Nakagawa Hiroshi, Tamada Taro
Materials Science Research Center, Japan Atomic Energy Agency, Ibaraki, Japan.
J-PARC Center, Japan Atomic Energy Agency, Ibaraki, Japan.
Front Chem. 2021 Oct 18;9:738077. doi: 10.3389/fchem.2021.738077. eCollection 2021.
Protein hydration is crucial for the stability and molecular recognition of a protein. Water molecules form a hydration water network on a protein surface via hydrogen bonds. This study examined the hydration structure and hydrogen bonding state of a protein, staphylococcal nuclease, at various hydration levels in its crystalline state by all-atom molecular dynamics (MD) simulation. Hydrophilic residues were more hydrated than hydrophobic residues. As the water content increases, both types of residues were uniformly more hydrated. The number of hydrogen bonds per single water asymptotically approaches 4, the same as bulk water. The distances and angles of hydrogen bonds in hydration water in the protein crystal were almost the same as those in the tetrahedral structure of bulk water regardless of the hydration level. The hydrogen bond structure of hydration water observed by MD simulations of the protein crystalline state was compared to the Hydrogen and Hydration Database for Biomolecule from experimental protein crystals.
蛋白质水合作用对于蛋白质的稳定性和分子识别至关重要。水分子通过氢键在蛋白质表面形成水合水网络。本研究通过全原子分子动力学（MD）模拟，研究了处于结晶态的蛋白质葡萄球菌核酸酶在不同水合水平下的水合结构和氢键状态。亲水残基比疏水残基具有更高的水合度。随着含水量增加，两类残基的水合度均均匀增加。单个水分子的氢键数量渐近地接近4，与体相水相同。无论水合水平如何，蛋白质晶体中水合水中氢键的距离和角度与体相水的四面体结构中的几乎相同。通过蛋白质结晶态的MD模拟观察到的水合水氢键结构与来自实验蛋白质晶体的生物分子氢和水合数据库进行了比较。
