Protein Folding

Protein Folding
General Structure of an amino acid

Primary Structure of Protein
Formation of a peptide bond by condensation

The pentapeptide serylglycyltyrosylalanylleucine or
Ser–Gly–Tyr–Ala–Leu.
Primary Structure of Protein
• The oxygen has a partial negative charge and the nitrogen a partial
positive charge, setting up a small electric dipole.
• The six atoms of the peptide group lie in a single plane, with the
oxygen atom of the carbonyl group and the hydrogen atom of the
amide nitrogen trans to each other.
The Function of a Protein Depends on Its
Amino Acid Sequence
• The bacterium Escherichia coli produces more than 3,000 different proteins.
• A human produces 25,000 to 35,000. In both cases, each type of protein has a
unique three-dimensional structure and this structure confers a unique function.
• First, as we have already noted, proteins with different functions always have
different amino acid sequences.
• Second, thousands of human genetic diseases have been traced to the
production of defective proteins. Perhaps one-third of these proteins are
defective because of a single change in their amino acid sequence; hence, if the
primary structure is altered, the function of the protein may also be changed.
• Finally, on comparing functionally similar proteins from different species, we find
that these proteins often have similar amino acid sequences.
Is the amino acid sequence absolutely fixed,
or invariant, for a particular protein?
• Answer: No
• Some flexibility is possible.
An estimated 20% to 30% of the proteins in humans are polymorphic,
having amino acid sequence variants in the human population. Many of these
variations in sequence have little or no effect on the function of the protein.
Amino acid sequence of same protein in different organisms

Structure of Protein
• The primary structure consists of a sequence of amino acids linked

together by peptide bonds and includes any disulfide bonds.
• The resulting polypeptide can be coiled into units of secondary
structure, such as an helix.
• The helix is a part of the tertiary structure of the folded
polypeptide, which is itself one of the subunits that make up the
quaternary structure of the multisubunit protein, eg: hemoglobin.
Three-dimensional structures of some small proteins.
Polypeptides Fold Rapidly by a Stepwise
Process
• Proteins are assembled from amino acids at a very high rate
How does such a polypeptide chain arrive at its
native conformation?
An Example: E. coli cells can make a complete, biologically active protein molecule
containing 100 amino acid residues in about 5 seconds at 37˚ C.
Assume conservatively that each of the amino acid residues could take up 10 different
conformations on average, giving 10100 different conformations for the polypeptide.
Let’s also assume that the protein folds itself spontaneously by a random process in
which it tries out all possible conformations around every single bond in its backbone
until it finds its native, biologically active form.
If each conformation were sampled in the shortest possible time (~10 13 second, or the
time required for a single molecular vibration), it would take about 1077 years to sample
all possible conformations.
• Thus protein folding cannot be a completely random, trial-and-error
process.
• This problem was first pointed out by Cyrus Levinthal in 1968 and is
sometimes called Levinthal’s paradox.
The folding pathway of a large polypeptide chain is
unquestionably complicated
#Model 1:
• The folding process is envisioned as hierarchical.
Local secondary structures form first.
• Certain amino acid sequences fold readily into
helices or sheets, guided by constraints we have
reviewed in our discussion of secondary structure.
• This is followed by longer-range interactions between
two helices that come together to form stable
supersecondary structures.
• The process continues until complete domains form
and the entire polypeptide is folded.
A simulated folding pathway.
#Model 2:
• Folding is initiated by a spontaneous collapse of the polypeptide into a
compact state, mediated by hydrophobic interactions among nonpolar
residues.
• The state resulting from this “hydrophobic collapse” may have a high
content of secondary structure, but many amino acid side chains are not
entirely fixed.
• The collapsed state is often referred to as a molten globule. Most proteins
probably fold by a process that incorporates features of both models.
• Instead of following a single pathway, a population of peptide molecules
may take a variety of routes to the same end point, with the number of
different partly folded conformational species decreasing as folding nears
completion.
Thermodynamically, the folding process can be
viewed as a kind of free-energy funnel.
The unfolded states are characterized by a high
degree of conformational entropy and relatively high
free energy.
As folding proceeds, the narrowing of the funnel
represents a decrease in the number of
conformational species present.
Small depressions along the sides of the free-energy
funnel represent semistable intermediates that can
briefly slow the folding process.
 At the bottom of the funnel, an ensemble of folding
intermediates has been reduced to a single native
conformation (or one of a small set of native
conformations).
The thermodynamics of protein folding
depicted as a free-energy funnel.
Protein Denaturation
• A loss of three-dimensional structure sufficient to cause loss of function is
called denaturation.
• Most proteins can be denatured by heat, which affects the weak
interactions in a protein (primarily hydrogen bonds) in a complex manner.
• Proteins can be denatured not only by heat but by extremes of pH, by
certain miscible organic solvents such as alcohol or acetone, by certain
solutes such as urea and guanidine hydrochloride, or by detergents.
• Each of these denaturing agents represents a relatively mild treatment in
the sense that no covalent bonds in the polypeptide chain are broken.
Amino Acid Sequence Determines Tertiary
Structure
• Certain globular proteins denatured by heat,
extremes of pH, or denaturing reagents will regain
their native structure and their biological activity if
returned to conditions in which the native
conformation is stable. This process is called
renaturation.
Renaturation of unfolded, denatured ribonuclease.

Protein Folding

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Protein Folding

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Protein Folding

General Structure of an amino acid

Formation of a peptide bond by condensation

Amino acid sequence of same protein in different organisms

• The primary structure consists of a sequence of amino acids linked

Renaturation of unfolded, denatured ribonuclease.

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