The Poisson-Boltzmann model for tRNA : Assessment of the calculation set-up and ionic concentration cutoff
(c) 2008 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 29(2008), 12 vom: 15. Sept., Seite 1970-81 |
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| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2008
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Ions Solvents Water 059QF0KO0R RNA, Transfer 9014-25-9 |
| Zusammenfassung: | (c) 2008 Wiley Periodicals, Inc. Using tRNA molecule as an example, we evaluate the applicability of the Poisson-Boltzmann model to highly charged systems such as nucleic acids. Particularly, we describe the effect of explicit crystallographic divalent ions and water molecules, ionic strength of the solvent, and the linear approximation to the Poisson-Boltzmann equation on the electrostatic potential and electrostatic free energy. We calculate and compare typical similarity indices and measures, such as Hodgkin index and root mean square deviation. Finally, we introduce a modification to the nonlinear Poisson-Boltzmann equation, which accounts in a simple way for the finite size of mobile ions, by applying a cutoff in the concentration formula for ionic distribution at regions of high electrostatic potentials. We test the influence of this ionic concentration cutoff on the electrostatic properties of tRNA |
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| Beschreibung: | Date Completed 11.09.2008 Date Revised 20.10.2021 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.20953 |