Chakraborty Sudip, Bandyopadhyay Sanjoy
Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India.
J Phys Chem B. 2007 Jul 5;111(26):7626-30. doi: 10.1021/jp072350e. Epub 2007 Jun 9.
An atomistic molecular dynamics simulation of the protein villin headpiece subdomain or HP-36 has been carried out with explicit water to explore the microscopic inhomogeneity of local density reorganization of the hydration layers of the three alpha-helical segments of the protein. The density reorganization of the hydration layer of helix-3 is found to occur faster than that for the hydration layers of the other two helices. It is noticed that such inhomogeneous density reorganization at the surface of different secondary structures exhibits excellent correlation with the microscopic dynamics of hydrogen bonds between the protein residues and the hydration water. Further, it is observed that the reorientation of water molecules involved in the formation and breaking of protein-water or water-water hydrogen bonds plays an important role in determining the dynamics of local density of the hydration layer. The faster density reorganization of the hydration layer of helix-3 is also consistent with the functionality of HP-36, as helix-3 contains several active site residues.
利用显式水对蛋白质绒毛蛋白头部结构域亚基（HP - 36）进行了原子尺度的分子动力学模拟，以探究该蛋白质三个α - 螺旋片段水化层局部密度重组的微观不均匀性。发现螺旋3水化层的密度重组比其他两个螺旋的水化层发生得更快。值得注意的是，不同二级结构表面这种不均匀的密度重组与蛋白质残基和水化水之间氢键的微观动力学表现出极好的相关性。此外，观察到参与蛋白质 - 水或水 - 水氢键形成和断裂的水分子的重新取向在决定水化层局部密度的动力学中起着重要作用。螺旋3水化层更快的密度重组也与HP - 36的功能一致，因为螺旋3包含几个活性位点残基。
