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Exploring Protein Stability by Comparative Molecular Dynamics Simulation of Homologous Hyperthermophilic, Mesophilic and Psychrophilic Proteins Sara Khan, Umar Farooq, and Maria Kurnikova J. Chem. Inf. Model., Just Accepted Manuscript • DOI: 10.1021/acs.jcim.6b00305 • Publication Date (Web): 26 Sep 2016 Downloaded from http://pubs.acs.org on September 28, 2016
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Journal of Chemical Information and Modeling is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.
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Journal of Chemical Information and Modeling
Exploring Protein Stability by Comparative Molecular Dynamics Simulation of Homologous Hyperthermophilic, Mesophilic and Psychrophilic Proteins Sara Khana, Umar Farooqa,*, Maria Kurnikovab
a
Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad-22060, Pakistan
b
Department of Chemistry, Carnegie Mellon University, Pittsburgh-15213, Pennsylvania, USA
*Corresponding Author Address
Dr. Umar Farooq Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad-22060, Pakistan. Ph. +92-992-383591–5; Email:
[email protected] 1 ACS Paragon Plus Environment
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ABSTRACT: In the present studies, we analyzed the influence of temperature on the stability and dynamics of α subunit of Tryptophan synthase from hyperthermophilic, mesophilic and psychrophilic homologous at different temperatures by MD simulations. This study employing different indicators such as RMSD, RMSF, PCA and FEL manifests the diverse behavior of all homologous with the change in temperature, especially an enhancement in the collective motions classified as representative motions, is observed at high temperature. Similarly the criterion for the selection of electrostatic interactions in term of their life span (duty cycle) has indeed helped in identifying the short and long lived electrostatic interactions and how they affect protein’s overall stability at different temperature. Rigidity and flexibility pattern of the homologue proteins is examined by employing FIRST software along with the calculation of duty cycles with various thresholds limit at different temperatures. Rigid cluster decomposition in TRPS of psychrophilic, mesophilic and hyperthermophilic origin identifies the flexible and rigid regions in the protein. Early loss of rigidity is observed in mesophilic TRPS via loss of the contact between major fragments of the protein compared to other homologue proteins. In spite of high similarity in 3D structure, the overall response of the three proteins to varying temperatures is significantly different.
Abbreviations: Tryptophan synthase (TRPS), PCA (Principal Component Analysis), FEL (Free Energy Landscape), HB (Hydrogen bond), HT (Hydrophobic tether).
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Journal of Chemical Information and Modeling
INTRODUCTION Life on earth is adapted to varying physiological conditions. Vast majority of living organisms survive around standard condition of temperature and pressure, but there exist a type of organisms embracing mechanistic features well designed to survive in extreme environmental conditions truly called extremophiles1. Among the wide class of extremophile, hyperthermophile (~120 ºC) and cold adapted organisms called psychrophiles (
