>> So we're going to pick up
where we left off last time.
Last time we were talking
about protein structure.
And, we're going to start
from first principles today,
looking at the most basic
elements of protein structure
and then kind of
building from there,
as we get more increasingly
more complicated.
OK. So quick announcements,
as you know, read chapter 5.
Get ahead and start
reading chapter 6.
We'll be working on
that chapter next week.
There'll be a midterm, which is
two weeks from the past Tuesday,
so about a week and a half
from now there'll be a
midterm, the second midterm.
And, that will cover
through the end of chapter 6.
OK, and I'll mainly focus
on the more recent material
since the last midterm,
and I believe that's
like chapter 3 through
chapter 6.
So sort of the last
half of chapter 3,
the last little quarter or
third of chapter 3 and then
on through the end
of chapter 6, OK,
that's what the midterm
will cover.
Let's see, today is the day that
we have assignments that are due
and so don't forget to
turn those in at the end
of the class today, just
leave them over here
or hand them to the TAs.
If you forget drop
them by my office.
OK, questions about we're
going, that sort of thing?
OK. Let's take a quick
look then at office hours.
I have office hours today,
immediately after class.
Mariam has office hour tomorrow
and next week we're back
on Tuesday, et cetera.
I expect my office
hour next week,
the floating office hour
will take place probably 2:15
to 3:15.
Let me just make that chance
just so that you know.
OK, so that's also going
to be the next week
office hour as well.
Let's see.
This would be a good
office hour to come
by to talk about your proposal.
Recall that the abstract to your
proposal is due next Thursday,
a week from today, right?
OK. So, a week from today
you're going to hand
in something that's page--
that's five sentences.
[ Laughter ]
I stopped myself just in time.
OK. So, let's talk very
briefly about the format
for those five sentences.
OK, this is what I like to see
in your proposal abstracts.
OK. OK. So, the proposal
abstract needs
to tell me two things.
OK. So, let's say-- yeah.
So, those two things
are your idea, and two,
how it fits the definition
of chemical biology.
[ Pause ]
I would say if you're
submitting a proposal
to the National Science
Foundation,
how it fits the definition
of chemical biology,
not so important.
But for Chem 128, it's
really important, OK?
Because I know everyone in
this classroom is a creative
individual who has lots of great
ideas but the vast majority
of those ideas aren't in the
area of chemical biology.
So, I'm interested in your
chemical biology ideas, OK?
So, here's what I would like to
see in your proposal abstract.
It must cover these two
topics and specifically,
let me show you the format.
Natalie [assumed spelling],
is this color showing
up OK or is it little dim?
>> If you get something
darker [inaudible]--
>> I'll get something darker.
OK. OK. So, abstracts
are at the start
of all scientific
communications.
The abstract is also known
as the executive summary
in business communication
and it's a very,
very short distillation of
the key ideas in a paper.
And so, the goal of the abstract
is to provide those ideas
and then, secondarily,
to hook the reader.
A good abstract should convince
the reader that they want
to read the rest of the paper.
And a great example of
this is PubMed right?
When you do searches
on PubMed, it turned--
you get these abstracts
that are turned up.
And I don't know about you,
but if the abstract doesn't
look very interesting
or the abstract isn't
covering the ideas
that I'm interested in, I
don't bother reading the paper.
I'm sure you're doing
this as well, right?
If you're not, then, boy,
you're reading a lot, OK?
So, abstracts are
absolutely crucial
to communicating
effectively with audiences.
And again, in the
business community,
this is called an
executive summary.
And, again, it's
absolutely essential.
So, for anything you're going to
be writing after you graduate,
there's a good chance
that you're going
to need an abstract.
The abstract in this
class should consist
of the following sentences.
OK. So, we'll call this
the abstract format.
And, in general, I'm expecting
something that's five sentences.
If it happens to be more
than five, that's fine.
If it happens to be a little
less than five like four,
that's probably OK as well.
But don't plan for something
that's like 10 pages, OK?
Don't hand me the
whole proposal.
The goal here is that I can
provide you a little bit
of feedback.
OK. So, the-- I'm going
to just number these.
Let's just say, number of--
numbered, we'll call this
numbered sentence, OK?
Numbered sentence.
OK. And, again, you--
don't number your sentences
but I'm going to just give you
what I expect each sentence
to look like.
OK. So, sentence number one is
kind of states the problem, OK?
So, diabetes affects two million
Americans per year sometimes
with great consequences.
OK. That's-- that kind
of states the problem,
the big picture of the problem.
By the way, I just made up
that statistic about diabetes.
I don't know what
the real number is.
I'm just making that up
just to give you an example.
OK. So, first sentence
states big picture, OK?
And I really mean big
picture of problem.
Big picture problem.
OK. So, start off big.
This really should
be something large.
If you're thinking
about, I don't know,
a better cosmetic or something.
You know, a better anti-wrinkle
cream, that might be nice.
But honestly, it's not going
to fly really as a proposal.
Like if you want to come up with
a better anti-wrinkle cream,
see me and we could talk
about how to like hook
up with a venture capitalist.
You can have money for
that kind of thing.
Separately, you submit proposals
to the National Science
Foundation
because they're not going
to fund that kind of stuff.
What I'm looking for is
I'm looking for things
that will either increase our
understanding of the world
around us or solve some problem
afflicting the human condition
on this planet.
And when I say that, I
mean that broadly, OK?
So, for example if you want to
solve, you know, some disease
that only affects
mountain gorillas,
which could be important, right?
Because we, humans, have a stake
in ensuring the biodiversity
of our planet.
So, that's a big problem.
I'd like to hear
about that as well.
OK. So I'm not going to
confine it just a human disease.
I'll say, you know,
chemical biology broadly.
But at the top, at the
outset, in that first sentence,
you have to show me what
the big picture problem is
that you're going to be
targeting with your idea.
And notice that you don't
lead off of the idea.
You're actually starting by
kind of setting up the story.
OK. And in fact, you
should be thinking
about this along the
lines of story telling.
Good proposals are kind
of like selling a story.
And so, the first sentence
is kind of setting the scene,
setting the dramatic mood
and telling us why it is
that we should be following
along with the next part.
OK. So that's sentence one.
Yeah? Any question over there?
>> So if we have like stats like
the diabetes stats [inaudible],
do we have to cite it in our
abstract or later on our paper?
>> Yeah, you could do both.
Yeah. So, oftentimes--
and I forget your name.
>> Rudyne [assumed spelling].
>> Rudyne?
>> Yeah.
>> OK. So Rudyne's question is
what if I want to cite the stats
that appeared in the first
sentence later in the paper
and that would be
perfectly acceptable.
Oftentimes, there's some
overlap between the abstract
and the rest of the paper,
and that's normal, right?
Because remember the
abstract is the distillation
of what's in the paper.
So, some overlap
is even expected.
OK. Second sentence is
kind of focuses reader
on your aspect of the problem.
Let's say on specific
aspect of problem, OK?
So the first sentence kind of
gets you in the door, right?
That first sentence is
the one that says, "Oh,
there's this huge
problem out there.
The barbarians are
at the gates."
Second sentence says, "And
here's what we're going to do
to counter the barbarians.
There's this back
gate that I know about
and I'm going to reinforce it."
OK. Obviously, you won't
be writing about barbarians
but that's a proposal I
can think of at the moment.
OK. So, focus the reader on a
specific aspect of the problem.
So, first sentence was the thing
about diabetes as, you know,
afflicting millions of people.
Second sentence says there's
a target for diabetes,
relatively unexplored
target for diabetes called,
I don't know, FoxA [phonetic].
Offers new opportunities
for controlling this
terrible disease, OK?
I'm making this up
as I go, all right?
So, now I know that the
next part of this is going
to be something about
FoxA and I'm going
to be looking out for FoxA.
Third sentence.
Third sentence now focuses
on your specific idea, OK?
So, third sentence is where
you're going to come in
and say state idea
as hypothesis.
OK. Now, I'm not going to
ask you to write a sentence
that says my hypothesis is X
and I will test this by doing Y.
But you should have
something that's a hypothesis.
Do you all know what
a hypothesis is?
Do we need to talk
about hypothesis?
If this word hypothesis
is unfamiliar
to you, you must look it up.
You must become familiar with it
because I will be
looking for a hypothesis.
Your ideas have to
be hypothesis driven.
OK. Now, I will tell you.
Now, I'm really burying
[phonetic] my soul,
90 percent of the stuff that I
think about and I want to work
on is not hypothesis driven.
I like the kind of
science where you go out
and you explore something
that you don't know what
you're going to get.
OK. I like fishing.
I love throwing a line in the
water and not knowing what kind
of beautiful fish is going
to get snagged by that line.
That absolutely fascinates me.
I will do that time and again
for, I don't know, hours per day
in miserable conditions
because I just love the thrill
of the venture of not knowing
what you're going to get.
But, I have learned to
frame my fishing expeditions
in terms of a hypothesis.
I have this hypothesis
that this particular area
of the lake is going to be
an effective one for fishing
because there's an outflow of
water into that particular area
of the lake and that's where
fish like to gather to--
or let's say inflow of water
and fish like to gather there
because there's going
to be abundant food
in that particular spot.
OK. So, if you have an
idea that you can not know
in advance really what
you're going to find,
you still frame it in terms
of I'm going to be doing this
but I have a hypothesis that
the way I'm doing this is going
to be more successful,
all right?
And let me give you an example
of this that's less abstract
like fishing and more
concrete like aptamers.
So, previous sentence I set up
this whole thing about FoxA.
So, RNA aptamer libraries have
emerged as a powerful technique
for studying proteins
in the cell and I want
to combine aptamers
together with studies of FoxA
to explore FoxA as a
target for diabetes.
OK. So I have a hypothesis
that if I could discover
a binding partner to FoxA,
then I will be able
to do something
about this terrible
disease called diabetes, OK?
And so, I can't tell you
in advance the design
of that aptamer.
I'm just going to make a whole
library of aptamers and it's
like fishing, I'm just going
to throw them all against FoxA.
But, I suspect that
this is going to be--
this is going to work.
OK. So, my hypothesis
is within this library,
I could find something
that's going to bind to FoxA.
And furthermore from the library
design, I'm going to set it
up so that we're going
to be more likely to
be successful, OK?
So, there has to be a hypothesis
embedded in your logic
of why it is that you want to
do what you want to do, OK?
But you don't necessarily have
to use the word hypothesis.
OK. Next sentence.
Next sentence is on how
it fits the definition
of chemical biology and
you must have a sentence
that says this in
your abstract, OK?
So, this-- and the sentence
must say this idea fits the
definition of chem bio because,
and then I'll leave a line here.
OK. This is essential.
Your abstracts must
all include a sentence
that says exactly this.
I've been doing this-- I've
been teaching in this class
for a long time in
think [inaudible] 12.
And I've learned that if I
don't have a sentence like this,
I will get all kinds
of unfocused ideas, OK?
And so, and I know from
talking to some of you
about book reports, this is
hell kind of a mysterious idea.
But review the definition
of chem bio and make sure
that your idea squarely targets
that definition of chem bio,
which is using techniques form
chemistry to understand biology
at the level of atoms
and bonds, OK?
Makes sense?
OK. Let's talk about the
most important sentence
of any proposal.
This is a sentence that
if it's a good one,
this will get you
funded every time.
And I guarantee it to you,
this trick works not just
with the NSF, not just
with funding agencies,
this will even work
with your parents.
OK? And those are your major
funders these days, I know.
OK. So, let's talk a little
bit about the last sentence.
This last sentence is one that
I like to call the payoff.
OK. In short, the
payoff sentence is
if this idea hits a home run,
here's what's in it for you.
Here's what is you or
needing society is going
to gain from this.
If every expectation that
I make, if every hypothesis
that I propose turns
out to be correct,
here's what you get
to benefit from.
OK. So, this is the one
where you imagine a
home run, now deliver.
OK. What happens?
What results?
So imagine a home run
and then what results.
All right.
Sorry, this is getting a
little jammed together.
I wanted all fit on one board.
OK. Makes sense?
So, every abstract is going
to end with the payoff.
This is easily the only sentence
that really matters in proposals
because your proposals
are going to be read
by a large number of people.
I'm not talking about Chem 128.
I'm talking about later
when you go up in front
of a research review board and
you're asking for more funding
for your, I don't know, oil
[phonetic] development team
or something like that.
That last sentence,
the what's in it
for the reader is really the
one that gets you funded, OK?
Because oftentimes, proposals
appear in front of people
who don't really
understand them, OK?
So, proposals have to appeal to
broad audience and typically,
proposals are read by
groups of 20 people.
There might be 20
people in front of you
between you and the check.
And those-- many of those
20 people are trained
in other areas.
They're really smart but
they might not know very much
about FoxA.
They might not be able
to evaluate whether
or not FoxA is a good target
for diabetes research.
However, they definitely
need to be able
to understand this payoff, OK?
And it really has to follow that
it's going to be useful, OK?
So, you don't want
to promise the moon
if you can't deliver the moon.
OK. So, a payoff sentence
for our hypothetical
proposal might be something
like inhibiting FoxA
with an aptamer would--
could provide a new mortality
for decreasing surges
in blood sugar amongst
diabetic patients.
OK. And that would
be useful, right?
That would be extremely
important, potentially,
for diabetes treatment, OK?
But I'm not going to say
it's going to cure diabetes
if I can't deliver
a cure for diabetes.
If you promise, you know, a
cure for cancer or something,
you know, disease, you'd
be able to back it up
or else the reviewer
reading this is going
to start holding her
nose or his nose, right?
Because they're going to be like
where is my cure for cancer?
I thought you promised
me a cure for cancer.
I don't see a cure for cancer.
This might be nice and all but
I don't see the-- anyway, right?
You get the idea.
So, you have to be able to
deliver what you are promising.
But on the other hand, you
don't want to under-promise
because this is really the
part where the, you know,
the person at the other
end holding the big bag
of cash decides whether or not
they want to invest in you.
OK. Makes sense?
OK. This is totally formulaic.
The formula I'm giving you,
this abstract format works
for all kinds of proposals.
It works for proposals that
are going to appear in front
of venture capitalists.
It will work with in front
[phonetic] of proposals
that appear in front
of your parents.
It will work for any sort of
group of foundation or group
of people holding money.
I know because this
is the formula I use.
OK. And I want you to do it.
I want you to follow
this formula as well, OK?
For this class, just try it.
Trust me, it works.
Other-- Any questions
about this abstract?
Yeah.
>> Now you mentioned
that would be a good idea
for journal reports to kind
of correlate with this.
>> Yeah.
>> So, since the ideas
behind probably sentence one,
two and five are going
to be really similar,
how can we like use those
ideas without plagiarizing?
>> OK. Great question.
And remind me of your name.
>> Yasmine.
>> Jasmine?
>> Yasmine, with a Y.
>> Yasmine, right, with a Y. OK.
So Yasmine with a
Y is asking why--
what happens if my background is
very similar to the background
that appeared in the
proposal-- not the proposal,
in the journal article, I would
say find another journal--
find another sentence one,
the big picture sentence.
That big picture sentence
has to be your interpretation
of why you think it's important
not why some other scientists
working at Johns Hopkins
thinks this is important, OK?
So you have to be spinning this
to fit your own interest, OK?
So, for example if the
journal article starts
with the sentence two million
people are going to be afflicted
with diabetes this year,
then maybe you want
to say 200,000 new cases
of diabetes are going
to be diagnosed next month.
You know what I mean?
So now you turned
it around, right?
And you focus on something
that you think is
particularly important.
And actually now
that I think about it
that if your target is
this thing that's going
to monitor your blood sugar,
maybe you want to say, you know,
10,000 diabetics are going
to have to have amputations
of their limbs because
of complications
from diabetes, right?
So basically you're
reinterpreting this big problem
and focusing on some aspect
that you think is important
because it's your
ideas that I care
about not somebody else's ideas.
And along those lines
on the payoff over here,
I want your ideas for where the
payoff is going to be useful.
OK. Why is this going to be
helpful for someone reading this
who might consider
funding it, OK?
OK. Final thought.
That was a great question.
Other questions?
Anyone else?
So, I've mentioned this
before in an e-mail
and I just want to reiterate it.
The very best proposals from
this class, I will submit
to the campus writing
coordinator
and I've been pretty
successful at getting--
at convincing the campus
writing coordinator
that my students are really
extraordinary writers.
And-- so I've been really
successful at getting students
from this class awards,
writing awards which is nice.
You get to add that to your CV.
I think they even
got you a check, OK?
So it's a rare time that
the regents, the University
of California will give you
money if you're successful.
So I'll be on the lookout
for the very top two
or three proposals
coming from this class.
Because I really could tend
[phonetic] that the top two
or three proposals from
this class are good enough
that I can put in front of the
National Institute of Health
and I bet they would get funded.
They're that good.
So, now-- OK, this also
reminds me of something.
Every year, when I get those
teaching evaluations back,
someone says Professor Weiss
is just fishing for new ideas.
I promise you that
is not the case.
OK. So, my laboratory
is stocked with ideas
for the next 20 years.
You can ask Miriam or Kritika.
They will assure you that
I'm always driving them nuts
with some crazy idea I think
of on the way into work.
And so, there's no way that no
matter how brilliant you are
that I'm going to be scooping
up your idea and then, you know,
running into the lab
and be like you got
to do this thing I just read it.
OK. So, don't worry about that.
Give me your best ideas.
Show me your best ideas.
It's a bad strategy to
hold back your best ideas
because you're afraid someone
is going to scoop them, OK?
Ideas are dime a dozen.
If you're smart enough to
come up with good ideas,
you're smart enough to
come up with one good idea.
You're smart enough to come up
with a dozen more good ideas.
OK. So give me your
best idea, OK?
And don't worry that someone's
going to end up scooping you.
If you do, you get to
claim some status, right?
You could say, well, I have
that idea 10 years ago back
when I took Chem 128
with that crazy guy.
And, you know, here's my report.
I got an A minus on it.
So, you know, maybe that person
goes on to win a Nobel Prize
and you look cool because you
thought that idea first, OK?
But don't hold back.
Don't worry about getting
scooped or anything like that.
The truth is any proposal
that you do, you're going
to have some situation
like that.
And if you're starting a new
company or something like that,
sometimes you sign
confidentiality disclosure
agreements, CDA's, in advance
with the people you're
disclosing ideas to.
But honestly, in science,
especially in academic science,
we're constantly
talking about ideas.
Even with my closest
competitors, OK?
My closest competitors,
I will tell them exactly
what we're working on.
Maybe not exactly but I might
hold back some key details.
But I'll certainly tell them the
general area that we're going
to be fishing in, right?
I'll be like, "Yeah, we're going
to be on this part of the lake."
I might not tell them exactly
what lure we're using or kind
of line but I'll them what we're
going to be doing, all right?
So, I want you to do the same.
Don't hold back.
Give me your best stuff.
I cannot wait to read this.
It's one of the real
rewards of the year I love.
Hearing about your creative
ideas really is invigorating.
It's really neat.
So, anyway, I'm looking
forward to that next Thursday.
Any questions about
the assignment?
Anything like that?
OK. I will get those
back next Thursday
and then it will take me a
week or so to process them.
I'll be in Brazil from
Friday onward of next week.
And so, there'll be--
you won't hear anything
from me for a few days.
Don't panic.
I'm reading them all while
I'm on the beach in Brazil.
Just kidding.
I won't be on a beach.
I'll be at meetings.
But I will be reading those
abstracts on the plane
and by the time I get back
I'll have them all commented
on for you, OK?
Yeah.
>> I just [inaudible] question.
Is there any effective
way to make sure
that our idea is
original and [inaudible]?
>> Yeah. Actually,
I'm so glad you asked.
OK. So the easy part of
this assignment is thinking
of a creative idea.
OK. That's the easy part,
the "eureka" moment.
The hard work is where you're
digging into the literature
to see if someone else has
already done that idea.
And it's essential
that you do this.
You must do this.
So, what I do is when
I think of some idea,
the first thing I do is I run--
well, I no longer have
to run to my laptop.
I pull up my cellphone and
then type it into Google
and do a quick Google search
and see what else has
been done in that area.
And then I'll do
PubMed searches.
And then I'll change
the wording around.
I'll do some more searches.
That's the hard stuff.
OK. So, thinking of the idea,
that's like five percent.
The much harder stuff is doing
all the background reading
to make sure that
it is original.
It is essential that you
propose an original idea.
If it's not an original idea,
I will give it back
to you ungraded, OK?
And I'm going to ask
Kritika and Mariam
to do Google searches
of everyone's idea.
OK. They will do a quick Google
search and they will tell me
if it's not an original idea.
If it's already been done,
it's going to be returned
to you ungraded, OK?
And that's not good.
That means you have to start
from the beginning, OK?
So, it's really important
that you do that.
Thanks for asking.
Any other questions?
Yeah.
>> Once we submit these
abstracts, are we allowed
to bring it all into
the actual [inaudible]?
>> Absolutely.
In fact, you will-- in fact,
it's absolutely mandatory
that you change your idea
based upon my comments,
based upon new reading
that you do, et cetera.
And what I'm going to do is I'm
going to give it back to you
but I'm going to ask you to hang
on to it and then turn it back
in with the proposal at
the very end because I want
to see the evolution
of your ideas
in response to my comments, OK?
So I'm going to tell
you, "Yeah, you know,
this idea would be a
lot better if you went
in this other direction
like there's a new type
of aptamer called mRNA display.
You should look into that."
And so, I'm going to be
looking for a proposal then
that is responsive
to that suggestion.
OK. And I'm going to give you
points for being responsive
to the suggestion
or take out points
for being unresponsive, OK?
So, yeah, there's going to be
considerable changes between now
and when the time when the
final proposal is submitted.
And, in fact, some of
you are going to end
up just totally chucking
the first idea
and coming up something new.
And that's fine too.
OK. Any other questions?
OK, very good.
Again, I look forward
to reading those.
Let's get back to proteins and
all things protein-related.
I want to-- let me see.
Let me just put down
these things.
Let's just quickly summarize
what we saw on Tuesday.
As I told you on Thursday,
I introduced you very,
very briefly to the 20
naturally occurring amino acids.
Id' like you to memorize
their structures,
their abbreviations,
their names.
We talked a little
about peptides can make
effective pharmaceutical
lead compounds.
Furthermore, when they're
cyclized, when their N
and C termini are
joined together in a ring
to form a ring, the
result in cyclized peptide
or cyclic peptide is amazingly
stable even in the stomach,
even in this very protease-rich
environment of the stomach.
It turns out this is
actually fairly generic.
It seems to work really well.
And cyclotides are
actually emerging
as an important pharmaceutical
class of compounds.
And we looked at how
peptides can also be used
as lead compounds to develop
small molecule therapeutics.
OK. And the next
topic was we looked
at a technique called
native chemical ligation
for stitching together
small peptides
into much larger proteins.
This actually works pretty well.
It actually-- This
is a good technique.
The nice thing about it is
because the peptides are
chemically synthesized.
You can include unnatural
amino acids pretty readily
and that allows hypothesis
testing, right?
If you replace say a
hydroxyl functionality
with the three functionality,
maybe you can test whether
or not the hydroxyl is donating
a hydrogen bond and you can look
at issues like the
fluorine-based hydrogen bond,
OK?
So you can look at stuff
in a unique ways using
unnatural amino acids
that are introduced
using chemical synthesis.
And along the lines
of chemical synthesis,
we very briefly reviewed that
carbodiimide coupling reactions
that you learned about back
in sophomore organic chemistry
and I suggested that if
those were unfamiliar to you,
you might want to
go back and review.
OK. And then finally,
we ended on talking
about how protein
splicing can result
in the spontaneous removal
of an intein using a
very similar mechanism.
All right.
Any questions so far?
All right, I want to go
and talk next about--
let me just skip on.
I want to talk next about
conformational analysis
which is trying to understand
why it is proteins adapt
specific configurations.
Last time, for example, we
learned about alpha helices
and we learned about
beta sheets.
And I haven't really
told you too much more
about how it is that this form.
What are the forces that
are driving these structures
into these particular
conformations?
And before you do, just a couple
of more quick words
about beta sheets.
Beta sheets come in two flavors.
They can be either parallel.
So the strands are running
from N terminus on the left,
C terminus on the right, N on
the left, C terminus at right.
These are now parallel
strands, OK?
So, notice N terminus
is on the left.
C terminus is on the right.
This is-- This strand is
going in this direction,
the next strand below it
going in this direction,
going in this direction.
On the other hand,
more commonly,
beta sheets can be found in
anti-parallel directions.
And I'm saying more commonly
because if you think about it,
there has to be a very long
linker between the C terminus
on this side and the N
terminus on this side.
All these gray stuff,
that's really long.
OK. Whereas, in an
anti-parallel fashion,
the beta sheet can very neatly
have a C terminus at one end,
a little linker that leads
neatly to the N terminus leading
to the C terminus and so on.
And recall that N to C
convention that we use
to describe peptides, that also
illustrates the directionality
of these arrows.
The arrows are going from
N terminus to C terminus
which is how we read
protein structure.
OK. Now, something that's
interesting about this as well,
notice that the hydrogen bonds
are at slightly different angles
between parallel beta sheets and
the anti-parallel beta sheets.
It turns out that nature
of hoarse flat surfaces.
Flat surfaces are
very, very really found
in biology more commonly
flat surfaces are curvy
and I'll tell you exactly
why beta sheets are curvy
in a moment.
But before we do, let me just
note that beta sheets fold
up into structures, surfaces
that aren't perfectly flat.
So, very commonly,
beta sheets will fold
up into this beta barrel.
Is this an anti-parallel
or parallel beta sheet?
>> Anti-parallel?
>> OK. Good.
Anti-parallel, right?
Because this one, the arrow
is going down here and this--
the next strand is going up
in the opposite direction,
down in opposite direction,
up in opposite direction,
et cetera.
And that's why we're going
to call anti-parallel, OK?
So, this is pretty common.
Beta sheets can form into
these barrel-like structures.
These barrels can be fit
into plasma membranes,
membranes on the
surface of the cell.
They also are used very commonly
as binding proteins and even
as active sites for
catalyzing reactions, OK?
And stuff can happen either on
the inside of the beta barrel
but also on the outside of
the beta barrel as well.
And-- OK. Oh, here's an example
of a parallel beta sheet,
over here on the right.
Notice all the arrows are
pointing in the same direction.
Notice that it, too, is curvy.
It's not forming a
perfectly flat beta sheet.
Instead, these things like
to curve and I'll explain
that more in a moment.
Even this one that
looks relatively flat
of an immunoglobulin
domain, curvy, right?
Curvy, it's curving out
slightly towards us.
I realize it's a
little hard to see, OK?
But on the other hand, you
know, these beta sheets,
they're called sheets but they
really look a lot more curvy
than that.
OK. Questions about beta sheets?
OK. OK. More pictures
of beta sheet.
I love looking at
pictures of proteins.
This, to me, it's like
visiting a zoo or something.
They are just so beautiful.
OK. So, here's one.
This is a nice side
view of a beta sandwich.
OK. These are two beta
sheets stuck on top
of each other like
slices of bread.
Notice how this forms this kind
of propellor like
twist over here.
This inside in here
is not empty.
The side-chains are sticking
in over here and over here
and the sheets are
packing together
to form a nice core
with each other.
The side-chains are tickling
each other from one sheet
to another and those
side-chains then form--
packed together to form a
core that consists largely
of hydrophobic residues.
We'll take a closer look
at that in a moment.
OK. Oh, actually
it's right here.
OK. So, here are the
side-chains of the beta sheet.
Notice that the side-chains
are perpendicular to the sheet.
This is due to something
called allylic strain
which we'll look more closely
at in just a moment, OK?
So, bear with me.
In about three minutes,
we're going to know--
yeah, I'm going to tell
you what allylic strain is.
But notice the consequence
of allylic strain is
that all these side-chains
are sticking
down perpendicular
to the beta sheet.
They're like leaves
of grass that are--
blades of grass that are
kind of sticking down.
And then this beta sheet
down here has side-chains
that are sticking
up to grass bond
to those side-chains up there.
OK. So, the beta
sheets tend to be curvy.
They have the side-chains
perpendicular
to the beta sheet
ready for interactions.
OK, one final element of
secondary structure in proteins
that I want to introduce you to.
The turns.
Turns are found at the ends
of each one of these sheets
or each one of these strands.
OK. So here's a beta
strand down here.
This is a turn and then it
leads to another strand,
so each one of these strands
are connected together
by loops and turns.
And let's take a closer look.
There's two kinds of
turns that are found.
A 180 degree turn
called a beta turn, OK?
So in this case, one
strand comes down here.
It turns around 180 degrees.
It heads back.
The other turn is kind of
like a right handed turn, OK?
So it comes in here
and then it turns
and this is called
a gamma turn, OK?
Sorry, this is-- yeah,
it's a right hand turn.
Notice that both of
these turns feature one
and only one hydrogen bond.
There's other elements that are
stabilizing the turn largely
from the strength of
these interactions
of the strands over here.
And there's residues over here
that critically staple
together the turns, OK?
So you have two side-chains that
are interacting with each other
such as two phenylalanine
side-chains.
Last time, on Tuesday, I showed
you how the FeFe side-chain
interaction was one
of the strongest
and the most over-represented
in the population of
protein structure.
So, somewhere over here, it's
likely that you'd have something
like that between
two phenyl groups
of phenylalanine side-chains.
And so, this one hydrogen bond
is not the world's greatest
accommodator of this turn but,
you know, it's not so strong
that it can force
the turn to happen
but there's other residues that
play more than a supporting role
in assuring that the
turn is happening.
OK. Now, here's the thing.
Because there's only
one hydrogen bond here,
what do you think happens to all
of those other hydrogen
bond donors and acceptors?
What do you think
they are doing?
[ Pause ]
>> Can you repeat the question?
>> Yeah. OK.
Carl [assumed spelling] asked
me to repeat the question.
So, you have one hydrogen bond.
So that has acceptor
and donor tied up
but then you have all these
other donors and acceptors.
These guys are available
to do things.
What do you think they're dong?
>> Would they be interacting
with other proteins?
>> Yeah. Chelsea [assumed
spelling] suggested
that these are interacting
with other proteins
and in fact that's why
these terms are often found
at positions that need
to accommodate other
binding partners.
You have all these extra
hydrogen bond donors
and acceptors that are
looking for business.
They're hanging out there.
They don't have anyone
to hydrogen bond to
and maybe they can pick up
some other binding partners.
Furthermore, because the
turn itself is set only
by this one hydrogen bond,
that means that the turn
can be relatively flexible
and the regions of
secondary structure.
This is the most flexible
region of the protein.
And so, oftentimes in areas
of protein structure that have
to accommodate large numbers
of different binding partners,
we find these turns
because they can change.
They can move around
and be flexible enough
to accommodate different
sizes of binding partners.
Yet at the same time,
they have lots
of hydrogen bond
functionalities,
hydrogen binding functionalities
that could then donate
to the binding partners, OK?
And let me show you
an example of this.
This is at the interphase
between two proteins
that are interacting
with each other.
And notice that there are
bunch of these turns or loops
that are reaching out
to touch each other.
OK, that's fairly typical where
you have two binding partners
that are interacting with
the sort of loopy regions.
Loopy regions are
flexible enough
to accommodate diverse
binding partners.
Excuse me.
Another example are found
in antibodies and we'll look
at that in a moment, OK?
Makes sense?
OK. Now, turns obviously
requires some amino acids.
Turns like this require
amino acids
that don't mind being torqued
quite dramatically, right?
If it's going to loop back over
here, you need some amino acids
that can handle that
kind of big turn, OK?
And not all amino acids
are so accommodating
with that kind of thing.
And when we look at trends in
the distribution of amino acids,
we find some amino
acids are better
at making these turns
than others.
And this also applies
as well to beta sheets.
The things that like to
do turns are not so good
at making strands of a beta
sheet where the peptide has
to be extended line, right?
If the thing wants to turn,
not going to be so good
in the middle of
a beta sheet, OK?
And so for this reason, we
can classify amino acids
as helix formers, helix breakers
present in coils, et cetera.
OK. And let me see.
Can you guys see
this way back here?
I wasn't sure when I put
these slides together
if would be visible.
Oh, actually, you
know, my prescription
for glasses is working
really well today.
I could see that pretty readily.
Can you see this as well?
>> Yup.
>> OK, good.
OK. So, the red numbers,
larger red numbers,
are a higher distribution
of amino acids
in these different
structures, OK?
So for example, alanine is found
very commonly in alpha helices.
Glutamic acid, very
commonly alpha helices.
Other ones like lycine,
not so much, OK?
Glycine might be
found more in coils.
Beta sheets, glycine isn't so
good because it's too flexible.
Glycine is also found very
commonly in these turns
that I showed on the
previous slide, OK?
So, beta turns commonly
have a glycine over here
and a proline over here.
So, G, P is a very
common motif in turns.
Glycine doesn't have
a side-chain.
It can be very readily
bend and bend
to accommodate this
dramatic 180 degree turn.
On the other hand, bendability,
not so good for beta sheets,
also not so good for alpha
helices and that's what you see
in this example over
here, right?
It has a number of 0.47.
So it's a very, very low
number of propensity.
OK. What else can I tell you?
Notice that the amino
acids that have carbons--
beta carbons, not found
so often in alpha helices.
Alpha helices are kind
of twisted or curled up.
And the beta-- functionalities
pass the beta carbon,
tend to run in to those
coils of the alpha helices.
So, instead, these
tend to be over--
in the large side-chains tend
to be over-represented
in beta sheets.
So they tend to be more
commonly found in beta sheets.
So these things like
phenylalanine, tryptophan,
tyrosine, these big aromatic
residues more commonly found
in beta sheets.
OK. Makes sense?
OK. Now, don't memorize this
table but get ready to kind
of prepare to explain
some of these trends, OK?
A totally legitimate problem
would be for me to ask you,
so here's, you know, what is
the structure of phenylalanine?
Would you expect it to be
more common in beta sheets
and gamma turns or
alpha helices and why?
OK? Right?
Makes sense?
OK. OK, I want to talk to you in
further detail about that kind
of conformational analysis.
And to do that, I'm going
to draw in the board, OK?
OK. Now, OK.
So, we're going to
start off very slow, OK?
We're going to start off easy.
I'm going to start
off with just ethane.
OK. So simple, you
know, two carbons.
I guess we don't spend enough
time thinking about ethane.
But let's imagine
that you looked
down this carbon-carbon
bond, OK?
This is going to be the
symbol for your eyes.
So imagine your eyes pointing
down this carbon-carbon bond.
If you did and you looked at
a projection down that bond,
what you would see then
is three hydrogens, OK?
So, three hydrogens
of the methyl group
that's closest to you.
And then we would have
the three hydrogens
of the methyl group
that's further away.
OK. Makes sense?
Everyone's still with me, right?
OK. Now, let's talk a little bit
about how much more energy is
required to go from this case,
this is staggered
versus eclipsed.
OK. So let's rotate
by-- what is this?
60 degrees?
OK. So, rotate down CC bond.
OK. So if we do this, we
will then have the hydrogens
eclipsing each other.
OK. When you make--
when you write the--
when you draw these projections,
draw them so that you always
have the Mercedes symbol, OK?
I find it easier
to do it that way.
OK. So, in this case,
we've rotated
down that carbon-carbon bond.
And now, instead
of having hydrogens
that are staggered
away from each other,
they're now eclipsed
on each other, OK?
This takes energy.
OK. So this is-- each one
of these hydrogens that's
eclipsing each other is
on the order of a kcal per mole.
So, the difference in
energy here is something
like 3 kcals per mole, OK?
And these are estimated numbers.
OK. Now, back in Chem 51-A
when you first learned
about this how the staggered
was greatly preferred
over the eclipsed, I think
it was described to you
as being due to steric
effects, right?
This hydrogen runs into this
hydrogen over here and the two
of them are repelling
each other.
It turns out those
hydrogens are really tiny, OK?
If we made models of
what was happening here,
each carbon would be about
the size of a balloon
and each hydrogen would
be like a little pimple
on the side of the balloon.
So these little pimples aren't
running into each other, OK?
It turns out that's actually
not the commonly accepted
explanation anymore
for why it is
that the staggered conformation
is greatly preferred
over the eclipsed conformation.
Instead, what we find
is actually it's due
to a hyperconjugative
effect and I'll attempt
to draw that for you here.
OK. So, in the staggered
case-- oops.
Let's [inaudible] this way.
OK. So this is a different
[phonetic] representation still
of the staggered case.
OK. So, here is that
one hydrogen.
There's one coming out
towards us, going down.
There's one going out
towards the back going down.
Up here, in the back.
There's one like that.
One like that.
OK. So, this is preferred
because there's actually
a very tiny resonance
called hyperconjugation.
OK. And so, what's going
to happen is the following.
That gives you H plus up
here and H minus down here.
OK. This is the world's lousiest
of resonance structures.
It's one that probably hasn't
event entered your radar.
It's not even on your
radar for consideration.
But it happens to a very-- it's
tiny but appreciable extents.
In order for this resonance
structure to take place,
for the resonance structure to
stabilize things, this hydrogen
and this hydrogen have
to be anti to each other.
And you can only have this
anti configuration in the case
of the staggered
conformation of ethane.
OK. It doesn't happen in
eclipse conformation, OK?
So for this reason, amino acids
and proteins will also adapt
and anti-configuration
were possible, OK?
They're also going
to be following a
hyperconjugative effect.
Now, I could tell
you that thinking
about hyperconjugation
will eventually start
to numb your mind and
kind of hurt the brain.
It just requires too much of
crazy brain power to think
about all these resonance
structures.
So it's simpler to think
about it in terms of sterics.
The steric arguments
are also correct, OK?
But keep it-- or also will
lead you to the correct answer
but keep in mind that the real
thing that's underlying this
steric business is actually
a hyperconjugative effect.
OK. Now, things get much more
complicated as we start building
up from two carbon
molecules, OK?
And let's get started
next with butane.
OK. So, butane can start
off as an anti-conformation.
All right.
Let's say.
OK. So here is butane.
One, two, OK.
Sorry. We're going
to do our projection
down this carbon-carbon
bond here.
This one is coming
out towards us.
There's a hydrogen here, methyl
group here and let's see.
Sorry. Methyl group
here, hydrogen, hydrogen.
[ Pause ]
OK. So, one possible
conformation of butane.
Here's another possibility.
Again, we're going to rotate
around this carbon-carbon bond.
And now against to what we were
doing up there with the ethane,
in this case we're going
to be rotating 120 degrees.
OK. And if we do that, what
will happen is we'll have a
conformation that has--
that looks like this.
OK. So, rotating and then always
keep one of these constant.
OK. And again, the projection
here now looks like this
where we have our methyl
group, hydrogen, hydrogen.
And now, OK.
Which of these two
is more stable?
One on the left or
the one on the right?
OK. Let's take a quick vote.
All in favor of right
raise your right hand.
All in favor of left
raise your left hand.
OK, rights had carried
[phonetic] the day.
So, yes, indeed.
This one is more stable.
It's called an
anti-configuration.
This one over here
is less stable
because these two
methyl groups are going
to be running into each other.
This is called the
gauche configuration.
OK. So, this happens to be
less stable by on the order
of one kcal per mole, OK?
So, this one over here requires
an additional one kcal per mole,
OK?
So, we're possible,
we're going to try
to find anti-conformations of
our amino acid side-chains.
OK. So, we've seen ethane.
We've seen butane.
Let's build up to
one more complicated.
Let's go up to pentane.
Pentane gets much more
interesting because it turns
out that in addition to
the gauche configuration,
you can get one more
conformation
of pentane that's relevant.
OK. So, here's pentane.
Here's one possibility.
Notice that there's
five carbons there.
This is one possibility.
Here is another possibility
of pentane.
Which of these two is preferred?
One on left, one on the right?
Right hands.
All in favor of right hand?
OK. So right hands.
All in favor of left hand?
Left hands.
All right.
Opinion's divided.
It turns out actually the
difference here is on the order
of three to four kcals per mole.
OK. And by the way,
where I put the numbers,
those numbers are at
the higher energy.
OK. So this one is going to be
greater in energy versus, well,
to say three kcals per mole.
It kind of depends on
what we start with.
The reason is these two
methyl groups are now banging
into each other very
strenuously.
OK. Whereas up here, this methyl
group is nicely out of the way.
This is going to be called
a syn-pentane conformation.
OK. So, there's terms that
we're going to be using.
Staggered, eclipsed, gauche
versus anti and then, finally,
syn-pentane versus
non syn-pentane, OK?
And this syn-pentane is pretty
big somewhere between three
and five kcals per mole.
It's really big.
OK. So proteins are going
to do everything possible
to avoid running into this
and they could run into this
when end up with beta
branched amino acids, OK?
So this, at its heart is
what's driving formation
of alpha helices
and beta sheets.
What's going to allow
some amino acids
to access beta sheets better
than other amino acids?
And why don't we take
a closer look at that?
OK. So these are the terms.
Everyone's comfortable now with
the definitions of these terms?
You kind of calibrate
in terms of numbers?
OK. Well, let's get
started then.
Oops. OK. So, we've
looked at eclipsed
versus staggered, ethane.
Here's some numbers.
This is-- oh, we didn't even
talk about eclipsed butane.
That's huge.
To my mind, five and
a half kcals per mole,
that just never going to happen.
That's so large to just
even enter the equation.
OK. So, I think we
can all agree.
Eclipsed butane, horrible, OK?
Gauche butane, higher by
about one kcal per mole,
0.9 kcals per mole.
Not so great either.
But anti, lowest in energy.
OK. So, next, I want to
look just very briefly
at a few amino acids.
It turns out that we
can very readily predict
which amino acids are going to
have preferred configurations.
OK. And unfortunately, I
have to go back up again.
Sorry. I realized there's
a lot of ups and downs.
OK. Why don't we take a look
at the amino acid valine?
Valine has a nicer
purple side-chain.
And it turns out that valine
actually will adapt one
and only one conformation-- will
largely adapt one conformation.
OK. So, what I'm going to do--
let me just think about
this for a second.
OK. So we're always
going to have NH
over here, carbonyl over here.
OK. So that would be our
backbone, OK, of the--
and so I'm talking about these
things not just valine by itself
but valine in the context
of being in a protein.
OK. So, valine has a
nicer purple side-chain.
So, one possible
conformation of valine is this.
OK. And yes, there's one other.
Just to make sure.
Yeah. OK. So, the angle
defined by C alpha
to C beta is called chi one.
And we're going to be
rotating down these chi ones
as we start looking at
amino acid side-chains.
OK. So, let's imagine
rotating 120 degrees
down this chi one angle.
OK. So this angle here in blue.
If we do that--
[ Pause ]
-- we'll have these two CH3's.
So, does everyone see that?
Rotate 120 degrees down chi
one, one methyl group used
to be sticking out over
here, one was pointing down.
We rotate 120 degrees,
one sticking off
to the right, one's
pointing down.
OK? Right?
You got from here, you rotate
120 degrees, you got at here.
Makes sense?
OK. What is the difference
in energy between these two?
Any difference in energy?
Come on, you guys.
>> One kcal.
>> OK. Well, I guess
it's always good guess.
The answer actually both
of these are the same.
It was a trick question.
Sorry. Right.
Because they both
have the same number
of gauche interactions, right?
So this one over here has one
gauche interaction, but this one
over here also has
one gauche interaction
and I'm not even worrying
about these two methyl
groups down here, right?
OK. Let's do one more rotation.
OK. Same idea, rotating
around the chi one angle.
OK. So, again, in blue, this
is plus 120 degrees again
around this chi one.
And if we do that, OK.
So, again, we keep
the backbone constant.
If we do that, we're going
to go from a situation
where we had methyl group
sticking up on the right,
one going down, we rotate
and now we have two
methyl groups sticking up.
One hydrogen down here.
OK. So, higher in
energy, lower in energy.
>> Higher in energy.
>> Higher.
>> Higher.
>> OK. OK.
OK. I hear a lot of guessing.
OK. So, up here, this
guy over here is subject
to two gauche interactions,
one there and one here.
So, three gauche interactions.
Down here, how many gauche
interactions are present--
gauche butane interactions
are present in this molecule?
>> Two.
>> Two. One, two.
Any others?
OK. So which ones
higher in energy?
Top one or lower one?
>> Top one.
>> By how much?
>> One kcal.
>> One kcal per mole.
OK. So this is lower and we'll
call this up here higher--
we'll say lower in energy,
lower by one kcal per mole, 0.9,
one relatively similar, OK?
So, when we look at
structures of proteins,
we find that this valine
side-chain is going
to be predominantly
in one conformation.
It is going to strongly
prefer this conformation
versus other conformations.
Notice that it can rotate
a little bit further.
It can result in
eclipsed interactions.
There's eclipsed interactions
are so high in energy.
I'm not even going
to consider them.
Just thinking about whether
you have gauche butanes and try
to minimize the number
of gauche butanes means
that valine will prefer one
and only one conformation.
Makes sense?
Proteins are a massive
minimization of interactions
like this gauche butane.
And one of the most dominant is
something called allylic strain.
And that's what I want to
talk to you about next, OK?
So, let me first show you
what allylic strain is.
So, the-- let's see.
Allylic strain results
from-- OK.
So, allylic strain
results from rotation
around a bond that's allylic
to a carbon-carbon double bond.
This is the allyl functionality.
It's three carbons, two are
forming our carbon-carbon
double bond.
No rotation across the
carbon-carbon double bond.
Here are two other ones.
And what happens is there's
two kinds of allylic strain.
They're numbered.
They're called A1, 3 and the
other one is called A1, 2.
In the case of A1, 2 strain,
two functionalities are running
into each other, one from the--
one that's attached
to the middle carbon
of the allyl functionality
and one that's attached
to the other side of the-- one
that's attached to the carbon
that doesn't do any
carbon-carbon double bonds, OK?
Now, there's free rotation
around this carbon-carbon
single bond, right?
The carbon-carbon
double bond is fixed.
It can't rotate.
But the single bond
is free to rotate.
So, it's going to rotate away
from this A1, 2 interaction.
Notice this 1, 2 because this is
carbon 1, this is carbon 2, A1,
2, allylic 1, 2 strain.
This is huge.
This is like a kcal
and a half or so.
So, as it rotates, it
can actually rotate
into a conformation--
configuration such as this one
up here where now it has
another, in this case,
methyl group banging into R. OK.
These two are going to be
approaching each other in space,
kind of like the
syn-pentane interactions.
And, again, this is going to be
on the order of 3 kcals per mole
of deleterious energy.
It's [inaudible] bad is.
Proteins hate this
kind of thing.
So, instead what will
happen is preferentially,
you'll get rotation around this
green carbon-carbon double--
carbon-carbon single bond
and that rotation will push the
hydrogen up into the same plane
as the R functionality.
Hydrogen though is small.
It doesn't-- it's not a
subject to this allylic strain.
On the other hand by doing this,
you avoid having any
functionality pointing down here
that could be interacting
with anything that's
on this carbon-carbon
bond right here.
OK. So you avoid A1, 2 strain
and you also avoid
allylic 1, 3 strain.
And again, this is
1, 3 because this is
between carbon 1
and carbon 3, OK?
1, 2, 3. Makes sense?
OK. So, now you're probably
wondering how could this
possibly affect proteins?
>> I just wonder like
you said the A1, 2 is--
tried to avoid, right?
>> Yes.
>> So, why these
are more preferable
in A1, 2 than that one?
>> Yeah. So-- yeah.
So-- actually, sorry.
This is-- these arrows
are incorrect.
OK. Very good.
Send me an e-mail you get points
for finding a mistake
in the [inaudible].
Ah, frustrating.
OK. Let's look at this
a little more closely.
Thank you for asking.
Here are some examples, OK?
So, in this case over here,
here's a functionality.
It has methyl groups.
In this case we have the
smallest functionality next
to that methyl group
avoiding allylic strain.
Over here, if it rotates
up, if we rotate around this
to have two methyl groups
next to the methyl--
next to the starting
methyl, higher in energy
by 3.4 kcals per mole.
And if the two of these are
right up close to each other,
that's like the syn-pentane
interaction
which we know is
highly disfavored, OK?
Over here, similar thing, OK?
So, even when you have a
hydrogen attached to the carbon
or the carbon-carbon
double bond,
you can still invoke
some strain as well.
I don't know why this
is not shutting off.
OK. OK. Makes sense?
Gees, sorry.
My thing is not shutting off.
All right.
All right.
Shoot. This stopped
working entirely.
Gees, [inaudible].
OK. Now, allylic strain,
it turns out dominates
the protein backbone
because there's partial double
bond character for each one
of those amides that is
joining together the amino acids
of the protein backbone.
And so it turns out that
that partial double bond
character is actually very
common like 40 percent
of the time.
Oh, thank you.
Thanks so much.
>> Thank you, sir.
>> Thank you.
>> Thank you.
So, here's a regular
amide and you get rotation
around this carbon-carbon
bond over here.
Totally free rotation.
Thank you.
But, 40 percent of the
time, this amide is going
to form a resonance structure
that gives you this
nitrogen-- carbon double bond.
And so now, you start
getting into allylic strain
between this oxygen up here and
then this hydrogen over here.
So, this conformation
is strongly preferred
but if you rotate around here,
you can't have a functionality
up in the same plane
as this oxygen due
to that allylic strain.
So the backbone of the
protein itself is not
at all wiggly flexible instead
it's going to adapt at each one
of these amide bonds one
and only one preferred
configuration.
This is really important
concept.
This is why we keep seeing
beta sheets and alpha helices.
This is why proteins aren't
folding all over that place
and giving you all
kinds of crazy stuff.
OK. There's only one
conformation that's going
to come out of this and it's too
largely to this allylic strain.
Does this make sense?
This concept?
OK. Thanks, Kritika.
OK. Here's what this looks like.
So, this is a histogram
of angles for a protein.
And these angles are defined
as the angle between nitrogen
and carbon as being
as a phi angle.
And the angle between the
carbonyl and the C alpha carbon,
that's psi angle
and they're graphed.
Here are the phi angles and
here are the psi angles.
And in colors, this is where
we actually find proteins.
OK. So if the spaces
in white over,
we've never found any protein
that's naturally occurring
that would occupy the space.
By the way, this map was made
originally by Ramachandran
and it's called a Ramachandran
Plot and it's used very commonly
to check the correct
structures of proteins.
OK. So, when we look at this,
we find that there's two
major mountains [phonetic]
that dominate in this histogram.
And one, these psi and phi
angles define the secondary
structure as that regular
right-handed alpha helix
that I've been showing you.
Less commonly, you can also
get a left-handed alpha helix
but this one is going
to be the dominant one.
We also find beta sheets, again,
with a certain psi
and phi angles.
And so because these psi and
phi angles are set by this A1,
2 strain or this A1, 3 strain,
there's very little room
for free rotation, OK?
This is why we only see two
types of secondary structure.
All of the stuff was worked
out by the great Linus Pauling,
almost before protein structures
were solved [phonetic]
or just likely before then, you
know, just by true brilliance
and just thinking about how
molecules rotate in space.
Make sense?
Any questions about this?
All right.
Well, let's look at some more
complicated protein structures.
The first kind of conformation
I want to talk to you
about are disulfide
bonds in proteins.
We're going to get
more complicated.
So, disulfide bonds in
proteins form a dihedral form.
These are two sulfurs,
the little shiny gold balls
are two sulfurs that are bonded
to each other to
form a disulfide.
And notice that the dihedral
angle here is nearly 90 degrees.
This form-- this tend to
prefer a 90 degree form.
There are two conformations, a
right hook and a left twist, OK?
So, right hook, left twist.
I don't know why I have them
reversed but that's the idea.
So, two possible conformation,
both with 90 degree dihedral
angles and you could see
that very clearly by looking
down the sulfur-sulfur
bond of the disulfide.
So, these are going to
help to stitch together
and provide spot welds to
hold together proteins.
They're not all that common.
A very large protein might have
one or two of these or maybe
as many as five but it's not
like they're going to be,
you know, every other
amino acid has a disulfide.
These are relatively
rare and they are
because they're covalent.
There are good ways
of covalently locking particular
conformations of proteins.
OK. So, this is a spontaneous
process to form disulfides
that occurs if you leave
out thiols just sitting
on your bench.
They will go to form
disulfides pretty readily
by an oxidation reaction
using air
as the oxidant to
form a disulfide.
OK. In biology, in
cells, there is a source
of thiol called glutathione
where the otherwise slippery
SH functionality is attached
to a larger handle that's
useful for enzymatic binding.
And in practice, disulfide
exchange happens very quickly
and very readily and
this is an important way
of reducing thiols
found in proteins.
OK. So I think I've
now introduced you
to all the elements
of conformational
structure in proteins.
We're now ready to look at
the proteins themselves.
OK. So now you understand all
of the elements that are kind
of the toolbox for building
large protein structure.
Let's put them together.
OK. So, first in
protein structure terms,
there are three levels
and descriptions of
protein structure.
The primary sequence
is simply the sequence
of amino acids typically
in one letter code.
The secondary structure
is the listing
of these alpha helices
and beta sheets.
I'm not sure exactly why
that's not being shown here.
Let me just show on this one.
So, primary structure,
the amino acids.
Secondary structures
are the alpha helices
and the beta sheets.
This oftentimes fold up
into discrete domains
and then these domains fold
up into larger structures
called tertiary structures
which in turn can interact with
other structures non-covalently
or covalently to result
in quaternary structures
and then even larger
biological assemblies, OK?
So, we now understand how to
get the primary structures
by forming amide bonds
either using carbodiimides
or the ribosome.
We now understand why it is
that secondary structure forms.
In our next step is
to understand tertiary
and quaternary structure.
And I think I am going to take
the full two minutes to try
to go as far as possible
and I'll pick
up whatever I don't
cover on Tuesday.
OK. So, individual domains
can fold independently.
That will be our
working definition
of domains of proteins.
These are regions of
proteins that you can clip
out of the larger
protein and they can fold
up without the larger
protein around.
A typical domain is this beta
sandwich structure called an
immunoglobulin domain.
Two beta sheets that are
stacked on top of each other.
This folding is driven
by hydrophobic collapse.
The interior of these beta
sandwiches is hydrophobic
and the exterior is hydrophilic
and that's a concept
we've looked
at in some detail a
couple of times before.
If we look at the most common
protein domains as listed
in the Human Proteome, what
we find is that there are few
that dominate over others.
And so, what I'm going to do is
I'm going to organize the rest
of this lecture according to
the most dominant structures.
OK. So, starting with
al-helical proteins,
Zinc fingers are
easily the most common.
We've seen this before.
We talked about this in the
case of transcription factors.
OK. So, in this case, the
structure is held in place
by the zinc ion and there's a
nice alpha helix on one side.
OK. Let's stop here.
When we come back on
Monday or Tuesday,
we'll be talking some more
about protein structure and then
on to protein function.
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