Nonuniform charge scaling (NUCS) : a practical approximation of solvent electrostatic screening in proteins
(c) 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1359-1371, 2005.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 26(2005), 13 vom: 02. Okt., Seite 1359-71 |
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| Weitere Verfasser: | , , |
| Format: | Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2005
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Peptides, Cyclic Proteins Solvents circular bovine pancreatic trypsin inhibitor Water 059QF0KO0R Tyrosine 42HK56048U Aprotinin mehr... |
| Zusammenfassung: | (c) 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1359-1371, 2005. 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 Tyr 35 ring flip in the bovine pancreatic trypsin inhibitor |
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| Beschreibung: | Date Completed 07.09.2005 Date Revised 21.11.2013 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |