The document discusses protein folding, emphasizing how amino acid sequences dictate a protein's native structure through physical forces and the challenges associated with predicting protein structure and folding mechanisms. It also details Anfinsen's experiments, which demonstrated that proteins can refold to their native state provided the correct conditions, and explains various folding models and the role of molecular chaperones in assisting protein folding. Additionally, it mentions the Levinthal paradox, which illustrates the complexity of protein conformations, and highlights the importance of hydrophobic interactions in the folding process.

1. IN THE NAME OF
ALLAH
THE MOST
BENIFICIENT
THE MOST MERCIFUL

2. PROTEIN
FOLDING
2

3. 3
Protein are amino acids chains that
acquire their biological properties by
folding in to unique 3 D structure i. e.
unfolded to native state.
Some physical forces help the protein
folding such as hydrophobic effect,
electrostatic interaction etc.
DEFINITION

4. 4
Three major problem of protein folding
 Protein code
 Structure prediction
 Folding speed and Mechanism
Folding problem

5. 5
ANFINSEN
EXPERIMENT
Denaturation of
ribonuclease A (4
disulfide bonds), with
8 M Urea containing
b-mercaptoethanol,
leads to random coil
and no activity

6. 6
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.

7. 7
 Remove b-mercaptoethanol only,
oxidation of the sulfhydryl group,
then remove urea → scrambled
protein, no activity
 Further addition of trace
amounts of b-mercaptoethanol
converts the scrambled form into
native form.
 Conclusion: The native form of
a protein has the thermodynamic-
ally most stable structure
Anfinsen Experiment

8. 8
 Under optimal experimental conditions, proteins
often fold more slowly in vitro than they fold in
vivo.
 Reason is that folding proteins often form disulfide
bonds not present in the native proteins, which
then slowly form native disulfide bonds through
the process of disulfide interchange.
 Protein disulfide Isomerase (PDI) catalyzes this
process.
 Indeed, the observation that RNase A folds so
much faster in vivo than in vitro led “Anfinsen” to
discover this enzyme.
Anfinsen discover Protein
Disulphide Isomerase (PDI)

9. 9
The Levinthal paradox
The Levinthal Paradox states that the number of possible
conformation available to a protein is astronomically large
Imagine a 100-residue protein so it has 99 peptide bonds so 198
phi and psi angles if each of these bond angles can be one of
3 stable conformation so maximum 3198 occure different
conformations so require a long time than the age of universe
to arise at its correct native conformation .
Conclusion : folding not a random but
have specific path way

10. 10

11. 11
Protein folding
models
Framework model
This suggest that folding is start with formation of
secondary structure which then interact to form a
more advanced folding intermediate.
Cont.

12. Framework
model
Supported by experimental observation of rapid
formation of secondary structure during protein
folding process

13. Framework
model
Formation of individual secondary structure
elements

14. Molten globule
state
The molten globule state is an intermediate
conformational state between the native and fully
unfold states of globular protein.
Some character of molten state:
The presence of native like content of secondary structure
The absence of specific tertiary structure produced by the
tight packing of amino acid side chain
 Model for early stages of protein folding (hydrophobic
collapse

15. COLLAPSE
MODEL OF
PROTEIN
FOLDING
 Experimental observations indicate that protein folding
begins with the formation of local segments of secondary
structure (α helices and ß sheets)
 Since native proteins contain compact hydrophobic cores,
it is likely that the driving force in protein folding is what
has been termed a hydrophobic collapse.
 The collapsed state is known as a molten globule, a
species that has much of the secondary structure of the
native protein but little of its tertiary structure.

16. 16
 During this intermediate stage, the native like elements
are thought to take the form of sub domains that are not
yet properly docked to form domains.
 In the final stage of folding, the protein undergoes a
series of complex motions in which it attains its relatively
rigid internal side chain packing and hydrogen bonding
while it expels the remaining water molecules from its
hydrophobic core.
Collapse model of protein
folding

17. 17
A folding protein must proceed from a
high-energy, high-entropy state to a
low-energy, low-entropy state.
An unfolded polypeptide has many
possible conformations (high entropy).
As it folds into an ever-decreasing number
of possible conformations, its entropy
and free energy decrease.

18. 18
Nucleation condensation model
In this modal the secondary and tertiary structure at a time made ,
the hydrophobic core collapse in random fashion and form a native
Structure.

19. 19
Formation of a nucleus of hydrophobic residues
Expansion of nucleus
Nucleation condensation model

20. “Evidently, proteins have evolved to have efficient
folding pathways as well as stable native
conformations.”
Nevertheless, misfolded proteins do occur in
nature, and their accumulation is believed to be the
cause of a variety of diseases.

21. MOLECULAR
CHAPERONES
ASSIST PROTEIN
FOLDING:
21
Definition
In molecular biology , Chaperones are proteins that
assist covalent folding or unfolding and assembly or
disassembly of other macromolecular structure.
They bind to unfolded and partially folded polypeptide
chains to prevent the improper association of exposed
hydrophobic segments that might lead to non-native
folding as well as polypeptide aggregation and
precipitation.

22. 22
There are two major classes of molecular
chaperones in both prokaryotes and
eukaryotes:
The Hsp70 family of 70-kD proteins
The chaperonins (large multisubunit proteins).
Chaperones

23. 23
Hsp70 proteins:
An Hsp70 protein binds to a newly synthesized polypeptide.
The Hsp70 chaperone probably helps prevent premature
folding.

24. 24
chaperon Protein Folding Process
Unfolded substrate proteins bind to a hydrophobic
binding patch on the interior rim of the open cavity of
GroEL.
Binding of substrate protein in this manner, in addition
to binding of ATP, induces a conformational change
that allows association of the binary complex with a
separate lid structure, GroES.
ATP is hydrolyzed and relase the GroES, which promote
folding of protein

25. 25

26. Thanks for your
attention please don’t
ask too much