Protein folding by KK Sahu

“Protein Folding”
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

CONTENTS
• Introduction
• Definition
• Levinthal’s Paradox
• Relation between folding & amino acid sequence
• Factors affecting protein folding
• Biophysical aspects
-Hierarchy in protein structure
-Thermodynamic consideration
• Conclusion
• References

INTRODUCTION
.[
Protein folding is the process by which a protein structure
assumes its functional shape or conformation.
 It is the physical process by which a polypeptide folds into its
characteristic and functional three-dimensional structure from
random coil.

Figure: Different level of Protein structure

LEVINTHAL’S PARADOX
• A newly synthesized polypeptide chain can theoretically assume high number of
conformation.
• Let’s assume 10100 different conformation for a polypeptide and if each
conformation were sampled in every ~10-13 seconds, it would take about 1077
years to sample all possible conformation.
• But experimentally it takes a few seconds or up to a minute for completion of
process.
• Thus protein folding can not be a completely random & error process. There must
be short cuts.
• This was first pointed out by CYRUS LEVINTHAL in 1968, which is also called
as Levinthal’s Paradox.

RELATION BETWEEN FOLDING & AMINO
ACID SEQUENCE
• Each protein exist as an unfolded polypeptide or random coil when translated
from a sequence of mRNA to linear chain of amino acid.
• This polypeptide lacks any three dimensional structure.
• However amino acids interact with each other to produce a well defined 3-
dimensional structure.
• The resulting 3-dimensional structure is determined by the amino acid sequence.
• It defines its native conformation.
• Folded proteins usually have a hydrophobic core in which side chain packing
stabilizes the folded state & charged or polar side chains occupy the solvent
exposed surface where they interact with surrounding H2O.

• Formation of intra molecular H-bond provides another important contribution to
protein stability.
• The process of folding in vivo often being co- translationally, so that the N-terminal
of the protein begins to fold while the C-terminal portion of the protein is still being
synthesized by the ribosome.
• Protein folding may involve covalent bonding in the form of Disulfide bond, formed
between Cystines residues.
Figure: Disulfide bond

FACTORS AFFECTING PROTEIN
FOLDING
• The passage of the folded state is mainly guided by hydrophobic
interaction, formation of intra molecular H-bonds of Van der Waal
forces & it is opposed by conformational entropy.
• The chemical interactions that counteract these effect & stabilizes
the native conformation include weak interaction & disulfide bonds.
• The non covalent interactions
-Hydrogen bond
-Hydrophobic interaction
-Van der Waal interaction

• When folding is initiated, much of the secondary structure present in
native protein, as small single domain proteins form within a few
seconds.
• About 200 to 460 kJ/mole required to break a single covalent bond,
whereas weak interaction can be disrupted by 4 to 30 kJ/mole.
• Hydrophobic interactions are clearly important in stabilizing a protein
conformation.
• The interior of a protein is generally a densely packed core of
hydrophobic amino acid side chains.
• Presence of polar or charged group in the protein interior have suitable
partners for H-bonding or ionic interactions.

Figure: H- bond
•The interior of a protein is
generally a densely packed core
of hydrophobic amino acid side
chains.
•They have a suitable partner for
H-bonding or Ionic interaction
due to which they form a cluster.
•This interaction are clearly
important in stabilizing protein
structure.

• Van der Waal interaction are
second order bond, often
found between apolar
molecules & hydrophobic
side chains of proteins.
• This interaction plays
important role in Packing
density of Protein.
Figure: High packing density of
Protein due to Van der waal
interaction

•One model views folding as a hierarchical process where local
secondary structures form first.
•Under this model, helices and sheets form first, with longer range
interactions between helices and sheets forming super-secondary
structures later.
• This process continues until the entire polypeptide folds. An
alternative model describes folding as a spontaneous collapse of the
polypeptide into a compact state. This collapsed state is known as a
molten globule.
MECHANISM OF PROTEIN FOLDING

•There are two models of protein folding that are currently being
confirmed:-
•The first: The diffusion collision model, in which a nucleus is
formed, then the secondary structure is formed, and finally these
secondary structures are collided together and pack tightly
together.
•The second: The nucleation-condensation model, in which the
secondary and tertiary structures of the protein are made at the
same time. Recent studies have shown that some proteins show
characteristics of both of these folding models.

BIOPHYSICAL ASPECTS
• Biophysical aspects gives a deep insight into the principles &
concepts of kinetic & structural resolutions of fast chemical &
biophysical reactions of protein folding.
• The study of fast protein folding reactions and understanding of
the folding paradox have significantly advance due to the recent
development of new biophysical methods which allow not only
kinetic resolution in the sub millisecond time scale but also
structural resolutions.

(A) HIERARCHY IN PROTEIN
STRUCTURE
• Local secondary structure form first, certain a sequences fold readily into α
helices and β sheets.
• This is followed by longer range interaction between, α helices that come
together to form stable super secondary structure.
• The process continues until complete domains form and the entire polypeptide
is folded.
Figure: Hierarchy in structure
• Folding is a hierarchal process in which it folds from its primary structure through
a series and attains its final folding.

Figure: primary structure of protein
(a) PRIMARY STRUCTURE

(b) SECONDARY STRUCTURE
• The term secondary structure refers to the local conformation of
some part of the polypeptide.
• It is the regular folding pattern of the polypeptide.
• Types are α-helix & β-conformation.

Figure:- . A β sheet is a common structure
formed by parts of the polypeptide chainsFigure : - Structure of
the a Helix.

(c) SUPER SECONDARY STRUCTURE
• Super secondary structure are also called motifs & are particularly
stable arrangements of several elements of secondary structure & the
connection between them.
• DOMAINS: polypeptide with more than a few hundred amino acid
residues often folds into 2 or more stable globular units.
Figure: Super secondary structure

(d) TERTIARY STRUCTURE
• The over all 3-Dimensional arrangements of all proteins is referred to
as protein’s tertiary structure.
• In this the folding of its 2 structural elements taken place together with
the spatial deposition of its side chains.
• The tertiary structure thus involves the folding of helix of globular
protein.
• Eg. Myoglobin.
Figure: Myoglobin

(e) QUATERNARY STRUCTURE
• It is the next level up from tertiary structure & is the particular
spatial arrangement interaction between 2 or more polypeptide
chains.
• Eg. Hemoglobin.
Figure: Hemoglobin

(B) THERMODYNAMIC CONSIDERATION
• Any system has maximum
stability if it is in lowest
possible energy state, this
principle applies to protein also.
• The mechanism & kinetics of
the folding process & the
thermodynamic stability of the
native protein depend on
polypeptide –water interactions.
• Native proteins are marginally
stable. Figure: Free energy funnel

CONCLUSION
Protein folding is a physical process by which a polypeptide folds
into its characteristic 3-Dimensional structure.
The correct 3-Dimensional structure is essential for proper function &
the biochemical property of this folded protein responsible for proper
function.
The improper folding may cause disease.

REFERENCES
BOOK AUTHOR
Principle of Biochemistry David L. Nelson
Michael M. Cox
Biochemistry J. L. Jain
Biochemistry Dr. U. Satyanarayan
Fundamental of
Biochemistry
Lubert Stryer
Websites
•www.pymol.org
•www.wikipedia.com
•www.kbiotech.com

Protein folding by KK Sahu

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