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A multicopy modeling of the water distribution in macromolecular crystals
Author(s) -
Podjarny Alberto D.,
Howard Eduardo I.,
Urzhumtsev Alexander,
Grigera J. Raul
Publication year - 1997
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199707)28:3<303::aid-prot1>3.0.co;2-d
Subject(s) - macromolecule , distribution (mathematics) , materials science , biology , mathematics , genetics , mathematical analysis
A multicopy protocol is proposed for modeling macromolecular hydration using diffraction experimental data (X‐ray or neutron) to search for a better description of delocalized water sites than that given by point water models. The model consists of one macromolecule and several copies of each water molecule, refined simultaneously against diffraction data using molecular dynamics techniques. The protocol was applied to BPTI and an RNA tetradecamer. The sites defined by the different copies range from very ordered ones to continuous channels; they fit the density maps and agree with the diffraction amplitudes with an accuracy comparable with usual crystallographic methods. The delocalization of water in channels agrees with the high mobility observed in NMR experiments. Proteins 28:303–312, 1997 © 1997 Wiley‐Liss, Inc.