A microscopic view of peptide and protein solvation.
The structure and dynamics of the water hydrating peptides and proteins are examined here at atomic resolution via molecular dynamics simulations. Detailed solvation density and residence time data for all 20 L-amino acids in an end-capped AXA tripeptide motif are presented. In addition, the solvation of the protein chymotrypsin inhibitor 2 is investigated as a point of comparison. Residues on the surface of proteins are not isolated; they interact both locally and non-locally in sequence space, and comparison of the solvation properties of each amino acid in both the peptide and protein allow us to distinguish inherent solvation properties from context-dependent perturbations due to neighboring residues. This work moves beyond traditional radial distribution functions and presents graphical representations of preferential solvation and orientation of water by side chains and the main chain. The combination of 0.3 micros of simulation data improves the statistical sampling over previous studies and reveals the significance of bridging water molecules that stabilize and mediate side chain-side chain, side chain-main chain and main chain-main chain interactions at the solvation interface.
Beck
David A C
DA
Biomolecular Structure & Design Program, University of Washington, Seattle, WA 98195-7610, USA.
Alonso
Darwin O V
DO
Daggett
Valerie
V
D000465:Algorithms; D004058:Diffusion; D008956:Models, Chemical; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry; D010100:Oxygen / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D010940:Plant Proteins; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012995:Solubility
D009842:Oligopeptides; D010455:Peptides; D010940:Plant Proteins; D011506:Proteins; C093336:chymotrypsin inhibitor 2; D010100:Oxygen