The document discusses protein folding, a process by which linear polypeptides achieve their functional three-dimensional structures from random coils. It addresses the Levinthal paradox, the hierarchical structure of proteins (primary, secondary, tertiary, quaternary), and the roles of chaperones and enzymes in facilitating proper folding. Additionally, it emphasizes the importance of correct folding for protein functionality and the potential consequences of misfolding.

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

2.  Introduction-
 Levinthal paradox
 Biophysical aspects of protein folding
 Hierarchy in protein structure
 Thermodynamic stability
 Cellular aspects of protein folding
 Self assembly (folding) of protein
 Molecular assistance – Chaperons
 Enzymes involved in protein folding
 Conclusions
 References
Synopsis

3.  Proteins are composed of a linear (not branched and not forming rings) polymer of amino acid.
 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.
Introduction

4. • 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.
Levinthal paradox

5.  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
 Protein folding may involve covalent bonding in the form of Disulfide bond, formed between Cystines
residues.
 Shortly before setting into more energetically favorable native conformation, molecules may pass through
on intermediate ‘ Molten Globule’ state.
Relationship between folding and amino acid
sequence

6.  Protein folding is a hierarchal process in which it folds from its primary
structure through a series and attains its final folding .These structures are :-
Biophysical aspects of protein folding

7. Primary structure
• The primary structure of protein refers to the number & sequence of amino acid.
• Linus Pauling & Robert Corey in 1930 demonstrated that the α- carbon atom of adjacent
amino acid are separated by three covalent bonds.
• The 4 atoms of peptide group lies trans to each other.

8. Secondary structure
 The secondary structure focuses on regular folding patterns of the polypeptide backbone.
 The most prominate are α helix and β –conformation.
 α- Helix
 The simplest arrangement of the polypeptide chain with right planer peptide bonds.
 In this the chain is tightly wound around an imaginary axis drawn longitudinally through middle of
helix.
 The R-group of amino acid residues protrude outward from helical backbone.

9.  b sheet-
 In the β conformation , the backbone of the polypeptide chains can be arranged into a zig-zag rather
than a α helix.
 The zig–zag polypeptide chains can be arranged side by side to form a structure resembling a series of
pleats .
 The β – sheet formation depends on intermolecular hydrogen bonding, although intermolecular H-
bonding is also present.
 There are two types of β- pleated sheet structures:-
 Antiparallel β-sheet.
 Parallel β- sheet
Figure:- . A β sheet is a common structure formed by parts of the polypeptide chains

10. Super secondary structure
 Super secondary structures, also called motifs or simply folds simply folds are particularly
stable arrangements of several elements of secondary structures and the connections
between them .
 Domains – polypeptides with more than a few hundred amino acid residues often folds
into two or more stable globular units called domains.
Figure:- Protein Domains. The cell-surface protein
CD4 consists of four similar domains.

11. Tertiary structure
 The tertiary structure of a protein is its three dimensional arrangement ; that is , the folding of
its 2 structural elements , together with the spatial dispositions of its side chains .
 The tertiary structure thus involves the folding of helices of globular proteins.
 Eg. Myoglobin
 Myoglobin is a single polypeptide chain of 153 amino-acid residues with one molecule of
heme.

12. Quaternary structure
 Multimeric proteins have quaternary structure in which different polypeptide
chains get associated and forms a quaternary structure .
 Eg . of multimeric protein is HEMOGLOBIN.
Figure: Hemoglobin

13. Thermodynamic consideration
 Any system has maximum stability if it is in the lowest possible energy state ,
this principles applies to proteins also .
 Thermodynamically, the folding process can be viewed as a kind of free energy
funnel
FIGURE: - The thermodynamics of protein
folding depicted as a Free-energy funnel.

14. (a) Self folding- e.g. Ribonuclease
(b) Molecular assistance-
Chaperons
Chaperonins
Cellular aspects of protein folding

15. By Chaperons
 Molecular chaperones are essential proteins that bind to unfolded and partially folded
polypeptide chains to prevent the improper association of exposed hydrophobic
segments that might lead to nonnative folding as well as polypeptide aggregation and
precipitation.
 1. Hsp 70 system-
 Identification of unfolded target protein
 Cycle of working of chaperons
Fig – Identification of unfolded target protein and Chaperones control protein folding interaction

16. Cycle of working of chaperons
Fig :- Cycle of binding and release of Hsp 40 – Hsp 70 .

17. By Chaperonins :- (Hsp60 / GroEL in E. Coli.)
 Chaperonin are the large structures
with hollow cavities often used for
handling the folding or degradation
of proteins
 The Hsp60 class of chaperones
forms a large apparatus that consist
of two types of subunit.
Fig :- Structure of Gro EL forming an oligomer of two ring
, each comprising a hollow cylinder made of 7 subunit.

18. Enzymes Involved In protein folding
 Protein disulfide isomerare ( PDI ) .
 Peptidyl prolylisomerase .
Fig :- Role of PDI in protein folding

19. Peptidyl prolyl isomerare
 This enzyme catalysis the isomerization of peptide bond .
 That involve protein reduce peptide bond between amino acid are almost always
in turns from .
Fig :- Isomers of protein

20.  Protein folding is the physical process by which a polypeptide folds into its
characteristics three dimensional structure.
 Failure to fold into native structure generally produces inactive proteins, but in
some instances misfolded proteins have modified or toxic functionality.
Conclusions-

21.  Books-
 Fundamental of biochemistry – Voet Voet Pratt – 4th edition
 Principle of biochemistry – David Nelson Michel M.Cox
 Websites-
 www.wekipidia.com
 www.KBiotech.com
 www.nature.com
References-