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Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline Staphylococcal nuclease

結晶の黄色ブドウ球菌由来核酸分解酵素の分子シミュレーションによる水和依存的な蛋白質ダイナミクス

城地 保昌*; 中川 洋   ; 片岡 幹雄; 北尾 彰朗*

Jochi, Yasumasa*; Nakagawa, Hiroshi; Kataoka, Mikio; Kitao, Akio*

結晶状態の黄色ブドウ球菌由来核酸分解酵素の分子シミュレーションを低い水和量と高い水和量で行って、蛋白質ダイナミクスに対する水和効果を調べた。高い水和量では結晶の隙間に水を充填させた。低い水和量では結晶水のみを入れた。ガラス性転移は220Kの温度で両者で見られたが、高い水和量の方が転移はより顕著であった。残基ごとの揺らぎの解析からは、ループや末端領域に揺らぎの増加が見られた。これら領域は低い水和量では分子間の接触によって揺らぎは抑制されていた。高い水和量での水分子の揺らぎは低い水和量よりも一桁大きい。転移温度以上では高い水和量では水分子はバルク水のように振る舞い、蛋白質ダイナミクスの潤滑剤として働く。一方、低い水和量では水分子は蛋白質と水素結合を形成し、蛋白質の揺らぎの大きさと同程度になる。分子間相互作用と溶媒の運動性は蛋白質のガラス性転移を理解するのに重要である。

Molecular dynamics simulations of crystalline Staphylococcal nuclease in full and minimal hydration states were 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 atomic mean-square fluctuation of protein as a function of temperature, known as the glass-like transition, is observed at 220 K in both cases, which is more significant in the full hydration state. By examining the temperature dependence 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 in other regions in the full hydration state, but the mobility of the corresponding regions are relatively restricted in the minimal hydration state by inter-molecular contact. The atomic mean-square fluctuation of water molecules in the full hydration state at 300 K is one order of magnitude greater than that in the minimal hydration state. Above the transition temperature, most water molecules in the full hydration state behave like bulk water, and act as a lubricant for protein dynamics. In contrast, 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, inter-molecular interaction and solvent mobility are important to understand the glass-like transition in proteins.

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パーセンタイル:25.5

分野:Chemistry, Physical

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