Department of Chemistry, Indian Institute of Technology, Kharagpur, India.
Phys Chem Chem Phys. 2012 Jan 14;14(2):899-913. doi: 10.1039/c1cp22575h. Epub 2011 Nov 25.
Water present near the surface of a protein exhibits dynamic properties different from that of water in the pure bulk state. In this work, we have carried out atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme. Attempts have been made to explore the correlation between the local heterogeneous mobility of water around the protein segments and the rigidity of the hydration layers with the microscopic dynamics of hydrogen bonds formed by water molecules with the protein residues. The kinetics of breaking and reformation of hydrogen bonds involving the surface water molecules have been calculated. It is found that the reformations of broken hydrogen bonds are more frequent for the hydration layers of those segments of the protein that are more rigid. The calculation of the low-frequency vibrational modes of hydration layer water molecules reveals that the protein influences the transverse and longitudinal degrees of freedom of water around it in a differential manner. These findings can be verified by appropriate experimental studies.
蛋白质表面附近的水表现出与纯体相状态下水不同的动态特性。在这项工作中，我们对鸡卵清溶菌酶的水溶液进行了原子分子动力学模拟。尝试探索蛋白质片段周围水分子的局部不均匀流动性与水合层的刚性之间的相关性，以及水分子与蛋白质残基形成氢键的微观动力学之间的相关性。计算了涉及表面水分子的氢键的断裂和形成的动力学。结果发现，对于蛋白质中更刚性的那些片段的水合层，断裂氢键的再形成更为频繁。水合层水分子的低频振动模式的计算表明，蛋白质以不同的方式影响其周围水的横向和纵向自由度。这些发现可以通过适当的实验研究来验证。
