Crystal water dynamics of guanosine dihydrate: analysis of atomic displacement parameters, time profile of hydrogen-bonding probability, and translocation of water by MD simulation.
The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism.
Yoneda
Shigetaka
S
School of Science, Kitasato University, Kitasato, Sagamihara, Kanagawa 228-8555, Japan. yoneda@sci.kitasato-u.ac.jp
Sugawara
Yoko
Y
Urabe
Hisako
H
D003198:Computer Simulation; D003460:Crystallization; D018360:Crystallography, X-Ray; D006151:Guanosine / Q000737:chemistry*; D006860:Hydrogen Bonding; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D013997:Time Factors; D014867:Water / Q000737:chemistry
D014867:Water; D006151:Guanosine