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

International Journal of Molecular Sciences

Xing-Lai Ji¹  Yun-Xin Fu¹  Shu-Qun Liu¹  Xing Du¹  Peng Sang¹  Li-Quan Yang¹  Qiong Yang¹  Nan Yang¹  Zhao-Hui Meng² 

[1] Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China;Laboratory of Molecular Cardiology, Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China;

关键词: solvent mobility;    hierarchical dynamics of proteins;    free energy landscape;    conformational sampling;   

DOI  :  10.3390/ijms17020254

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown