A Molecular Dynamics Study of Fast Side Chain Motions in Proteins Origin Diversity and Responses to Perturbations

Abstract

Fast side chain conformational dynamics play a vital role in the biological functions of proteins. High-resolution nuclear magnetic resonance studies continue to evolve in important ways to elucidate the structure, dynamics and thermodynamics of proteins in natively folded, unfolded, invisible excited states, and in ligand-bound complexes. Since the side chain motions and thermodynamics are governed by the underlying conformational energy landscape, it is essential to understand the interrelationship between protein energy landscape, protein-mediated biological processes, side chain dynamics and their responses to external perturbations. The derived correlations between O2axis, Sconf and strengths of noncovalent interactions reveals that side chain flexibility and conformational entropy decrease with increasing strength of its noncovalent interaction with surrounding evironment in a sigmoidal-like fashion for all residue types. Using fundamental statistical mechanical principles, an exact relationship between noncovalent interaction strengths, the relative stabilities of side chain conformational states and rotamer barriers of protein side chains is derived. The distribution of rotamer barriers follows a trimodal distribution both in ligand-free and ligand-bound states of CaM and CAP. Further, the side chains with O2axis 0.3 are observed to be least perturbed for all methyl-containing residues. A non-linear correlation between O2axis and the side chain rotamer population and linear relationship between O2axis and conformational entropy are observed even in the presence of significant site-specific perturbations in protein complexes. The investigation on the effect of external pressure on the fast side chain dynamics reveals a heterogenous distribution of side chain dynamics and local compressibility of proteins. Structural characterization of ubiquitin at different pressures indicated that even at 2.5 kbar pressure it remains in its native folded state.