Computation of ionic distributions around charged biomolecular structures: results for right-handed and left-handed DNA.
Open Access
- 1 June 1991
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 88 (11) , 4631-4635
- https://doi.org/10.1073/pnas.88.11.4631
Abstract
We introduce an efficient computational methodology employing the potentials of mean force approach for estimating the detailed three-dimensional ionic distributions around arbitrarily complex charged biomolecular structures for all monovalent salt concentrations of practical interest (e.g., 0.1-5.0 M NaCl). Such distributions are required for specifying thermodynamic and structure-specific features of ion-mediated interactions of charged proteins, DNA and RNA, membranes, and macromolecular assemblies. As a first application, we present results for distributions around the B and ZI conformers of the DNA oligomer d(C-G)18.d(C-G)18. The ionic microenvironment depends strongly on the DNA conformation, sequence, and bulk salt concentrations.Keywords
This publication has 14 references indexed in Scilit:
- Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution.Proceedings of the National Academy of Sciences, 1989
- The electrostatic potential of B‐DNABiopolymers, 1989
- Salt Dependence of DNA Structural Stabilities in Solution. Theoretical Predictions Versus ExperimentsJournal of Biomolecular Structure and Dynamics, 1988
- B‐Z DNA conformational transition in 1:1 electrolytes: dependence upon counterion sizeFEBS Letters, 1987
- Relative Stabilities and Transitions of DNA Conformations in 1:1 Electrolytes: A Theoretical StudyJournal of Biomolecular Structure and Dynamics, 1987
- Generalized Poisson‐Boltzmann calculation of the distribution of electrolyte ions around the B‐ and Z‐conformers of DNABiopolymers, 1984
- Statistical mechanics of the B----Z transition of DNA: contribution of diffuse ionic interactions.Proceedings of the National Academy of Sciences, 1984
- Simulations of the solvent structure for macromolecules. III. Determination of the Na+ counter ion structureBiopolymers, 1982
- Double Helical DNA: Conformations, Physical Properties, and Interactions with LigandsAnnual Review of Biochemistry, 1981
- Optimised parameters for A-DNA and B-DNABiochemical and Biophysical Research Communications, 1972