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1 Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, USA
2 Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California, San Diego, California 92093, USA
Reprint request to: Richard Henchman, Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive Dept 0365, La Jolla, California 92093, USA; e-mail: rhenchma{at}mccammon.ucsd.edu; fax: (858) 534-7042.
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 Å 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.
Keywords: Solvation; hydration; hydration site; molecular dynamics; acetylcholinesterase
Abbreviations: AChE, acetylcholinsterase • ARC/TAP, averaged residue coordinate/time-averaged position
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