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Published online before print July 6, 2004, 10.1110/ps.04748404
Protein Science (2004), 13:2120-2129. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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H-bonding in protein hydration revisited

Michael Petukhov1,2, Georgy Rychkov1, Leonid Firsov1 and Luis Serrano2

1 Division of Molecular and Radiation Biophysics (OMRB), St. Petersburg Nuclear Physics Institute, RAS, Gatchina, 188350, St. Petersburg, Russia
2 European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg D-69117, Germany

(RECEIVED March 17, 2004; FINAL REVISION March 17, 2004; ACCEPTED April 27, 2004)

H-bonding between protein surface polar/charged groups and water is one of the key factors of protein hydration. Here, we introduce an Accessible Surface Area (ASA) model for computationally efficient estimation of a free energy of water–protein H-bonding at any given protein conformation. The free energy of water–protein H-bonds is estimated using empirical formulas describing probabilities of hydrogen bond formation that were derived from molecular dynamics simulations of water molecules at the surface of a small protein, Crambin, from the Abyssinian cabbage (Crambe abyssinica) seed. The results suggest that atomic solvation parameters (ASP) widely used in continuum hydration models might be dependent on ASA for polar/charged atoms under consideration. The predictions of the model are found to be in qualitative agreement with the available experimental data on model compounds. This model combines the computational speed of ASA potential, with the high resolution of more sophisticated solvation methods.

Keywords: protein; hydration; water; H-bonding; solvent-accessible surface area

Abbreviations: ASA, solvent-accessible surface area • MD, molecular dynamics • PDB, Brookhaven Protein Data Bank • ASP, atomic solvation parameters

Reprint requests to: Michael Petukhov, Division of Molecular and Radiation Biophysics (OMRB), St. Petersburg Nuclear Physics Institute, RAS, Gatchina, 188350, St. Petersburg, Russia; e-mail: pmg{at}omrb.pnpi.spb.ru; fax: 7-812-552-3019.

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04748404.


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