User:Jamesef

James Fitzgerald

I am an undergraduate majoring in physics and mathematics. I work on computational and theoretical aspects of protein folding with Professors Tobin Sosnick[1] and Karl Freed[2].

Past Research

• My primary research interest has been the dynamics of proteins. My first project was to investigate the fundamental local motions of proteins. Through numerous simulations we find a fundamental anticorrelation between the motions of the phi torsion angle of the ith residue and the psi angle of the (i-1)st residue. This motion is accomplished through the rocking of the rigid peptide group. This motion is independent of solvent model, force field, and is seen both in the presence and absence of long range interactions. This fundamentally local motion is robust enough to describe both equilibrium fluctuations of the backbone and basin transitions. No longer range correlations are necessary in either type of motion to retain the global structure of the peptide.

Current Research

• More recently I have been studying the fundamental motions of proteins by investigating topological constraints in protein folding. Using a mixture of classical differential geometry, knot theory, and computer simulations I am attempting to delineate the conditions under which certain conformational transitions of proteins are probable (or even possible). This is a work in progress, but interesting progress and been made and further results will follow when available.

• This winter I will begin working on the theory for the long time dynamics of proteins which has been developed by Professor Freed and his students [3]. This statistical mechanical theory using equilibrium averages (which can be obtained by any desired method) to retrieve information about the slow modes of polymers and peptides. I will begin by considering a simple polymer melt and will later consider a small folded protein.

• In addition to my work with protein dynamics, I have been considering the energetic and entropic content of protein sidechains. Using the information learned in this process I have developed a new force field for use in protein structure prediction which is currently in the testing stage. I am also developing a slight variation on this force field in hopes of better achieving the desired additivity of individual energy terms in this reduced potential.

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