Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica.
Buried water molecules and the water molecules in the active-site gorge are analyzed for five crystal structures of acetylcholinesterase from Torpedo californica in the resolution range 2.2-2.5 A (native enzyme, and four inhibitor complexes). A total of 45 buried hydration sites are identified, which are populated with between 36 and 41 water molecules. About half of the buried water is located in a distinct region neighboring the active-site gorge. Most of the buried water molecules are very well conserved among the five structures, and have low displacement parameters, B, of magnitudes similar to those of the main-chain atoms of the central beta-sheet structure. The active-site gorge of the native enzyme is filled with over 20 water molecules, which have poor hydrogen-bond coordination with an average of 2.9 polar contacts per water molecule. Upon ligand binding, distinct groups of these water molecules are displaced, whereas the others remain in positions similar to those that they occupy in the native enzyme. Possible roles of the buried water molecules are discussed, including their possible action as a lubricant to allow large-amplitude fluctuations of the loop structures forming the gorge wall. Such fluctuations are required to facilitate traffic of substrate, products and water molecules to and from the active-site. Because of their poor coordination, the gorge water molecules can be considered as "activated" as compared to bulk water. This should allow their easy displacement by incoming substrate. The relatively loose packing of the gorge water molecules leaves numerous small voids, and more efficient space-filling by substrates and inhibitors may be a major driving force of ligand binding.
Koellner
G
G
Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel. koellner@chemie.fu-berlin.de
Kryger
G
G
Millard
C B
CB
Silman
I
I
Sussman
J L
JL
Steiner
T
T
D000110:Acetylcholinesterase / Q000737:chemistry* / Q000378:metabolism*; D000470:Alkaloids; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002800:Cholinesterase Inhibitors / Q000378:metabolism; D003460:Crystallization; D018360:Crystallography, X-Ray; D000077265:Donepezil; D004491:Edrophonium / Q000378:metabolism; D006860:Hydrogen Bonding; D007189:Indans / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010880:Piperidines / Q000378:metabolism; D017433:Protein Structure, Secondary; D015203:Reproducibility of Results; D012717:Sesquiterpenes / Q000378:metabolism; D055672:Static Electricity; D014101:Torpedo; D014867:Water / Q000737:chemistry / Q000378:metabolism*
D000470:Alkaloids; D002800:Cholinesterase Inhibitors; D007189:Indans; D008024:Ligands; D010880:Piperidines; D012717:Sesquiterpenes; C050426:huperzine A; D014867:Water; D004491:Edrophonium; D000077265:Donepezil; D000110:Acetylcholinesterase