Properties of water molecules in the active site gorge of acetylcholinesterase from computer simulation.
A 10-ns trajectory from a molecular dynamics simulation is used to examine the structure and dynamics of water in the active site gorge of acetylcholinesterase to determine what influence water may have on its function. While the confining nature of the deep active site gorge slows down and structures water significantly compared to bulk water, water in the gorge is found to display a number of properties that may aid ligand entry and binding. These properties include fluctuations in the population of gorge waters, moderate disorder and mobility of water in the middle and entrance to the gorge, reduced water hydrogen-bonding ability, and transient cavities in the gorge.
Henchman
Richard H
RH
Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0365 USA. rhenchma@mccammon.ucsd.edu
Tai
Kaihsu
K
Shen
Tongye
T
McCammon
J Andrew
JA
D000110:Acetylcholinesterase / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D003198:Computer Simulation; D006860:Hydrogen Bonding; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D014867:Water / Q000737:chemistry / Q000378:metabolism*
D008024:Ligands; D014867:Water; D000110:Acetylcholinesterase