CMSE SEMINAR Protein Folding mechanisms By Sefer Baday

OUTLINE Ø Ø Ø 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 PRIMARY STRUCTURE (amino acid sequence) SECONDARY STRUCTURE (helices, strands) VHLTPEEKSAVTALWGKVNVD EVGGEALGRLLVVYPWTQRFF ESFGDLSTPDAVMGNPKVKAH GKKVLGAFSDGLAHLDNLKGTF ATLSELHCDKLHVDPENFRLLG NVLVCVLAHHFGKEFTPPVQAA YQKVVAGVANALAHKYH QUATERNARY STRUCTURE (oligomers) 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 Ø Ø Ø 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 n n Let have Protein composed of 100 amino acids. Assume that each amino acid has only 3 possible conformations. Total number of conformations = 3100 ~= 5 x 1047. If 100 psec (10 -10 sec) were required to convert from a conformation to another one, a random search of all conformations would require 5 x 1047 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 n n Interactions between atoms within the protein chain Interactions between the protein and the solvent

Electrostatic Interactions n Interaction of charged side chain with the opposide charged side chain.

Hydrogen Bonds n n n Noncovalent bond Energy: 10 -40 k. J/ mol Strength varies with angle of hydrogen bond interaciton.

van der Waals forces n Between all atoms Approximately 1 kj/mol Van der Waals potential Van der Waals Force n Van der waals radii of common atoms (nm): H 0. 1 nm C 0. 17 nm N 0. 15 nm O 0. 14 nm P 0. 19 nm S 0. 185 nm r 0 r

Average Strength of Interactions Bond Type k. J/mol Covalent Bond 250 Electrostatic 5 van der Waals 5 Hydrogen bond 20

The Hydrophobic Interaction n n Hydrophobic means afraid of water Hydrophobic residues are buried in while hyrophilic residues stay outside.

Hydrogen Bonds

The kinetic Theory of Protein Folding Ø Folding proceeds through a definite series of steps or a Pathway. Ø A protein does not try out all possible rotations of conformational angles, but only enough to find the pathway.

Energy Landscape

Molten Globule

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

Phi Value Analysis n n 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 n Local interactions are main determinants of protein structures native state unfolded state Transition state

Hydrophobic Collapse n Hydrophobic core forms first. collapse unfolded state native state

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

Nucleation Model n Unites hydrophobic collapse and frame work model unfolded state formation of a nucleus native state

Nucleation Model n n 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 Ci 2

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 n n n The folding process is hierarchical Native topology affects the folding mechanism. Nucleation method explains folding mechanism better than framework and hydrophobic collapse methods.

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