Conformational stability Protein folding and denaturation Video Lecture

Let's talk about
conformational stability
and how this relates
to protein-folding
and denaturation.
So first, let's review
a couple of terms
just to make sure we're
all on the same page.
And first, let's start out
with the term conformation.
And the term
confirmation just refers
to a protein's
folded, 3D structure,
or in other words, the
active form of a protein.
And next we can review what
the term denatured means
when you're talking
about proteins.
And denatured
proteins just refer
to proteins that have become
unfolded, or inactive.
So all conformational stability
is really talking about
are the various forces
that help to keep
a protein folded
in the right way.
And these various forces are
the four different levels
of protein structure,
and we can review those
briefly right here.
So recall that the primary
structure of a protein
just refers to the actual
sequence of amino acids
in that protein, and
this is determined
by a protein's peptide bonds.
And then next, you have
secondary structure,
which just refers to the local
substructures in a protein.
And they are determined
by backbone interactions
held together by hydrogen bonds.
Then you have
tertiary structure,
which just talks
about the overall 3D
structure of a single
protein molecule.
And this is described by distant
interactions between groups
within a single protein.
And these interactions
are stabilized
by van der Waals interactions,
hydrophobic packing,
and disulfide bonding, in
addition to the same hydrogen
bonding that helps to
determine secondary structure.
And then quaternary
structure just
describes the
different interactions
between individual
protein subunits.
So you have the
folded-up proteins
that then come together
to assemble the completed,
overall protein.
And the interaction of these
different protein subunits
are stabilized by the
same kinds of bonds
that help to determine
tertiary structure.
So all of these levels
of protein structure
help to stabilize the
folded-up, active confirmation
of a protein.
So why is it so
important to know
about the different levels
of protein structure
and how they contribute to
conformational stability?
Well, like I said, a
protein is only functional
when they are in their
proper conformation,
in their proper 3D form.
And an improperly folded
or degraded, denatured,
protein is inactive.
So in addition to the four
levels of protein structure
that I just reviewed,
there is also
another force that
helps to stabilize
a protein's conformation.
And that force is called
the solvation shell.
Now, the solvation shell
is just a fancy way
of describing the
layer of solvent that
is surrounding a protein.
So say I have a protein
who has all these exterior
residues that are overall
positively charged.
And picture this protein
in the watery environment
of the interior of
one of our cells,
then the solvation shell is
going to be the layer of water
right next to this
protein molecule.
And remember that water
is a polar molecule,
so you have the
electronegative oxygen atom
with a predominantly
negative charge leaving
a positive charge over
next to the hydrogen atoms.
The same is true for each
of these water molecules.
So now, as you can see, the
electronegative oxygen atoms
are stabilizing all the
positively charged amino acid
residues on the exterior
of this protein.
So as you can see, the
conformational stability
of a protein depends
not only on all
of these interactions
that contribute
to primary, secondary, tertiary,
and quaternary structure,
but also what sort of
environment that protein is in.
And all of these
interactions are
very crucial for keeping
a protein folded properly,
so that it can do its job.
Now, what happens
when things go wrong?
How does a protein become
unfolded and thus inactive?
Well, remember that this
is called denaturation.
And this can be done by changing
a lot of different parameters
within a protein's
environment, including
changing the
temperature, the pH,
adding chemical denaturants,
or even adding enzymes.
So let's start with what
happens if you alter
the temperature
around a protein.
And we can use the
example of an egg
when we put it into a
pot of boiling water,
because an egg, especially the
white part, is full of protein,
and this pot of boiling
water is representing heat.
And remember that heat is
really just a form of energy.
So when you heat an
egg, the proteins
gain energy and
literally shake apart
the bonds between the parts
of the amino acid chains.
And this causes the
proteins to unfold.
So increased
temperature destroys
the secondary, tertiary,
and quaternary structure
of a protein, but the primary
structure is still preserved.
So the take-away
point is that when
you change the temperature of
a protein by heating it up,
you destroy all of the different
levels of protein structure
except for the
primary structure.
So now, let's say you
were to take an egg
and then add vinegar, which
is really just an acid.
The acid in the vinegar will
break all the ionic bonds
that contribute to tertiary
and quaternary structure.
So the take-away point when
you change the pH surrounding
a protein is that you have
disruption of ionic bonds.
And if we think about this
a little bit more deeply,
it kind of makes sense,
because ionic bonds
are dependent upon
the interaction
of positive and
negative charges.
So when you add either
an acid or a base, which
in the case of an acid
is just like adding
a bunch of positive
charges, you kind of
disrupt the balance between
all these interactions
between the positive
and negative charges
within the protein.
So now let's look at how
chemicals denature proteins.
Chemical denaturants often
disrupt the hydrogen bonding
within a protein.
And remember that
hydrogen bonds contribute
to secondary, tertiary, all the
way up to quaternary structure.
So all these levels
of protein structure
will be disrupted if you
add a chemical denaturant.
So let's take our same example
of a protein with an egg,
and say, if you were
21 years or older,
you got your hands
on some alcohol,
and you added this to the egg.
Then, all the hydrogen
bonds would be broken up,
leaving you with just
linear polypeptide chains.
And then finally, let's
take our hard-boiled egg
from the temperature
example, and let's eat it.
So here's my beautiful
drawing of a person,
representing you, eating
this hard boiled egg.
Once the egg enters
our digestive tract
we have enzymes that break down
the already denatured proteins
in the egg even further.
They take the linear polypeptide
chain, whose primary structure
is still intact.
And they break the bonds between
the individual amino acids,
the peptide bonds, so that we
can absorb these amino acids
from our intestines
into our bloodstream.
And then we can use
them as building blocks
for our own protein synthesis.
And that's how enzymes can alter
a protein's primary structure
and thus the protein's overall
conformational stability.
So what did we learn?
Well, we learned that the
conformational stability
refers to all the forces
that keep a protein properly
folded in its active form.
And this includes all
the different levels
of protein structure, as
well as the salvation shell.
And we also learned
that a protein
can be denatured into
its inactive form
by changing a variety of
factors in its environment,
including changing the
temperature, the pH,
adding chemicals, or enzymes.