Harold Scheraga, Cornell University: “Physics-based Calculation of Protein Structure and Protein-folding Pathways”

Apr 21 2009, 10:00 am
Distinguished Lecture Series Guest Speaker: 

Harold Scheraga

George W. and Grace L. Todd Professor of Chemistry, Emeritus
Baker Laboratory of Chemistry and Chemical Biology
Cornell University

Date & Time: 
Tuesday, April 21, 2009, 10:00AM
Location: 
MoSE, Room 3201A
Host: 
Jeffrey Skolnick
Abstract: 
Using a coarse-grained united-residue (UNRES) force field and simulation methods (Langevin molecular dynamics and multiplexed replica exchange molecular dynamics), it is possible to compute the folding pathways, folding kinetics, and final folded native structure of a globular protein. Progress has been made in refining the parameters of the UNRES force field and, by extensive parallelization of the code, in extending the size of proteins (to about 1000 residues) that can be treated in the available time with current computers. The current state of these computations will be discussed.
Additional Info: 

We are investigating the interactions that (a) dictate the folding of a polypeptide chain in water into the three-dimensional structure of a native protein and (b) determine the reactivity of such a protein molecule (e.g., as an enzyme) with other small and large molecules.

Both experimental and theoretical methods are used in this research. The experimental work involves genetic engineering and hydrodynamic (e.g., sedimentation and viscosity), spectroscopic (Raman, infrared, fluorescence, nuclear magnetic resonance, electron spin resonance, ultraviolet absorption, circular dichroism, and optical rotatory dispersion), immunochemical, and other physicochemical measurements on proteins, synthetic polymers of amino acids, and model compounds. The theoretical work involves statistical mechanical studies of aqueous solutions of amino acids and peptides, and of conformational changes in proteins and polypeptides, and empirical energy calculations to determine the stable conformations of proteins, polypeptides, and enzyme-substrate complexes.

Much of the experimental and theoretical work involves the determination of the pathways of folding of proteins, and the mechanism of action of thrombin on fibrinogen (an important reaction in the blood clotting process).
Faculty Research Page
Harold Scheraga - Seminar Flyer 4-21.jpg