get radioactive amino acids
00:17:24.21 incorporated into it.
00:17:26.18 That allows us, then, to visualize it... what's happened.
00:17:30.08 We spread those proteins out on a gel,
00:17:32.25 and we put a film on top of it,
00:17:35.01 and wherever there's radioactivity
00:17:37.20 from a newly made protein,
00:17:39.11 we can see the imprint and a line on the gel.
00:17:41.26 And so, you can see that at 25 degrees,
00:17:45.12 the normal temperature for this organism,
00:17:47.01 it's making one group of proteins.
00:17:49.04 At 39 degrees, it started making a whole bunch of other proteins.
00:17:52.28 And the sole function of all of those proteins
00:17:55.17 is to cope with this protein folding problem,
00:17:58.18 to help other proteins in the cell
00:18:00.16 maintain their normal shapes,
00:18:02.10 or to get rid of them when they've lost their normal shapes.
00:18:07.06 Now, this is a very broadly used survival response.
00:18:11.06 We first started working with it with heat
00:18:14.00 because that's an awfully simple manipulation to make within the laboratory.
00:18:18.12 But it turns out these same proteins provide protection
00:18:22.06 against all sorts of different difficult conditions:
00:18:25.20 changes in pH, changes in the energy balance of the cell,
00:18:28.28 changes in osmotic strength...
00:18:30.28 many, many, many different changes in the cell.
00:18:34.26 In fact, these proteins are constantly being made...
00:18:37.20 made in smaller amounts,
00:18:39.19 over and over and over again,
00:18:41.13 to help cope with this very broad problem in protein folding.
00:18:46.11 So, this very broadly used survival response, as...
00:18:49.10 I showed you yeast cells.
00:18:51.01 I showed you Arabidopsis seedlings.
00:18:52.23 Arabidopsis is a small little mustard plant.
00:18:55.07 I showed you human cells.
00:18:57.10 Every organism on Earth is making very highly conserved,
00:19:00.09 very similar patterns of proteins under these stress conditions.
00:19:03.21 And it turns out that that plays into human biology and medicine
00:19:07.13 in just an extraordinary variety of different ways.
00:19:11.16 One of the major reasons
00:19:13.28 why we want so deeply to understand this problem
00:19:17.00 is that it drives many aspects of human disease.
00:19:21.11 So, one of the things that it drives
00:19:23.22 is the process of infection.
00:19:25.21 When organisms come into our body...
00:19:29.13 and you can see here we've got a fungus
00:19:32.15 that is growing under normal conditions...
00:19:35.04 not inside the body.
00:19:36.23 But when it starts to grow inside the body,
00:19:38.16 it senses this change in temperature,
00:19:41.07 and it... and it starts to realize
00:19:43.25 that it can invade the biological system.
00:19:46.07 And the only way it can do that
00:19:49.02 is by making new proteins
00:19:51.20 and by making this survival response
00:19:53.19 that allows those new proteins to fold properly.
00:19:57.22 So, that's one aspect of...
00:19:59.29 of disease biology that uses that survival response
00:20:03.00 all of the time.
00:20:04.29 Here's another aspect of human biology
00:20:06.18 that uses this survival response.
00:20:08.16 So, what you have in blue is normal proteins,
00:20:12.10 and what you have labeled in brown here
00:20:15.18 is the master regulator of this survival response.
00:20:20.14 And that's normal tissue over there.
00:20:22.20 And you can see that the survival response protein
00:20:27.16 is kind of tucked away in little corners of the cells,
00:20:30.26 because it's not being used under...
00:20:32.20 in this normal biological system.
00:20:35.11 But in the cancer cells,
00:20:37.08 you can see that that master regulator
00:20:39.05 has been amplified a great deal.
00:20:41.05 It's actually present, now, in the center of the cell,
00:20:44.03 and it's directing a whole new program of gene expression,
00:20:47.18 whole new sets of proteins that are being made,
00:20:51.14 at the dictum of the cancer cells
00:20:53.20 to help protect those cancer cells
00:20:56.12 and drive the malignant state.
00:20:58.06 And neurodegenerative disease...
00:21:00.26 these are two brain sections,
00:21:04.22 from a normal person and from someone with a...
00:21:07.13 who has died from neurodegenerative disease.
00:21:10.05 And what you're seeing here is the devastation
00:21:12.17 brought by misfolded proteins in the brain.
00:21:16.19 So, it turns out that,
00:21:18.19 in terms of human beings,
00:21:20.20 we are a bit between a rock and a hard place
00:21:23.19 with regard to this problem in protein folding.
00:21:27.28 Because cancer cells and infectious organisms
00:21:29.19 are using their resp...
00:21:32.09 their survival response, this heat shock response,
00:21:35.05 to kill us, because it strengthens them
00:21:38.04 and allows them to survive the rigors
00:21:40.26 of a living...
00:21:44.06 of a living system. And our brains, conversely,
00:21:47.01 are not using this survival response
00:21:50.06 when we would normally think they should be.
00:21:52.09 Because when we die of neurodegenerative diseases,
00:21:54.12 it's because proteins have misfolded, misfunctioned,
00:21:56.28 and just like those instruments that are not playing right with the orchestra,
00:22:01.23 they're causing devastating disease.
00:22:04.17 Now, this puts us in a difficult position,
00:22:08.00 but it's not a place where we can't move
00:22:10.06 and we can't do something important
00:22:12.20 in biological experimentation.
00:22:14.07 And the reason why we can do things
00:22:16.26 that will help to fix these problems
00:22:18.21 is because it is such a universal problem.
00:22:22.06 And so, we can take these very simple organisms
00:22:25.07 here, these yeast cells,
00:22:26.19 and understand more about how that...
00:22:29.04 the biology of that system is driven,
00:22:31.11 how to correct protein folding
00:22:33.26 and how it goes wrong,
00:22:35.21 in order to help these people over here
00:22:37.29 with all those different protein folding problems
00:22:40.13 I just mentioned to you.
00:22:42.06 So, I'll be talking to you about that in the next lectures.

This Talk

Speaker: Susan Lindquist

Audience:

General Public
Educators of H. School / Intro Undergrad
Student
Educators of Adv. Undergrad / Grad
Researcher
Educators

Recorded: January 2015

Talk Overview

Proteins are complex structures folded from a linear strand of amino acids. These structures are involved in almost every process in the cell. In this iBiology talk, Susan Lindquist discusses the incredible diversity of protein structures, the importance of proper protein folding, and the problems that arise when proteins are misfolded.

Speaker Bio

Susan Lindquist

Susan Lindquist was a member and former Director of the Whitehead Institute for Biomedical Research. She was also a Howard Hughes Medical Institute Investigator and Professor of Biology at the Massachusetts Institute of Technology. She received her Ph.D. in biology from Harvard and was a postdoctoral fellow of the American Cancer Society. Lindquist was on… Continue Reading