Henchman Richard H, McCammon J Andrew
Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, USA.
Protein Sci. 2002 Sep;11(9):2080-90. doi: 10.1110/ps.0214002.
Structural and dynamic properties of water molecules around acetylcholinesterase are examined from a 10-nsec molecular dynamics simulation to help understand how the protein alters water properties. Water structure is broken down into hydration sites constructed from the water density <3.6 A from the protein surface. These sites are characterized according to occupancy, number of water neighbors, hydrogen bonds, dipole moment, and residence time. The site description provides a convenient means to describe the extent and localization of these properties. Determining the network of paths that waters follow from site to site and measuring the rate of flow of waters from the sites to the bulk make it possible to quantitatively study the time scales and paths that water molecules follow as they move around the protein.
通过10纳秒的分子动力学模拟，研究了乙酰胆碱酯酶周围水分子的结构和动力学性质，以帮助理解该蛋白质如何改变水的性质。水结构被分解为由距蛋白质表面<3.6 Å的水密度构建的水化位点。这些位点根据占有率、水邻居数量、氢键、偶极矩和停留时间进行表征。位点描述提供了一种方便的方式来描述这些性质的范围和定位。确定水分子从一个位点到另一个位点所遵循的路径网络，并测量水分子从这些位点流向本体的流速，使得定量研究水分子在蛋白质周围移动时所遵循的时间尺度和路径成为可能。
