Paper Citing NAMD - Abstract
Paliwal, A.; Asthagiri, D.; Abras, D.; Lenhoff, A.M.; Paulaitis, M.E.
Light-scattering studies of protein solutions: Role of hydration in weak protein-protein interactions
BIOPHYSICAL JOURNAL, 89:1564-1573, SEP 2005
We model the hydration contribution to short-range electrostatic/ dispersion protein interactions embodied in the osmotic second virial coefficient, B-2, by adopting a quasi-chemical description in which water molecules associated with the protein are identified through explicit molecular dynamics simulations. These water molecules reduce the surface complementarity of highly favorable short-range interactions, and therefore can play an important role in mediating protein-protein interactions. Here we examine this quasi-chemical view of hydration by predicting the interaction part of B-2 and comparing our results with those derived from light-scattering measurements of B-2 for staphylococcal nuclease, lysozyme, and chymotrypsinogen at 25 degrees C as a function of solution pH and ionic strength. We find that short-range protein interactions are influenced by water molecules strongly associated with a relatively small fraction of the protein surface. However, the effect of these strongly associated water molecules on the surface complementarity of short-range protein interactions is significant, and must be taken into account for an accurate description of B-2. We also observe remarkably similar hydration behavior for these proteins despite substantial differences in their three-dimensional structures and spatial charge distributions, suggesting a general characterization of protein hydration.
