H-bonding in protein hydration revisited.
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.
Petukhov
Michael
M
Division of Molecular and Radiation Biophysics (OMRB), St. Petersburg Nuclear Physics Institute, RAS, Gatchina, 188350, St. Petersburg, Russia. pmg@omrb.pnpi.spb.ru
Rychkov
Georgy
G
Firsov
Leonid
L
Serrano
Luis
L
D031218:Crambe Plant / Q000737:chemistry*; D006860:Hydrogen Bonding; D008956:Models, Chemical; D015394:Molecular Structure; D010940:Plant Proteins / Q000737:chemistry*; D011487:Protein Conformation; D012639:Seeds / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D010940:Plant Proteins; D014867:Water; C024934:crambin protein, Crambe abyssinica