Coarse-Graining the Accessible Surface and the Electrostatics of Proteins for Protein-Protein Interactions.

Abstract

This study is concerned with the development and test of a coarse-grained representation specifically constructed for proteins and peptides, where each amino acid of the sequence is represented by a charged dipolar sphere. The model was parametrized from the physical properties of individual amino acids and applied to the study of the interaction between solvated proteins. Using an implicit solvent approach and our coarse-grained model, we computed the potential of mean force for the association of well-known proteins, such as the Cu-Zn superoxide dismutase, lysozyme, and basic pancreatic trypsin inhibitor, and a peptide, Aβ7. The coarse-grained potentials of mean force were systematically compared with their all-atoms counterpart. For both the polar and nonpolar contributions to this potential, the results of our calculations show that the coarse-grained model provides a good approximation of the all-atoms potential when the distance between the molecule surfaces is greater than a solvent molecular diameter. For shorter distances and for specific interactions, like those found between the SOD monomers, the electrostatic desolvation effect appears to be underestimated by our coarse-grained representation. The possibility of a very short range all-atom refinement to better describe the interaction at close contact is explored. We find also that the most important contribution to the association free-energy comes from the hydrophobic solvent accessible surface area term, which is well reproduced by our coarse-grained approach.