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A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides

✍ Scribed by Pavelites, Joseph J.; Gao, Jiali; Bash, Paul A.; Mackerell, Alexander D.

Publisher: John Wiley and Sons
Year: 1997
Tongue: English
Weight: 453 KB
Volume: 18
Category: Article
ISSN: 0192-8651
DOI: 10.1002/(sici)1096-987x(19970130)18:2<221::aid-jcc7>3.0.co;2-x

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✦ Synopsis

Ž

q . Empirical force field parameters for nicotinamide NIC and 1,4-Ž . dihydronicotinamide NICH were developed for use in modeling of the Ž q . coenzymes nicotinamide adenine dinucleotide NAD and NAD hydride Ž . NADH . The parametrization follows the methodology used in the development of the CHARMM22 all-hydrogen parameters for proteins, nucleic acids, and lipids. Parametrization of inorganic phosphate for use in adenosine di-and Ž . triphosphates e.g., ADP and ATP is also presented. While high level ab initio data, such as conformational energies, dipole moments, interactions with water, and vibrational frequencies, were adequately reproduced by the developed parameters, strong emphasis was placed on the successful reproduction of experimental geometries and crystal data. Results for molecular dynamics crystal simulations were in good agreement with available crystallographic data.

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