IIIT Hyderabad Publications |
|||||||||
|
A Molecular Dynamics Study of Fast Side Chain Motions in Proteins: Origin, Diversity and Responses to PerturbationsAuthor: Rajitha Tatikonda Date: 2017-09-12 Report no: IIIT/TH/2017/73 Advisor:Marimuthu Krishnan AbstractFast side chain conformational dynamics play a vital role in the biological functions of proteins. High-resolution nuclear magnetic resonance (NMR) 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. NMR spectroscopy uses methyl spin probes of methyl-containing residues to characterize the sitespecific side chain motions and to establish a molecular-level connection between the dynamics and thermodynamics of proteins. 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 major aim of this thesis is to investigate the origin, diversity, functional roles of the fast side chain motions of proteins and their responses to external perturbations (ligand-binding and pressure) using molecular dynamics simulations. The universal features of fast side chain motions in proteins are characterized by examining the conformational energy surfaces of individual residues obtained using enhanced sampling molecular dynamics simulation. The free energy barriers separating side chain rotamer states follows a trimodal distribution. A hierarchical grading of rotamer states based on the conformational free energy barriers, conformational entropy (Scon f), and probability flux revealed three distinct classes of side chains in proteins. A unique nonlinear correlation is established between NMR order parameters (O 2 axis ) and the side chain rotamer populations (ρ). The apparent universality in O 2 axis versus ρ correlation, trimodal barrier distribution, and distinct characteristics of three classes of side chains observed among proteins with different secondary structures and molecular weights indicated a hidden regularity (or commonality) in the dynamical heterogeneity of fast side chain motions in proteins. The influences of ligandbinding, pressure and noncovalent interactions on the fast internal motions of proteins are examined. The derived correlations between O 2 axis, Scon f and strengths of noncovalent interactions reveals that side chain flexibility and conformational entropy decrease with increasing 9 strength of its noncovalent interaction with surrounding evironment in a sigmoidal-like fashion for all residue types. The results also showed that there exists a critical range of noncovalent interaction strength for each residue type determined primarily by the mean side chain conformational barriers, beyond which side chain flexibility and conformational entropy are insensitive to noncovalent interactions. 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. Using calmodulin (CaM) and catabolite activator protein (CAP) complexes as model systems, the site-specific ligand-induced changes in thermodynamical properties and side chain dynamics of proteins are investigated. The distribution of rotamer barriers follows a trimodal distribution both in ligand-free and ligand-bound states of CaM and CAP. The distributions of changes in O 2 axis, for all complexes followed a Gaussian-like unimodal distribution and the width of the distribution varied among different complexes. Further, the side chains with O 2 axis ≈0.3 are observed to be least perturbed for all methyl-containing residues. A non-linear correlation between O 2 axis and the side chain rotamer population (ρ) and linear relationship between O 2 axis and conformational entropy (Scon f) 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 (0.001- 2.5 kbar) indicated that even at 2.5 kbar pressure it remains in its native folded state. The present thesis has illustrated the use of advanced enhanced sampling methods and molecular dynamics simulation to gain new molecular-level insights into fast conformational dynamics and to relate side chain dynamics and thermodynamics of proteins to the underlying conformational landscape. Full thesis: pdf Centre for Computational Natural Sciences and Bioinformatics |
||||||||
Copyright © 2009 - IIIT Hyderabad. All Rights Reserved. |