cmse seminar

CMSE SEMINAR

Protein Folding mechanisms

By

Sefer Baday

OUTLINE

Proteins Protein Folding Forces Driving Folding Energy landscape The folding mechanism models Conclusion

Some Facts about Proteins

Composed of amino acids.

Each sequence fold in unique structure-native structure

Proteins are functional only in their native states

Folding is reversibe unfolding or re-folding is possible

Modest changes in the environment can cause structural

changes in the protein,thus affecting its function

Protein structure hierarchical levels

VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

PRIMARY STRUCTURE (amino acid sequence)

QUATERNARY STRUCTURE (oligomers)

SECONDARY STRUCTURE (helices, strands)

TERTIARY STRUCTURE (fold)

What is Protein Folding ?

• Protein folding is the process by which a protein

assumes its functional shape or conformation.

Random Coil Native conformation

Why is the “Protein Folding” so important

Most of the proteins should fold in order to function Misfolding cause some diseases. Cystic Fibrosis ,affects lungs and digestive system

and cause early death Alzheimers’s and Parkinson's disease It may help us to understand the structure of proteins

which has not been known

LEVINTHAL PARADOX

Let have Protein composed of 100 amino acids. Assume that each amino acid has only 3 possible

conformations. Total number of conformations = 3100 ~= 5x1047 . If 100 psec (10-10 sec) were required to convert from a

conformation to another one, a random search of all conformations would require

5x1047 x 10-10 sec = 1.6 x 1030 years.

However, folding of proteins takes place in msec to sec order.

Forces that stabilize protein structure

Interactions between atoms within the protein chain

Interactions between the protein and the solvent

Electrostatic Interactions

Interaction of charged side chain with the opposide charged side chain.

221

Dr

qqF

NH3+ O

CO

CH2

H2C C

O

O- NH3+

(CH2)4

Hydrogen Bonds

Noncovalent bond Energy:10-40 kJ/ mol Strength varies with angle of hydrogen bond

interaciton.

van der Waals forces

Between all atoms Approximately 1kj/mol

r

Van d

er

Waals

pote

nti

al

Van d

er

Waals

Forc

e

r0

r0Van der waals radii of common atoms (nm):

H 0.1 nm C 0.17 nmN 0.15 nmO 0.14 nmP 0.19 nmS 0.185 nm

Average Strength of Interactions

Bond Type kJ/mol

Covalent Bond 250

Electrostatic 5

van der Waals 5

Hydrogen bond 20

The Hydrophobic Interaction

Hydrophobic means afraid of water Hydrophobic residues are buried in while

hyrophilic residues stay outside.

Hydrogen Bonds

The kinetic Theory of Protein Folding Folding proceeds through a definite series of

steps or a Pathway. A protein does not try out all possible

rotations of conformational angles, but only enough to find the pathway.

Energy Landscape

Energy Landscape

Molten Globule

Contact Order

The average separation in the sequence between residues that are in contact with each other in native structure

Phi Value Analysis

Experimental method to study of the structure of the transition state

Using mutations as a structural report Phi=1, transition state has native like

structure Phi=0, transition state has denatured like

structure

The Framework Model

Local interactions are main determinants of protein structures

unfolded stateTransition state

native state

Hydrophobic Collapse

Hydrophobic core forms first.

unfolded state

collapsenative state

Hydrophobic Collapse

Formation of hydrophobic globule may hinder the reorganization of both side chains and whole protein

Nucleation Model Unites hydrophobic collapse and frame work

model

unfolded state

formation ofa nucleus

native state

Nucleation Model

Substantial expulsion of water from the burial of non polar surfaces

Good correlation between decrease in hyrodynamic volume and increase in secondary structure

Unfolding simulation of Ci2

The folding Pathways of Barnase

Conclusions

Non local interactions( Hydrophobic effect and van der waals ) are needed to bring protein into a globular conformation.

Chemically specific interactions( hydrogen bonds, electorstatic interactions) determine the fine detail of the protein structure

Conclusions

The folding process is hierarchical Native topology affects the folding

mechanism. Nucleation method explains folding

mechanism better than framework and hydrophobic collapse methods.

THANK YOU

QUESTIONS

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