Structural and dynamic properties of water around acetylcholinesterase.
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.
Henchman
Richard H
RH
Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, USA. rhenchma@mccammon.ucsd.edu .
McCammon
J Andrew
JA
D000110:Acetylcholinesterase / Q000737:chemistry*; D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D014867:Water / Q000737:chemistry*
D014867:Water; D000110:Acetylcholinesterase