Conformational Response to Solvent Interaction and Temperature of a Protein (Histone h3.1) by a Multi-Grained Monte Carlo Simulation

Authors

Ras B. Pandey, University of Southern MississippiFollow
Barry L. Farmer, Wright Patterson Air Force BaseFollow

Document Type

Article

Publication Date

10-18-2013

Department

Physics and Astronomy

School

Mathematics and Natural Sciences

Abstract

Interaction with the solvent plays a critical role in modulating the structure and dynamics of a protein. Because of the heterogeneity of the interaction strength, it is difficult to identify multi-scale structural response. Using a coarse-grained Monte Carlo approach, we study the structure and dynamics of a protein (H3.1) in effective solvent media. The structural response is examined as a function of the solvent-residue interaction strength (based on hydropathy index) in a range of temperatures (spanning low to high) involving a knowledge-based (Miyazawa-Jernigan(MJ)) residue-residue interaction. The protein relaxes rapidly from an initial random configuration into a quasi-static structure at low temperatures while it continues to diffuse at high temperatures with fluctuating conformation. The radius of gyration (R_g) of the protein responds non-monotonically to solvent interaction, i.e., on increasing the residue-solvent interaction strength (f_s), the increase in R_g (f_s≤f_sc) is followed by decay (f_s≥f_sc) with a maximum at a characteristic value (f_sc) of the interaction. Raising the temperature leads to wider spread of the distribution of the radius of gyration with higher magnitude of f_sc. The effect of solvent on the multi-scale (λ: residue to R_g) structures of the protein is examined by analyzing the structure factor (S(q),|q| = 2π/λ is the wave vector of wavelength, λ) in detail. Random-coil to globular transition with temperature of unsolvated protein (H3.1) is dramatically altered by the solvent at low temperature while a systematic change in structure and scale is observed on increasing the temperature. The interaction energy profile of the residues is not sufficient to predict its mobility in the solvent. Fine-grain representation of protein with two-node and three-node residue enhances the structural resolution; results of the fine-grained simulations are consistent with the finding described above of the coarse-grained description with one-node residue.

Publication Title

PLoS ONE

Volume

8

Issue

10

Recommended Citation

Pandey, R. B., Farmer, B. L. (2013). Conformational Response to Solvent Interaction and Temperature of a Protein (Histone h3.1) by a Multi-Grained Monte Carlo Simulation. PLoS ONE, 8(10).
Available at: https://aquila.usm.edu/fac_pubs/7873