title: Do homologous thermophilic-mesophilic proteins exhibit similar structures and dynamics at optimal growth temperatures? A molecular dynamics simulation study.
abstract: Structure and dynamics both are known to be important for the activity of a protein. A fundamental question is whether a thermophilic protein and its mesophilic homologue exhibit similar dynamics at their respective optimal growth temperatures. We have addressed this question by performing molecular dynamics (MD) simulations of a natural mesophilic-thermophilic homologue pair at their respective optimal growth temperatures to compare their structural, dynamical, and solvent properties. The MD simulations were done in explicit aqueous solvent under periodic boundary and constant pressure and temperature (CPT) conditions and continued for 10.0 ns using the same protocol for the two proteins, excepting the temperatures. The trajectories were analyzed to compare the properties of the two proteins. Results indicated that the dynamical behaviors of the two proteins at the respective optimal growth temperatures were remarkably similar. For the common residues in the thermophilic protein, the rms fluctuations have a general trend to be slightly higher compared to that in the mesophilic counterpart. Lindemann parameter values indicated that only a few residues exhibited solid-like dynamics while the protein as a whole appeared as a molten globule in each case. Interestingly, the water-water interaction was found to be strikingly similar in spite of the difference in temperatures while, the protein-water interaction was significantly different in the two simulations.
authors.affiliation: Molecular modeling Section, Biolab, Chembiotek, TCG Lifesciences Ltd., Bengal Intelligent Park, Tower-B 2nd Floor, Block-EP & GP, Sector-V, Salt Lake Electronic Complex, Calcutta-700091, India.
authors.forename: Sohini
authors.initials: S
authors.lastname: Basu
authors.forename: Srikanta
authors.initials: S
authors.lastname: Sen
mesh_terms: D000595:Amino Acid Sequence; D001407:Bacillus / Q000737:chemistry*; D001412:Bacillus subtilis / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011487:Protein Conformation; D016415:Sequence Alignment; D013696:Temperature; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; C077188:cold-shock protein CspB, Bacteria