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Digitale Medien

Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects (1999)

Srinivasan, Jayashree ; Trevathan, Megan W. ; Beroza, Paul ; [weitere]

Springer

Theoretical chemistry accounts 101 (1999), S. 426-434

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ISSN: 1432-2234

Schlagwort(e): Key words: Solvation ; Electrostatics ; Generalised Born theory ; Salt effects ; Continuum solvent

Quelle: Springer Online Journal Archives 1860-2000

Thema: Chemie und Pharmazie

Notizen: Abstract. The Poisson–Boltzmann (PB) continuum solvent model shows considerable promise in providing a description of electrostatic solvation effects in biomolecules, but it can be computationally expensive to obtain converged results for large systems. Here we examine the performance of a pairwise generalized Born approximation (GB) method on multiple conformations of a small peptide, three proteins (protein A, myoglobin, and rusticyanin) and four RNA and DNA duplexes and hairpins containing 20–24 nucleotides. Charge and dielectric radii models were adapted from the CHARMM and Amber force fields. Finite difference PB calculations were carried out with the Delphi and PEP programs, and for several examples the matrix of all pairwise interaction energies was determined. In general, this parameterization of the GB model does an excellent job of reproducing the PB solvation energies for small molecules and for groups near the surface of larger molecules. There is a systematic tendency for this GB model to overestimate the effects of solvent screening (compared to PB) for pairs of buried atoms, but individual errors tend to cancel, and a good overall account of conformational energetics is obtained. A simple extension to the GB model to account for salt effects (in the linearized Debye–Hückel approximation) is proposed that does a good job of reproducing the salt dependence of the PB calculations. In many cases, it should be possible to replace PB calculations with much simpler GB models, but care needs to be taken for systems with extensive burial of charges or dipoles.

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/s002140050460

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Digitale Medien

An all atom force field for simulations of proteins and nucleic acids (1986)

Weiner, Scott J. ; Kollman, Peter A. ; Nguyen, Dzung T. ; [weitere]

New York, NY [u.a.] : Wiley-Blackwell

Journal of Computational Chemistry 7 (1986), S. 230-252

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Details

ISSN: 0192-8651

Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry

Quelle: Wiley InterScience Backfile Collection 1832-2000

Thema: Chemie und Pharmazie , Informatik

Notizen: We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc., 106, 765 (1984). The parameters of our function are based on calculations on ethane, propane, n-butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, deoxyadenosine, base paired dinucleoside phosphates, adenine, guanine, uracil, cytosine, thymine, insulin, and myoglobin. We have also used these parameters to carry out the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach.

Zusätzliches Material: 6 Ill.