PROFESSOR: It's going to
be a great lecture today. It's about proteins. I love proteins. Don't forget the handout, yeah. OK, so I'm going
to briefly wrap up the lecture we were doing
on Friday because there were a couple of things that I
wanted to make a note of, and then we'll move
on to section 2.3 about amino acids,
peptides, and proteins. Now, in the last
class, I introduced you to the lipidic molecules,
and you can pick them out of a lineup because they are
rich in carbon-carbon and carbon-hydrogen bonds. As you can see here in
these line-angled drawings, the majority of a lot
of these molecules is carbon-carbon or
carbon-hydrogen hydrogen. They are molecules that are
mostly hydrophobic, so there are some terminologies here. Whoops. Hydrophobic, which can also
be referred to as lipophilic. You either-- you can hate water
and love fatty acid or fatty types of materials, so those
both terms are synonymous. And some of the lipids are
what are known as amphipathic, and they include hydrophobic
and hydrophobic components. There are a couple
of tiny terms that I didn't mention
explicitly, so I just want to go ahead
and do that now. For example, in this
phospholipid structure-- and we'll talk about these-- they have long chain fatty
acids attached via esters to this glycerol
unit, so there's one here and the
second one here, and then what's known
as the polar head group. In those fatty acids, they
could be fully saturated. It means they have no double
bonds in the structure, so that term saturated is
equivalent to no double bonds, so no carbon-carbon
double bonds. Or they could be
unsaturated, where there is a double
bond within it, so that's one or
more double bonds. And those double bonds
take on a particular shape because there's not freedom of
rotation around double bonds the same way there is
around single bonds. So those single bonds,
you can twist them around and twist them around, but the
double bond geometry is fixed. And so double bonds,
we refer to them as either trans, where the two
groups are on opposite sides, leaving the double bond,
or we refer to them as cis, where the two groups
are on the same side. And we tend to use
that cis and trans sort of naming system in a
lot of other contexts as well, but you almost always
want to remember that trans is as far
away as possible, cis is closer than trans. All right, so I'm just
going to take you forward to the phospholipid structure. This is a very important
semi-permeable membranes are made up through the
non-covalent, supramolecular association of
phospholipid monomer units. Here's a monomer unit up here. You see it has an
amphipathic structure, with a lot of hydrophobicity
but also hydrophilicity, and these molecules assemble
into supramolecular structures that form the boundaries
of your cells. Saying they are semi-permeable
tells us a little bit about what can go through them. If they were fully permeable,
anything could come and go and they wouldn't
be much use frankly. It's like leaving the
door open the whole time. But because they're
semi-permeable, only a few things can come
and go without extra help, and other things need active
mechanisms to go through. So let's take a look
at the boundary here. So when you see a
membrane bilayer, they are-- they're often
shown looking like this, where every one of these
units is a phospholipid, and there's water on both
sides of the phospholipid, because that polar head
group is interacting with water on both sides. So down here could be
the inside of the cell. Up here could be the
outside of the cell. And a lot of cells,
especially eukaryotic cells, the ones that make us up,
have a lot of endomembranes, membranes within the cells. For example, forming the
boundary to the nucleus or to the mitochondria. Yes? AUDIENCE: Why is
there a [INAUDIBLE] PROFESSOR: Oh,
this guy must be-- so this looks like it's
probably a saturated fatty acid. So what do you think
this one might be, folks? Unsaturated. And what's the
double-bond geometry? AUDIENCE: Cis. PROFESSOR: Cis. Yeah, it is. It's like a-- it looks like
a ballerina or something. OK, so we have a
lot of concerns, and we'll see later about how
things get in and out of cells. But most commonly, things
like oxygen or water and other small
hydrophobic molecules can pass readily in and out
through the semi-permeable barrier, but other things,
things that are charged, things that are big, need
a different mechanism to get in and out. And we will see later
on how proteins provide the opportunities
to cargo things into cells or out of cells,
even very large entities, and there are certain
mechanisms whereby that happens through a
semi-permeable membrane, OK? I want to show you the
other feature of membranes. They are self-healing. What this means is
if you poke them, you poke a hole in a
cellular membrane, You? Basically push apart
those non-covalent forces. Once you take the thing
away, be it a needle or a very fine glass capillary,
they seal right back up to close to close the
hole in the cell wall, so that kind of tells us that
they're non-covalent forces. So this is a really
cool video of someone doing micro-injection
into eukaryotic cells. The needle points to the
cell, approaches the surface. You can drop something
into the cell, and then the cell
closes and maintain-- regains its integrity
of the barrier, so this is a very
cool observation. People do this. They have to not
drink too much coffee because it's quite complicated
to do a lot of micro-injection, because you can really cause
carnage in your cell population if you're not very dexterous
with the micro-injection but people can be
very good at it. So I just want to ask
a couple of questions before, give you a couple
of things to think about before we close up. The lipids. So here's a typical
lipid bilayer, where I've highlighted
a single lipid. And the colors, those
are the head groups, and all in white and gray are
the hydrophilic components, and just one of the
phospholipids is highlighted, and that would be this
molecular structure here. So first of all, what do you
think the non-covalent forces at that membrane
interface may be? That is, what's going on
here at the interface? What are the types
of interactions that you might have there? Give you a minute
to think about it, and I want to show you that
I'm actually giving you a clue here, because you can see
the structure, negative charge, positive charge,
but also remember this is a barrier to water, so
there are other things going on with the solvent that the
membrane is sitting in because there's water
surrounding that barrier layer. Anyone want to tell me what
the answer is, and why? Yeah, did you-- are you-- yeah. AUDIENCE: Hydrogen bonding. PROFESSOR: Yeah,
between what and what? AUDIENCE: Like the
oxygen and [INAUDIBLE] PROFESSOR: Right, so water. Water is a good hydrogen
bond donor and acceptor, so there will be
hydrogen bonding. What about amongst
all those lipid head groups, what's
the other major force? Yeah? AUDIENCE: Electrostatic force. PROFESSOR: Between
the different charges. So the correct answer
here is both of them. Don't think it's just
electrostatic, it's both. It's electrostatic amongst the
head groups, hydrogen bonding between all that sort of dense
bunch of charge, and the water. And then the other question,
what type of molecules can get across? I've already answered
that question to you. Salts are going to need
ways to get in and out. Small proteins are too big
to dissolve in that membrane through passive
mechanisms, so we're going to have to figure
out how to get proteins in and out of cells. Neurotransmitters,
such as this, this is GABA, or gamma
aminobutyric acid. It's charged. It just can't get through
without a transporter of some kind, and
it's actually proteins that end up doing the heavy
lifting of the transport processes that we'll see. OK, so moving along. This section will be about the
building blocks of your protein macromolecules, which
I want to remind you comprise 50% of all
of the macromolecules, so that suggests it's a
pretty important class of macromolecules that has a
lot of different functions. Now, the amino acid
building locks-- blocks look pretty simple. They're called amino
acids because they have an amine, the
carboxylic acid, and there's a carbon that
is tetrehedral between the carboxylic acid and the amine. And the simplest of those is
when those are both hydrogen, but most of the amino
acids are differentiated from that-- this one I've
showed you on the board. This amino acid is glycine. Usually, when it's just a lonely
amino acid in aqueous solution, it's in a different
charged form, just consistent with what we
talked about in the last class. And I put it here. So this is glycine. It's one of the 20
encoded amino acids. That means the
amino acids that are made through
ribosomal biosynthesis through a code that's
provided by the messenger RNA, so they are encoded
by messenger RNA. Later on, you'll see all
of the beautiful mechanics of those processes. Now, this table looks
pretty complicated, so I'm going to
deconstruct it a bit. But what I first of all want
to assure you is that these-- you will always get a handout
with these structures on them. We are not asking you to
remember these structures. You might become familiar
with some of them, but you do not have
to remember them. You'll have a table that
shows them, but on that table, I won't necessarily
give you the information on what their properties
are, because those are things that you should be able to spot
by looking at their chemical structures, all right? So that's important. So these are all
line-angled drawings, so you see the carbon. The hydrogens aren't
shown in there. The charges are shown for
what's called the side chain, because most of the
amino acids have a side chain. The amino acids are
also chiral, but you'll learn more than you ever wanted
to know about chirality in 512, so I won't weigh you down
with any of those properties. So there is a side chain
that dictates the properties of the amino acids. One tiny detail,
the amino acids that are encoded in our
proteins are all what are known as alpha amino acids. There are other amino acids. GABA, that I showed you
on the previous slide, is not an alpha amino acid. Actually it's, a
gamma amino acid. These are called amino acids
because the amine group is at the alpha position
relative to the carboxyl. Don't need to know a lot
more about that with respect to that. So let's take a look at
this set of amino acids, and what you see is amino
side chains with rather different properties. I've amassed-- here's
glycine at the very top. All amino acids have
a three-letter code or a one-letter code. I particularly enjoy
using one letter codes and spelling out people's
names in peptides and things like that. I'll let you do that in the
privacy of your own room. It's kind of amusing to see if
your name actually spells out a peptide. Some of us-- if I get a little
stopped stuck with Barbara because there are no B amino
acid one letters with a B. The next most abundant
type of amino acid have hydrophobic side chains. What that means is
they have a lot of CHs, but not a lot else, right? So take a look at them. Alanine has a methyl group,
for example, where I've shown the R, that would be alanine. And they get increasingly big. They're quite large. Some of them have quite
extended size chains. Other ones have side
chains with rings with double bonds in them. Those are what we would
designate in organic chemistry as aromatic. They show-- they are
still hydrophobic, but they show
different properties to this other set
of amino acids. Some of these amino
acids may actually have polar groups in them,
but their major feature is that they're hydrophobic. But in an amino acid,
such as tyrosine, you could not only have
hydrophobic interactions with that ring system, but also
hydrogen bonding with the OH on the tyrosine, so
some of the amino acids can do a few different things. The next set of
amino acids are those that are polar and
charged, and I've shown you the most common state
of all of those amino acids, but you already know
that the amine of lysine is likely to be charged. This quanidinium group of
arginine, take my word for it, it's charged. It's a bit more
complicated to draw. Histidine is also one of
those that's annoying to draw, but the negatively-charged
side chains with a carboxylate are both negatively
charged, and that's something you would remember
from the previous class hopefully. And then finally,
there are amino acids with polar uncharged
side chains, such as those shown here. Now, this doesn't look
like a very exciting set of building blocks. How can life run on things
made of 20 relatively simple building blocks
with functional groups? And it's that the building
blocks are not functional themselves. It is the polymers that
are made up of amino acids, and I'll always call them AAs
because it's easier for me. The polymers of amino
acids are heteropolymers. That means they're made up of
a bunch of different monomer units when they're
called heteropolymers. And the other important
thing about these polymers is that they are of
defined sequence. What is the sequence? It's the order in which
the amino acids appear. So I'm writing that down, order. And all the
functions of proteins are dictated by the
order of the amino acids, so let's take a look
at the sidebar here. So once again, remember
a couple of things that we will always give you
this table to think about. Ooh, come back. There are a couple of outliers
I just want to mention quickly. So I talked to
you about glycine, the simplest amino acid with
no elaborate side chain. Proline is a little odd because
its side chain is kind of in a cyclic structure, and
towards the end of the class, I'll talk to you about
collagen, whose structure is totally dependent on
the involvement of proline in the sequence of the amino
acids that make up collagen. And then the last sorts of
unusual amino acid is cysteine. It has a thiol, and the one
clever thing about cysteine-- I'm just going to put a
bit of a peptide here. One cysteine, and then I'm
going to put a second cysteine, and these are going to be
deemed in a peptidic structure. What cysteine can do
is it can exist either with the thiol side
chain, SH, or it can be at a different
oxidation state where the two sulfurs
are joined to each other. So for the most part,
your linear arrangement of amino acids that dictates
sequence is solely held by-- together by the covalent
bonds and the peptide backbone that we'll talk
about in a minute. But occasionally,
enfolded structures, if two cysteines are
close to each other and the environment
is oxidizing, they will form a cross-link. But they're not
what drives folding. They kind of fall
into place later on, but that just sort of sets
cysteine apart a little bit for its properties, all right? OK, so coming down
the side here. Amino acids are assembled
in a unique linear polymer of defined order, and we
designate that defined sequence the primary sequence. And proteins can be 1,000 amino
acids, 1,500, 100 amino acids. They can be various lengths
where they, you know, we would generally
consider the smallest protein to be about
400 amino acids, and you might go up to
thousands of amino acids. I'm going to write
2,000 or more here. When the proteins
are smaller, they are not capable of adopting
too much ordered structure, and we mostly call
them peptides. Peptides are sort of
shorter sequences, so peptide sequences. So this would be a protein,
and peptides, probably two to 39 amino acids,
but these breakpoints are a little bit more vague. So the primary sequence
will define the structure of a protein, and
we're going to start to talk about the hierarchical
structure of proteins as put in place, and that's
the primary sequence, And that primary sequence
is kind of a cool thing because it's very specific. It defines-- it's got
encoded into its structure, the three-dimensional
fold of the protein, OK? All the information for the
folded, compact, globular structure that's
functional is encoded in that primary sequence. It's a cryptic code. We may not be able to
tell by looking at it what it really looks like,
but all the information is there in order to program
the folding into a globular structure. So the primary sequence
determines the fold, and it's the fold of the protein
that mandates its function. It's not the sequence
of the protein. The sequence defines the fold. The fold, the three-dimensional
form, defines the function, OK? So that's very important. And I think it's
absolutely amazing that with a relatively limited
set of building blocks, we can define so many different
functions of all the proteins in our body that
may be structural, they may be catalysts,
they may be things that transfer information
from the outside to the inside of cell. All of that is programmed
with this rather limited set of building blocks, OK? Now, let's now
talk about peptides because one gets a
little frustrated looking at single amino acids. They don't tell us so much
about the peptidic structure, so I'm going to draw
two amino acids, and then I'm going to tell
you one important thing. So let's put R1, and I'm going
to draw another amino acid, and I'm putting it in a
particular orientation. R2, because that
designates that these might be different amino acids. For example, if R1 is H, there's
an implied hydrogen here, that would be glycine. If R2 is a methyl group, there's
an implied hydrogen there, that would be
alanine, all right? When nature bonds all
these amino acids together, it carries out a
condensation reaction to form a peptide
bond between these two components of the
amino acid, the amine and the carboxylic acid. And now I'm going to draw you
the first of the dipeptides that you'll meet. And there are so many
things to tell you about these
structures, it sort of drives me crazy
thinking about, oh, I must remember to tell
them that or I've got to remember to tell them
that, because the structures are cool. R1, R2. OK, so this is a
dipeptide, two amino acids, and there are some
characteristics I want you to remember. When we write out peptides,
we always write them N to C. So in that peptide, this would
be the carboxyl terminus, and this would be
the amino terminus. If you don't always remember
to write things in this order, and you tell your friend,
oh, go and get this peptide made, and you put it
down in the wrong order, they'll make the wrong peptide. So you always-- there is
basically an agreement amongst everyone that we always
write from left to right, the sequence of peptides. The next important thing
about this structure, as you look at it, there
are several bonds joining the polymeric structure. Many of these bonds
show free rotations. You can twist them
around, there's nothing stopping that conversion. All of these show
freedom of rotation. But the amide, or
peptide bond, is unique in that
there's restricted rotation about that bond. So it's as if you've
got a linear polymer, but every third bond
has kind of stuck in a particular
orientation, which starts to define a lot of
details about protein tertiary structure. It's not complete spaghetti. It's like spaghetti with little
bits that haven't been cooked. They're stiffer than the
rest of the sequence. And the other really
important thing about the peptide
structure is that embedded within that structure, there is
the amide or peptide functional group where, remember, this can
be a hydrogen bond acceptor, and this can be a
hydrogen bond donor. Once you know that, the next few
slides will make a lot of sense as we talk about higher-order
structure of proteins. So let's just take
a look at that with a slightly longer peptide. By convention, if I'm
going to draw a peptide that's methionine
isoleucine threonine-- you can look up that names-- those names on the chart-- that would be the MIT peptide. These are the three amino acids. I'm going to condense
them into a tripeptide. When I condense
three amino acids, I spit out two
molecules of water, and I put in place two
amide or peptide bonds. If I go down this
backbone, every third bond is going to be
fixed, fairly fixed. There's not freedom
of rotation around it, and every third bond is
going to have the capacity to be involved in hydrogen
bonding interactions, as I've suggested
here, all right? What else is there here? When I write the MIT
peptide, I write M first, I second, T third. If I wrote TIM, it would be a
completely different chemical structure with different
chemical properties, so the directionality is
important to understand, and there you have it. So now you can go home
and practice your name in amino acids
and draw them out. If you draw them out
fairly sort of sharply, then you'll never get
confused about what end's what and where
the substitutes are, but it's important
to remember as you're making a dipeptide-- oops,
I forget this doesn't work. As you're condensing
a dipeptide, when you're putting these
R groups on, one goes up, one goes down, but
these are nuances of the structure that
may be lit for-- good for a later discussion. So here is now a longer linear
peptide, and the suggestion of a globular structure
that might be found if that peptide was folded up. And the primary sequence here
defines the globular structure, and the process whereby you
go from the extended primary sequence to the folded structure
is called protein folding. And physical chemists
and physicists and computational
chemists have for years tried to understand how we could
predict the folded structure from the primary sequence. It's not simple because
what you're doing is you're solving a
massive energy diagram, where as you fold
a structure up, you're trying to maximize
all those non-covalent forces for maximum thermodynamic
stability, right? It's kind of a three-dimensional
puzzle where you're trying to have as
many hydrogen bonds, electrostatic interactions,
and so on, as you can possibly make. So when computational
chemists try to fold proteins, they're basically solving
a three-dimensional puzzle where they are
maximizing interactions. And there are a lot of ab
initio and molecular dynamics programs that are now starting
to be able to fold proteins into fairly reliable structures,
but they don't always get them right
because they haven't gotten all the clues yet. And also while they may
be able to do ab initio or computational folding
with small structures, the headache gets way bigger
the larger the structures get. So the predictors aren't
very good at predicting big structures,
they're getting better at predicting small structures. And so just to reinforce to
you, the primary sequence is established by covalent
bonds, the peptide bonds, but the globular
tertiary structure is based on non-covalent
covalent interactions, OK? Now, I want to ask you this. I love cartoons with
science in them, but you know, 10%, 20% of
the time, they make mistakes, and I felt this one was
particularly pertinent. So a bunch of guys lugging
around in a lab and says, well, we finished
the genome map, now we just have to
figure out how to fold it. What is wrong with that cartoon? What fold? Yeah? AUDIENCE: You want
to [INAUDIBLE].. PROFESSOR: Yeah. AUDIENCE: [INAUDIBLE] PROFESSOR: Yeah, the
genome doesn't fold. It's double helical,
duplex DNA or something. You're actually
folding proteins, so the cartoon is
not quite right, but it's sort of kind of cute. All right, now, when we talk
about the non-covalent forces that hold proteins
together, I just want you to remember
from last time this set of non-covalent forces,
because if you understand them and recognize them, you'll
understand how they may occur in folded protein structures. All right, so here's
a peptide sequence. Here's a puzzle for you. You can go back and figure out
what the one-letter code spells there. Just take out your table
with all the amino acids. It's appended to the
back of your P-set, and you'll be able to see what
that very large peptide spells. All right, I don't
want you working it out while you're here. You've got to listen to
me for the time being. OK, so the first order, we get
it, there's a primary sequence. The next thing to
think about is what's known as secondary structure. It's a higher order than
just the primary sequence, and it's established
by non-covalent bonds, and it's called secondary--
oof, my writing's horrid today. Secondary structure. And those are interactions that
are put in place exclusively by interactions between
the peptide bonds of what's known as the peptide backbone. So if I look at the structure,
these are the side chains. The peptide backbone is this
continuous linear sequence. That's what we would call
the peptide backbone, and the secondary
structure is put in place by hydrogen bonding
between components of the peptide backbone. So for example,
a hydrogen bonds, such as that, or a different
hydrogen bonding interaction, such as that. Between the atoms that have
lone pairs of electrons and the other atoms-- heavy atoms that hold a
hydrogen that's quite acidic. And there are a couple of major
forms of secondary structure. What I'm showing
you here is what's known as the alpha helix. First deduced by Pauling, in
fact, through model building, he said, proteins could form
these ordered structures, and an alpha helix is an ordered
structure exclusively made up from the hydrogen-bonding
interactions of the peptide backbone. And you can look at
this helical structure. It's a continuous
strand of peptide, but there are hydrogen bonds
between COs and NHs all the way through the backbone, such
that this strand of peptide can fold up into a cylindrical,
helical structure, where all those R groups, the side
chains of the amino acids, are on the perimeter
of that helix. So this secondary structure
is an important one because it's very prevalent
in a lot of proteins. The next secondary structure
is also held together by hydrogen bonding,
and it's interactions between stretched out strands
of peptides that may not be close to each other
in the primary sequence, but they align in
the folded structure. And so for example,
what I've shown you here is what's known as a-- this guy is then to say this
is an anti-parallel beta sheet. And across that sheet, there
are continuous opportunities for hydrogen
bonding interaction. If the strands run in opposite
directions, it's anti-parallel. If they're in the same
direction, it's parallel. These two secondary
structure elements make up a lot of
the sort of basics of how proteins start to fold. They're key non-covalent
forces, and there are also other smaller motifs. One is called a beta turn,
where the peptide sequence may go through a chain
reversal, so the sequence would look like this. I'm going to just
draw it, and I'll talk to you in a moment
about ribbon diagrams. And this piece here
would be the turn, whereas that would be
the interactions enforced by the sheet. These are the ordered elements
of secondary structure. You don't have to be
able to figure them out, but you have to be
able to pick them out in order to understand
the structure, OK? So even those simple
elements still it's hard to make big enough
structures to have functions. So as I mentioned in a
continuation of the theme, the protein folding
is hierarchical, you can start to put together
elements of secondary structure to make things that
are a little larger. Helix, turn, helix. Helix with a different
kind of turn, maybe put in place by a metal
ion or something, or a strand, turn, strand, or
now something that's a composite of these two major
types of secondary structure, the helix and the turn. And these really
start to be proteins that might be big enough
to be able to do something, but they're all
exclusively held together by non-covalent forces between
the amides or peptide bonds in the backbone of
the protein, OK? Not very exciting just yet. Now, one other little
clue that people will-- you might see and you
might be confused, people sometimes, when
they're drawing sort of a quick picture of a protein,
they might draw a helix, but instead of really
showing it in detail, they might show
it as a cylinder, so you might need to pick
that out of a structure. And then I want to call
your attention to that, that in all those motifs, when
you join one helix to another, you might need to turn a
strand to another strand you need to turn, and so on. OK, so this is like taking
your very extended stored of polymer, knowing there are
different kinks in it, because of the backbone bonds,
but folding it up in a structure that
maximizes the opportunity for another order of structure,
which we'll talk about now. All right, so
we've seen primary. Secondary is just with backbone. And things start to get
much more interesting when we get to
tertiary structure, because tertiary
structure is enabled by all these other interactions,
electrostatic, hydrogen bonding, hydrophobic
forces, that can be put in place
due to the side chains of amino acids
interacting with each other or with the backbone structures. So I'm going to walk you through
this, so you can sort of get a sense of how these
three-dimensional puzzles work on a very small scale. So look here, that's
a very small motif. And what I'm going to
call your attention to is when you fold
up these motifs, when the secondary
structure is in place, a lot of the side chains
are near each other, and they can engage in
long-distance contacts. And so for example,
I'm going to show you interactions
between side chains, between side chains and
the peptide backbone, or side chains and water. But what I want to do is
take a look at this and see, can you put any of those
potential interactions on the drawing that's
on your handout? It's pretty obvious
where there's an electrostatic
interaction, right? Boop. OK, between plus-- get
those out of the way, those are the easy ones. And then interactions
between hydrophobic groups, where they want to amass
that lipophilic structure, so it's not exposed
as much to water, so they cluster,
so those are easy. And then you can start thinking
about what are all of hydrogen bonds you could draw. Here I've shown one
between side chains, between side chains
and backbone, between side chains and
water, and those may all contribute to the ultimate
thermodynamic stability. Make sure you get your
hydrogen bonds right. Remember, two donors don't
interact with each other into acceptors, don't-- so this might describe
the folding possibilities of that small motif. Now what I want to show you-- I'm going to-- let me-- is an ab-initio simulation
of a folding process. So let me just get that a
little bigger on the screen. So this is computing. GB1 is a very small protein
that holds reversibly under appropriate conditions,
and what I'm going to do is forward you
through this video. This is a simulation. This is all computation. It's not looking at anything
by spectroscopy or in solution or anything like that. And what I'm going to do
is I'm going to forward you through the structure. This is multi-scale modeling. It's got a lot of
details in how it's done, but the starting point is
a very denatured protein, all stretched out, right? And what I'm going to do is
just show you for a few seconds, you know, this
thing's like trying to find its
thermodynamic minimum, and it's actually
failing pretty badly. And it does that for about 30-- 60 seconds of the simulations,
so I made a point to myself to take you to about minute
one, where things start to get fairly interesting. And you're saying, well,
what's interesting about that? You see that nascent helix,
in the background, the red and the blue, is starting
to form strands that are a little bit
aligned, and it's trying to find as many
connections as possible to satisfy a stable structure. At a certain point
in the simulation, five of the hydrophobic
groups are in a little pea. They're in a little
hydrophobic cluster, and that's a breakpoint
in the folding process, because that gets everything
glued together better, so that the rest
of it now can start to really find its final
place in the folded structure. These early structures are
known as molten globules. A lot of the interactions
are not yet in place, but the hydrophobic
cluster is critical. But then after
that, it's almost as if you're sliding
downhill to get all the remaining interactions
in place to fold the protein, OK? So protein folding
is a puzzle that can be solved
computationally by maximizing thermodynamic interactions. So it's sigma this, sum of
this, sum of this, sum of that. That's going to get difficult
the larger the protein gets, but for small proteins,
those simulations really start to make sense, OK? All right, so let's
just move on here. Lost-- ah, good. What did you think
of the simulation? It's kind of cool, right? So you can find the
link in the sidebar. So just pop these back
on now, and that's the folded structure. All right, so with
many proteins, they're much more
complex than that. So for example, here's cyclin
A. It's involved in cell cycle, and you can see its alpha
helix structure dominantly, very clearly, all those
beautiful alpha helices. Next to it is the green
fluorescent protein, which is a cylindrical
structure made up of anti-parallel beta sheets. What's really cool is when
you sort of rotate it, you can see all those
sheets, but then it does this little sort of
curtsy to the audience, and you can look
down into the barrel. And then in some
cases, proteins may be a mixture of a secondary
structure elements. Here it's a little hard to tell. This is triose
phosphate isomerase, but if you look down it,
you can see the helices, and there's also a group of beta
strands that are held together. So in that protein, it's a
mixture of alpha helix and beta sheet. Now, I'm not going to tell
you much about pulling up Protein Data Bank files
right now because I want to cover the next topic. And then when we have
a few minutes later on, I'll show you. But wherever I show
you a structure, I'm trying to show you the
Protein Data Bank code, and in the web site,
you can see there is a free download
of PyMOL, which is the program I used to
create all these structures and movies, so you can
really look at things. And believe me, it took
me about three years to learn how to use it properly. It'll probably take you about a
week or maybe a couple of days. So if I can learn it, you
can certainly learn it. Now, there is one final
element of protein structure that people get
kind of hung up on, and it's what's called
quaternary structure. It's like, aren't we done yet? So in addition to all
of these, let's say I have a folded motif,
and there's its structure. That would be have primary,
secondary, between the strands or the helix, and
tertiary structure, right? But in some cases, proteins
hold up to quaternary structure, where it's multiple of these
units joined together-- hoo, I could have
picked a simpler fold, but that will get you
the general gist of it-- all right, where these
are actually associated by non-covalent forces. So there's more than
one polypeptide chain. In fact, here would be four
peptide chains coming together in a higher-order
structure that's made up of four of those units. The prototypic example
of this is the protein that carries oxygen around
in your blood, which is hemoglobin, and it has
four primary sequences that have come together
in a tetrameric quaternary structure. Hemoglobin is kind
of interesting, because it's made up of two
alpha and two beta subunits. If All these subunits
were identical, they would be called
homooligomers, all the same pieces. If they are different, they
are called heterooligomers. We'll see a little
bit more about this when I talk about hemoglobin
in the next class, because the features of
the quaternary structure are very, very important for
the proper transport of oxygen, and single mutations can
really mess things up, and you'll see more about
that in the next class. So just wrap that
little bit up, proteins are condensation
polymers of amino acids. Each protein sequence is
defined by covalent bonding. Native proteins. Most of them that are not have
quite quaternary structure are folded through secondary
and tertiary interactions, these things that we
already talked about, and folding is defined
by how to maximize all those non-covalent
forces to get the maximum
thermodynamic stability with the maximum
number of interactions. And subunits may
also come together through quaternary structure. OK, so I'm going to talk to
you about several proteins throughout the
course, but for now, I want to focus you in on
a structural protein that provides mechanical
support for tissues. In the next class, we'll talk
about transporters and enzymes, and as we move on
to signaling, things like receptors and membrane
proteins and so on. So the protein I'm going to
describe to you is collagen. It is the most abundant
protein in the human body. It plays enormous roles. It's not an enzyme,
it's not a catalyst, it's not a transporter. It is one of those
structural proteins, where the structure of
collagen has evolved to provide a mechanical
stability to lots of essential components
of complex organisms. And there are many
different types of collagens that are found in
different parts of the body. For example, bone, tendon,
cartilage, and so on. They are all college
and structures, but they have
subtle differences, maybe some have different,
slightly different, mechanical properties to
adapt to the functions that they perform, OK? And what I'm going to show you
is that a single amino acid change in the primary
sequence of collagen can destabilize the structure,
so it is no longer viable. And the disease type
I'm going to talk to you about is a set of diseases
known as collagenopathies, and the particular one is
called osteogenesis imperfecta. Osteo always refers to
bone because college and plays a critical role
in the structure of bone. Bone isn't just bone, it's
collagen involved in it. And it's also this disease is
called brittle bone syndrome. And here's the X-ray of a
baby born with brittle bones syndrome, and you'll see that
the long bones in the upper arm are all irregular because
the bones are brittle, and they'll break even in utero. A lot of babies with
this defect can't even be born through the
birth canal because it would crush the bones,
and many of them don't survive very long at all. Some survive with
different kinds of cases, but their lives are
greatly impacted, and they could just
sort of hit a table and the bones would
break, all right? There are those sort
of serious situations where parents are actually
accused of abuse to the child, but the child actually
had brittle bone syndrome, and it was just through helping
them put their clothes on or taking them upstairs, the
bones got broken very readily. So osteogenesis
imperfecta really describes a collection
of these defects. Now the collagen tertiary
structure is shown here. It's actually made up
of a type of helix. It's not an alpha helix. It's a polyproline helix,
where the individual subunits in that tertiary in the
structure are fairly long and extended, and I
show you three strands in this polymeric structure,
a yellow, a red, and a green. And these rolled together
into a three helix bundle that has a fibrillous structure,
and then all these structures come together to make the
macromolecular structure that is collagen. It's not just one
of those fibrils. It's bundles of those fibrils in
a very organized pattern where you could even see that
patterning in electron microscopy. And there are many genetic
defects of collagen, and what's so important
to think about is if you have a
defect in one strand that defect will propagate
through every single strand. If this is one strand made up
of three polypeptide chains, it propagates all the way
through the structure. And I believe I have little
time to just show you, here's the collagen structure. I'm just showing you
how it's extended. Those are three
independent strands, and there's a set of magenta
residues in the middle, which come from a defect
in the sequence where a glycine has been
changed to an alanine. So I'm going to show you
this movie because it shows you right at the center
of the structure, there are residues painted in pink. And what I'm going to do is show
you close up of that segment. If you look at
those cells they're all nicely organized,
except where that defect is, and that defect is caused
by the change of a hydrogen to a methyl group on three
residues that come together, and that bulges out that
fibrillous structure and makes it not as
compact and beautiful as it should be in the version
that's got the glycine there. So if you look at
it, you can even see that helix gets
bulged out and it's not as well-aligned as the
rest of the structure. And then that defect
gets propagated into all the fibrils and results
in the weakening of the bones. Either the collagen
fails to form properly, or the collagen,
when it forms, it has much less
mechanical stability. So I think that's a
good place to stop and I'll pick up next
time with hemoglobin. Oh, one last little thing, a
couple of things for you to do. There's a great link on the
website to the Protein Data Bank to see how enzymes work. And if you have
a little time, it would be awesome
if you could just take a quick flick through
those parts of the text. These slides are posted with
these reading assignments, and they're posted in color if
you want to look at them again.
