Hydration-Dependent Protein Dynamics Revealed by Molecular Dynamics Simulation of Crystalline Staphylococcal Nuclease

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• 作者：Yasumasa Joti ; Hiroshi Nakagawa ; Mikio Kataoka ; Akio Kitao
• 刊名：Journal of Physical Chemistry B
• 出版年：2008
• 出版时间：March 20, 2008
• 年：2008
• 卷：112
• 期：11
• 页码：3522 - 3528
• 全文大小：297K
• 年卷期：v.112,no.11(March 20, 2008)
• ISSN：1520-5207

文摘

Molecular dynamics simulations of crystalline Staphylococcal nuclease in full and minimal hydration stateswere performed to study hydration effects on protein dynamics at temperatures ranging from 100 to 300 K.In a full hydration state (hydration ratio in weight, h = 0.49), gaps are fully filled with water molecules,whereas only crystal waters are included in a minimal hydration state (h = 0.09). The inflection of the atomicmean-square fluctuation of protein as a function of temperature, known as the glass-like transition, is observedat ~220 K in both cases, which is more significant in the full hydration state. By examining the temperaturedependence of residual fluctuation, we found that the increase of fluctuations in the loop and terminal regions,which are exposed to water, is much greater than that in other regions in the full hydration state, but themobilities of the corresponding regions are relatively restricted in the minimal hydration state by intermolecularcontact. The atomic mean-square fluctuation of water molecules in the full hydration state at 300 K is 1 orderof magnitude greater than that in the minimal hydration state. Above the transition temperature, most watermolecules in the full hydration state behave like bulk water and act as a lubricant for protein dynamics. Incontrast, water molecules in the minimal hydration state tend to form more hydrogen bonds with the protein,restricting the fluctuation of these water molecules to the level of the protein. Thus, intermolecular interactionand solvent mobility are important to understand the glass-like transition in proteins.