Protein folding protein structure by anant mohan sharma

1. Protein Folding
Anant mohan sharma
M.Sc. 2nd sem

2. Introduction
Translation completes the flow of genetic information within the cell. The
sequence of nucleotides in DNA has now been converted to the sequence of
amino acids in a polypeptide chain. The synthesis of a polypeptide, however, it is
not equivalent to the production of a functional protein. To be useful,
polypeptides must fold into distinct three-dimensional conformations, and in
many cases multiple polypeptide chains must assemble into a functional
complex. In addition, many proteins undergo further modifications, including
cleavage and the covalent attachment of carbohydrates and lipids, that are
critical for the function and correct localization of proteins within the cell.
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3. Protein folding
Let’s start with the protein structure
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4. “
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Proteins have several layers of structure each of which is important in the
process of protein folding.
The first most basic level of this structure is the sequence of amino acids
themselves.(primary structure)
The next layer in protein structure is the secondary structure. Secondary
structure includes α-Helixes and β-sheets.
The tertiary structure is the next layer in protein structure. This takes the
α-Helixes and β-sheets and allows them to fold into a three dimensional
structure.
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5. Protein folding
● Proteins are folded and held together by several
forms of molecular interactions. The molecular
interactions include the thermodynamic stability
of the complex, the hydrophobic interactions and
the disulfide bonds formed in the proteins.
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6. Protein folding depends upon
The process depends upon;
 The solvent (water or lipid bilayer)
 The concentration of salt
 The PH
 The temperature
 The possible presence of cofactor
 Molecular chaperones
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7. Stages of protein folding
Primary structure
The primary structure of a protein its linear
amino-acid sequence, determines its native
conformation. The specific amino acid residues
and their position in the polypeptide chain are the
determining factors for which portions of the
protein fold closely together and form its three-
dimensional conformation. The amino acid
composition is not as important as the sequence.
Amino acid are linked together by peptide bond
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8. Secondary structure
● Formation of a secondary structure
is the first step in the folding process
that a protein takes to assume its
native structure.
● Characteristic of secondary
structure are the structures known
as alpha helices and beta sheets that
fold rapidly because they are
stabilized by intramolecular
hydrogen bonds, as was first
characterized by Linus Pauling.
● Formation of intramolecular
hydrogen bonds provides another
important contribution to protein
stability.
● Protein secondary structure takes
on the three forms
● Alpha helix
● beta sheet
● Turn , coil or loop
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9. ● The α helix, a common
structural motif of
proteins, consists of a
right-handed helix with a
repeat length of 3.6
amino acid residues per
helical turn.
● Beta sheets consist
of beta strands (β-
strands) connected
laterally by at least two
or three backbone
hydrogen bonds, forming
a generally twisted,
pleated sheet.
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10. Tertiary structure
● The alpha helices and beta pleated sheets can be
amphipathic in nature, or contain a hydrophilic portion and a
hydrophobic portion. This property of secondary structures
aids in the tertiary structure of a protein in which the folding
occurs so that the hydrophilic sides are facing the aqueous
environment surrounding the protein and the hydrophobic
sides are facing the hydrophobic core of the protein.
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11. Quaternary structure
● Tertiary structure may give way to the formation
of quaternary structure in some proteins, which
usually involves the "assembly" or "co assembly"
of subunits that have already folded; in other
words, multiple polypeptide chains could interact
to form a fully functional quaternary protein.
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12. Driving force of
protein folding
Folding is a spontaneous process that is
mainly guided by hydrophobic interactions,
formation of intramolecular hydrogen bonds,
van der Waals forces, and it is opposed by
conformational entropy. The process of
folding often begins co-translationally, so
that the N-terminus of the protein begins to
fold while the C-terminal portion of the
protein is still being synthesized by the
ribosome; however, a protein molecule may
fold spontaneously during or after
biosynthesis.
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13. Anfinsen's Experiment of Protein
Folding
● Anfinsen’s experiment describe protein folding by two process:
● Denaturation and Refolding
● He uses following compound for preform experiment
● Ribonuclease A (124 amino acid residue)
● Urea, guanidine HCl - denaturants
● β-mercaptoethanol - breaks disulfide bonds
● He perform 3 experiment as follow;
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Conclusion:
All the information necessary for
folding into its native structure is
contained in amino acid sequence of
protein which is thermodynamically
most stable

15. Molecular Chaperones
● molecular chaperones are proteins that assist the covalent folding or unfolding and
the assembly or disassembly of other macromolecular structures.
● Chaperones may assist in folding even when the nascent polypeptide is being
synthesized by the ribosome.
● Molecular chaperones operate by binding to stabilize an otherwise unstable structure
of a protein in its folding pathway,
● They assist the de novo folding of proteins or they form repair machines for
misfolded or even aggregated proteins, and they are therefore especially important
for the survival of cells during stress situations.
● A well studied example is the bacterial GroEL system, assists in the folding of globular
proteins.
● In eukaryotic organisms chaperones are known as heat shock proteins
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16. ● These are basically proteins that are involved in the folding and unfolding of other
proteins.
● Various approaches have been applied to study the structure, dynamics and
functioning of chaperones.
● Chaperone-assisted folding is required in the crowded intracellular environment to
prevent aggregation and Used to prevent misfolding and aggregation which may
occur as a consequence of exposure to heat or other changes in the cellular
environment .
● There are two major families known as Hsp60 and Hsp70
● Hsp70 family members (Hsp70. Hsc70, Hsp40 and GrpE) act at early stages before
protein leaves the ribosome they prevent premature folding.
● The Hsp60 family (chaperomins) forms barrel shaped structure that act later in
protein life after it has been fully synthesized
● Chaperonins binds unfolded, partly folded and incorrectly folded protein molecule
but mot protein in their native state
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Reference
Slide share/SABAHAT ALI
The cell – ncbi bookshelf
Life sciences