00:01
within a protein; we change the other properties
of the protein.
00:01
The secondary structure of amino acid describes
regular repeating structures that arise from
interactions between amino acids that are
close to each other but not distant, that
is, amino acids that are typically between
about three and ten amino acids apart.
00:17
There are three common structures that I want to
discuss here. The first of these structures
is shown in blue with coils. These coils are
alpha helices and as I noted, Linus Pauling
discovered these back in the 1940s and won
the Nobel Prize for his discovery. The second
type of secondary structure I want to mention
are those of the beta strands. Beta strands
were also discovered by Linus Pauling, and
for also which he won the Nobel Prize, and
like the alpha helices they form interactions
between amino acids that are close in primary
sequence. The actual structure of beta strands
is not a coil, like it is in the alpha helix,
but instead resembles a pleat, like that found
on drapes.
00:59
The third type of structure that's found in
proteins, that is predictable, that it involves
secondary structure, is what we refer to as
reverse turns. Now reverse turns are important,
because as you see on the image in front of
you, an alpha helix may start, but doesn't
stay going on, and on, and on, in fact there
is usually some sort of connecting turn that
occurs between individual units of beta strands
and alpha helices. These reverse turns are
predictable based on sequence as we shall
see. Now the alpha helix, as I showed earlier,
is depicted in this image here. We can see
that the alpha helix is a coil, and that coil
has a regular repeating nature to it. Further
we can see that there's interactions between
the carboxyl oxygen and the amine hydrogen
as shown on here. These interactions between
the carboxyl oxygen and the amine hydrogen
give rise to hydrogen bonds, and hydrogen
bonds are very, very important for stabilizing
the structure of alpha helices. They are also
very important, as we will see, in stabilizing
the structure of beta strands. Beta strands
as I noted have a structure that resembles
a pleat. Now individual beta strands can form
inside of proteins, but as you can see in
this image, beta strands in one part of the
protein, can interact with beta strands in
another part of the protein, and give rise
to a structure that is commonly referred to
as a beta sheet. Now on the right I've shown
sequences here of individual beta strands
and the interactions between those beta strands
to form beta sheets. There are two different
sets of interactions here, and for our purposes
it doesn't really matter which one is there.
In both cases we see that the forces that
hold together the beta strands in a beta sheet
form are also hydrogen bonds like what we
saw in the alpha helix, but in this case,
the zigzag structure of the backbone of each
of the strands is different from the coil
that we saw in the alpha helix.
03:06
Reverse turns differ from the alpha helices
and beta strands in not having a repeating
structure like we saw, either the coil or
the pleats, instead, beta turns are fairly
short sequences consisting of about four amino
acids as shown on the screen here. Now the
composition of the amino acids
comprising beta turns varies a bit, but one
of the interesting things that we see when
we compare many reverse turns is that frequently
the amino acid proline is involved in those
turns. Proline you may recall from the earlier
discussion is an amino acid that has less
flexibility than the other amino acids do.
03:45
As a result of that lack of flexibility, proline
tends to have restrictions on the angles that
it can project out and allow amino acids to
be attached to. Consequently proline is very
commonly found in reverse turns. Another interesting
amino acid we commonly see in reverse turns
is the amino acid glycine. Now glycine, you
remember, had the R group that contained only
hydrogen and had what I described as the most
flexibility. So in combining the amino acid
with the least flexibility with the one that
has the most flexibility, changes in structure
are possible that would not otherwise be possible.
04:22
One of the things that we can do knowing the
structure of all the amino acids, is again
use a computer to ask the question, what types
of structures do each of these amino acids
have and how do these structures allow an
amino acid to be a part of an alpha helix,
a beta strand or a reverse turn. Now what the
computer will do is take that information
and give predictions or numerical values assigned
to each one, that will indicate the tendency
of each amino acid to be in any of these structures.
So we can say for example, alanine has a value
of 1.41 for being in an alpha helix, a value
of 0.72 for being in a beta strand and a value
of 0.82 for being in a reverse turn. What
does this mean? Well in general, the higher
the value that the computer assigns, the more
likely that amino acid will be found in the
structure shown. These plots and these evaluations
for all 20 of the amino acids are known, and
you can see the some amino acids have a greater
tendency to be in one structure than another.
05:25
Alanine for example, is more likely to be
found in an alpha helix than it is to be found
in a beta strand or a reverse turn. But you'll
notice also that no amino acid has a value
of zero, meaning that there is
no amino acid that isn’t found in some of
the structures, just the frequency is all
that really matters. Now we can use this information
to help us to predict what types of secondary
structure appear in a protein if we know the
sequence of the protein. So for example if
we have a protein that has a section that
has alanine, that has a high value for alpha
helix, adjacent to a glutamic acid that has
a high value for an alpha helix, adjacent
to a leucine, that also has a high value for
an alpha helix, that we might begin to think
that this portion of a protein has an alpha
helical structure. Well, this is shown for
some of the different amino acids here, so
for example, as I noted for alanine and glutamic
acid, you can see they have high values of
being in an alpha helix. By contrast, isoleucine
and valine have high values and will tend
to be found in beta strands. And as I mentioned
earlier, glycine and proline have high values
for being located in reverse turns. Now the
beauty of this analysis is that with fairly
good accuracy, the scientist can predict the
secondary structure of a protein based on
its primary sequence. Now the same is not
true for predicting the tertiary structure
as I will discuss in just a bit.
06:56
Now there are proteins that are interesting
in the sense that they only have primary and
secondary structure. These are proteins that
are known as fibrous proteins, they have very
little tertiary structure which I will describe
in just a minute. Proteins that are fibrous
in nature have important functions in our
body, so for example, our hair is comprised
of a protein known as keratin. The glue that
sticks ourselves together is a protein known
as collagen. If we look at silk for example,
we're talking about a protein that's called
fibroin. Now the interesting thing about these
proteins is as I said, they are fibrous in
nature. The protein I showed you earlier,
showed an alpha helix and then bends and then
it showed beta strands and then bends and
so forth. These fibrous proteins will not
have those bends. They will typically have
a repeating structure of either an alpha helix,
or a beta strand, or some other type of helix,
which is what we find in collagen that is
a repeating over and over and over and over.
Now this can be seen an electron micrograph showing
some of the proteins and their fibrous nature
as you can see on the screen here.