title: Structural characteristics of hydration sites in lysozyme.
abstract: A new method is presented for determining the hydration site of proteins, where the effect of structural fluctuations in both protein and hydration water is explicitly considered by using molecular dynamics simulation (MDS). The whole hydration sites (HS) of lysozyme are composed of 195 single HSs and 38 clustered ones (CHS), and divided into 231 external HSs (EHS) and 2 internal ones (IHS). The largest CHSs, 'Hg' and 'Lβ', are the IHSs having 2.54 and 1.35 mean internal hydration waters respectively. The largest EHS, 'Clft', is located in the cleft region. The real hydration structure of a CHS is an ensemble of multiple structures. The transition between two structures occurs through recombinations of some H-bonds. The number of the experimental X-ray crystal waters is nearly the same as that of the estimated MDS hydration waters for 70% of the HSs, but significantly different for the rest of HSs.
authors: Laboratory for Computational Molecular Design, Center for Computational Life Science, RIKEN, Minatojima-Minami-machi, Chuo-ku, Kobe, Hyogo, Japan. soda@riken.jp
authors: Kunitsugu
authors: K
authors: Soda
authors: Yudai
authors: Y
authors: Shimbo
authors: Yasutaka
authors: Y
authors: Seki
authors: Makoto
authors: M
authors: Taiji
mesh_terms: D000818:Animals; D002645:Chickens; D018360:Crystallography, X-Ray; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry*; D011487:Protein Conformation; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D009113:Muramidase