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Titolo:
Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics
Autore:
Tsui, V; Case, DA;
Indirizzi:
Scripps Clin & Res Inst, Dept Mol Biol, La Jolla, CA 92037 USA Scripps Clin & Res Inst La Jolla CA USA 92037 iol, La Jolla, CA 92037 USA
Titolo Testata:
JOURNAL OF PHYSICAL CHEMISTRY B
fascicolo: 45, volume: 105, anno: 2001,
pagine: 11314 - 11325
SICI:
1520-6106(20011115)105:45<11314:COTAFE>2.0.ZU;2-9
Fonte:
ISI
Lingua:
ENG
Soggetto:
NUCLEIC-ACIDS; RIBOZYME DOMAIN; MAJOR GROOVE; FORCE-FIELD; PROTEINS; SOLVENT; DNA; ASSOCIATION; COMPUTATION; INCLUSION;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
35
Recensione:
Indirizzi per estratti:
Indirizzo: Case, DA Scripps Clin & Res Inst, Dept Mol Biol, La Jolla, CA 92037 USA Scripps Clin & Res Inst La Jolla CA USA 92037 olla, CA 92037 USA
Citazione:
V. Tsui e D.A. Case, "Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics", J PHYS CH B, 105(45), 2001, pp. 11314-11325

Abstract

The calculation of binding free energies between highly charged species isa major challenge for free energy simulations. In this study, we applied acombination of molecular dynamics simulations and continuum electrostatics, along with normal-mode analysis, to compute the absolute free energies ofbinding between cobalt (III) hexammine and two RNA fragments for which NMRstructures have been determined. The predicted affinities, using the finite-difference Poisson-Boltzmann method with a solute dielectric constant of I to treat solvation, were overall underestimated relative to the experimental values. However, internal consistency in the calculated energies was maintained between the different trajectories, and the structures in the simulations gave excellent agreement with NMR data. Various models for obtaining the electrostatic contributions were analyzed, including the effects of solute dielectric constants and van der Waals radii, linear and nonlinear salt contributions, as well as results from generalized Born versus finite-difference Poisson-Boltzmann models. These provide insight into the strengthsand limitations in the current methods and force fields for free energy calculations.

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Documento generato il 12/12/19 alle ore 15:05:02