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Protein Folding
PROTEIN FOLDING
• Process in which a polypeptide chain goes from a
linear chain of amino acids with vast number of more or
less random conformations in solution to the native,
folded tertiary (and for multichain proteins, quaternary)
structure
Protein Folding
• Protein folding considers the question of how
the process of protein folding occurs, i. e.
unfolded  native state.
• This very challenging problem has been
described as the second half of the genetic
code, and as the three-dimensional code, as
opposed to the one-dimensional code involved
in nucleotide/amino acid sequence.
• Importance:
– Predict 3D structure from primary sequence
– Avoid misfolding related to human diseases
– Design proteins with novel functions
Why do proteins fold?
In order to carry out
their function (for
instance as enzymes or
antibodies), proteins
must take on a particular
shape, also known as a
"fold." Thus, proteins are
truly amazing machines:
before they do their
work, they assemble
themselves! This selfassembly is called
"folding."
Forms determines function
Suppose you have some molten iron. You may
turn it into nails, hammers, wrenches, etc. What
makes these tools different from each other is
their form (i.e. their shape and structure).
PRIMARY STRUCTURE DETERMINES TERTIARY (AND
QUATERNARY) STRUCTURES.
– demonstrated by the fact that many proteins can refold from a
more or less "random coil" set of conformations without
"instructions" from any other cellular components
– All the information for 3-dimensional structure is provided by
the amino acid sequence.
Proteins fold on a defined pathway (or a small number of
alternative pathways); they don't randomly search all possible
conformations until they arrive at the most stable (lowest free
energy) structure.
Anfinsen Experiment
•Denaturation of
ribonuclease A (4 disulfide
bonds), with 8 M Urea
containing bmercaptoethanol, leads to
random coil and no activity
Anfinsen Experiment
• After renaturation, the refolded protein has native
activity, despite 105 ways to renature the protein.
• Conclusion: All the information necessary for
folding into its native structure is contained in the
amino acid sequence of the protein.
How do proteins fold?
Proteins have primary structures, which is their sequence
of amino acids, and secondary structures, which is the
three dimensional shape that one or more stretches of
amino acids take. The most common shapes are the alpha
helix and the beta conformation.
Proteins fold, amazingly quickly: some as fast as a
millionth of a second (microsecond)
The normal protein is called PrPC (for cellular). Its
secondary structure is dominated by alpha helices.
Interactions between the side chains of amino acids
determine how a long polypeptide chain folds into the
intricate three-dimensional shape of the functional
protein. Protein folding, which occurs within the cell
in seconds to minutes, employs a shortcut through the
maze of all folding possibilities. As a peptide folds, its
amino acid side chains are attracted and repulsed
according to their chemical proper-ties. For example,
positively and negatively charged side chains attract
each other. Conversely, similarly charged side chains
repel each other. In addition, interactions involving
hydrogen bonds, hydrophobic interactions, and
disulfide bonds all exert an influence on the folding
process. This process of trial and error tests many, but
not all, possible configurations, seeking a compromise
in which attractions outweigh repulsions. This results
in a correctly folded protein with a low-energy state
CHAPERONES
It is generally accepted that the information needed for
correct protein folding is contained in the primary
structure of the polypeptide. Given that premise, it is
difficult to explain why most proteins when denatured do
not resume their native conformations under favorable
environmental conditions. One answer to this problem is
that a protein begins to fold in stages during its synthesis,
rather than waiting for synthesis of the entire chain to be
totally completed. This limits competing folding
configurations made available by longer stretches of
nascent peptide. In addition, a specialized group of
proteins, named “chaperones,” are required for the proper
folding of many species of proteins.
HSPs in protein folding
The chaperones—also known as “heat shock” proteins—interact with
the polypeptide at various stages during the folding process. Some
chaperones are important in keeping the protein unfolded until its
synthesis is finished, or act as catalysts by increasing the rates of the
final stages in the folding process. Others protect proteins as they
fold so that their vulnerable, exposed regions do not become tangled
in unproductive interactions
•The diagram shows the role of heat-
shock proteins and a chaperonin in
protein folding. As the ribosome moves
along the molecule of messenger RNA,
a chain of amino acids is built up to form
a new protein molecule. The chain is
protected against unwanted interactions
with other cytoplasmic molecules by
heat-shock proteins and a chaperonin
molecule until it has successfully
completed its folding.