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Int. J. Mol. Sci. 2016, 17(2), 254; doi:10.3390/ijms17020254

Effect of the Solvent Temperatures on Dynamics of Serine Protease Proteinase K

1
Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China
2
Laboratory of Molecular Cardiology, Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
3
College of Agriculture and Biological Science, Dali University, Dali 671003, China
4
Human Genetics Center, School of Public Health, the University of Texas Health Science Center, Houston, TX 77030, USA
5
Key Laboratory for Tumor molecular biology of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming 650091, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editor: Christo Z. Christov
Received: 12 December 2015 / Revised: 21 January 2016 / Accepted: 6 February 2016 / Published: 19 February 2016
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
View Full-Text   |   Download PDF [2952 KB, uploaded 19 February 2016]   |  

Abstract

To obtain detailed information about the effect of the solvent temperatures on protein dynamics, multiple long molecular dynamics (MD) simulations of serine protease proteinase K with the solute and solvent coupled to different temperatures (either 300 or 180 K) have been performed. Comparative analyses demonstrate that the internal flexibility and mobility of proteinase K are strongly dependent on the solvent temperatures but weakly on the protein temperatures. The constructed free energy landscapes (FELs) at the high solvent temperatures exhibit a more rugged surface, broader spanning range, and higher minimum free energy level than do those at the low solvent temperatures. Comparison between the dynamic hydrogen bond (HB) numbers reveals that the high solvent temperatures intensify the competitive HB interactions between water molecules and protein surface atoms, and this in turn exacerbates the competitive HB interactions between protein internal atoms, thus enhancing the conformational flexibility and facilitating the collective motions of the protein. A refined FEL model was proposed to explain the role of the solvent mobility in facilitating the cascade amplification of microscopic motions of atoms and atomic groups into the global collective motions of the protein. View Full-Text
Keywords: solvent mobility; hierarchical dynamics of proteins; free energy landscape; conformational sampling solvent mobility; hierarchical dynamics of proteins; free energy landscape; conformational sampling
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MDPI and ACS Style

Sang, P.; Yang, Q.; Du, X.; Yang, N.; Yang, L.-Q.; Ji, X.-L.; Fu, Y.-X.; Meng, Z.-H.; Liu, S.-Q. Effect of the Solvent Temperatures on Dynamics of Serine Protease Proteinase K. Int. J. Mol. Sci. 2016, 17, 254.

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