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Nonuniform charge scaling (NUCS): A practical approximation of solvent electrostatic screening in proteins
Author(s) -
Schwarzl Sonja M.,
Huang Danzhi,
Smith Jeremy C.,
Fischer Stefan
Publication year - 2005
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20274
Subject(s) - solvation , poisson–boltzmann equation , chemistry , scaling , implicit solvation , partial charge , solvent models , electrostatics , computational chemistry , molecular mechanics , poisson's equation , coulomb , molecule , solvent effects , aqueous solution , chemical physics , solvent , molecular dynamics , statistical physics , quantum mechanics , ion , physics , electron , organic chemistry , geometry , mathematics
In molecular mechanics calculations, electrostatic interactions between chemical groups are usually represented by a Coulomb potential between the partial atomic charges of the groups. In aqueous solution these interactions are modified by the polarizable solvent. Although the electrostatic effects of the polarized solvent on the protein are well described by the Poisson–Boltzmann equation, its numerical solution is computationally expensive for large molecules such as proteins. The procedure of nonuniform charge scaling (NUCS) is a pragmatic approach to implicit solvation that approximates the solvent screening effect by individually scaling the partial charges on the explicit atoms of the macromolecule so as to reproduce electrostatic interaction energies obtained from an initial Poisson–Boltzmann analysis. Once the screening factors have been determined for a protein the scaled charges can be easily used in any molecular mechanics program that implements a Coulomb term. The approach is particularly suitable for minimization‐based simulations, such as normal mode analysis, certain conformational reaction path or ligand binding techniques for which bulk solvent cannot be included explicitly, and for combined quantum mechanical/molecular mechanical calculations when the interface to more elaborate continuum solvent models is lacking. The method is illustrated using reaction path calculations of the Tyr35 ring flip in the bovine pancreatic trypsin inhibitor. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1359–1371, 2005