Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model.

ABSTRACT: When proteins bind to their DNA target sites, ordered water molecules are often present at the protein-DNA interface bridging protein and DNA through hydrogen bonds. What is the role of these ordered interfacial waters? Are they important determinants of the specificity of DNA sequence recognition, or do they act in binding in a primarily nonspecific manner, by improving packing of the interface, shielding unfavorable electrostatic interactions, and solvating unsatisfied polar groups that are inaccessible to bulk solvent? When modeling details of structure and binding preferences, can fully implicit solvent models be fruitfully applied to protein-DNA interfaces, or must the individualistic properties of these interfacial waters be accounted for? To address these questions, we have develope

SUBMITTER: Li S 

PROVIDER: S-EPMC3904374 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature