Excluded volume approximation to protein-solvent interaction. The solvent contact model.
Important properties of globular proteins, such as the stability of its folded state, depend sensitively on interactions with solvent molecules. Existing methods for estimating these interactions, such as the geometrical surface model, are either physically misleading or too time consuming to be applied routinely in energy calculations. As an alternative, we derive here a simple model for the interactions between protein atoms and solvent atoms in the first hydration layer, the solvent contact model, based on the conservation of the total number of atomic contacts, a consequence of the excluded-volume effect. The model has the conceptual advantage that protein-protein contacts and protein-solvent contacts are treated in the same language and the technical advantage that the solvent term becomes a particularly simple function of interatomic distances. The model allows rapid calculation of any physical property that depends only on the number and type of protein-solvent nearest-neighbor contacts. We propose use of the method in the calculation of protein solvation energies, conformational energy calculations, and molecular dynamics simulations.
Colonna-Cesari
F
F
Laboratoire d'Enzymologie Physico-Chimique et Moleculaire, Universite de Paris Sud, Orsay, France.
Sander
C
C
D000596:Amino Acids; D006860:Hydrogen Bonding; D008961:Models, Structural; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins; D012997:Solvents; D013499:Surface Properties; D014867:Water
D000596:Amino Acids; D011506:Proteins; D012997:Solvents; D014867:Water