Computation of Ionic Distributions Around Charged Biomolecular Structures: Results for Right-handed and Left-handed DNA

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1991 Jun 1

PMID 1711205

Citations 11

Authors

R Klement

D M Soumpasis

T M Jovin

Affiliations

Soon will be listed here.

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.

Citing Articles

Solvent-induced free energy landscape and solute-solvent dynamic coupling in a multielement solute.

San Biagio P, Martorana V, Bulone D, Palma-Vittorelli M, Palma M Biophys J. 2010; 77(5):2470-8.

PMID: 20540927 PMC: 1300523. DOI: 10.1016/S0006-3495(99)77083-9.

Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms.

Thiyagarajan S, Rajan S, Gautham N Nucleic Acids Res. 2004; 32(19):5945-53.

PMID: 15534365 PMC: 528804. DOI: 10.1093/nar/gkh919.

A unified theory of the B-Z transition of DNA in high and low concentrations of multivalent ions.

Gueron M, Demaret J, Filoche M Biophys J. 2000; 78(2):1070-83.

PMID: 10653820 PMC: 1300710. DOI: 10.1016/s0006-3495(00)76665-3.

Conformational equilibria of alkanes in aqueous solution: relationship to water structure near hydrophobic solutes.

Ashbaugh H, Garde S, Hummer G, Kaler E, Paulaitis M Biophys J. 1999; 77(2):645-54.

PMID: 10423414 PMC: 1300360. DOI: 10.1016/S0006-3495(99)76920-1.

Ion-induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study.

Bassi G, Murchie A, Walter F, Clegg R, Lilley D EMBO J. 1998; 16(24):7481-9.

PMID: 9405376 PMC: 1170347. DOI: 10.1093/emboj/16.24.7481.

References

Soumpasis D, Jovin T . B-Z DNA conformational transition in 1:1 electrolytes: dependence upon counterion size. FEBS Lett. 1987; 213(2):341-4. DOI: 10.1016/0014-5793(87)81519-3. View

Jayaram B, Sharp K, Honig B . The electrostatic potential of B-DNA. Biopolymers. 1989; 28(5):975-93. DOI: 10.1002/bip.360280506. View

Garcia A, Soumpasis D . Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution. Proc Natl Acad Sci U S A. 1989; 86(9):3160-4. PMC: 287086. DOI: 10.1073/pnas.86.9.3160. View

Soumpasis D . Salt dependence of DNA structural stabilities in solution. Theoretical predictions versus experiments. J Biomol Struct Dyn. 1988; 6(3):563-74. DOI: 10.1080/07391102.1988.10506507. View

Soumpasis D, Wiechen J, Jovin T . Relative stabilities and transitions of DNA conformations in 1:1 electrolytes: a theoretical study. J Biomol Struct Dyn. 1987; 4(4):535-52. DOI: 10.1080/07391102.1987.10507658. View

Pack G, Klein B . Generalized Poisson-Boltzmann calculation of the distribution of electrolyte ions around the B- and Z-conformers of DNA. Biopolymers. 1984; 23(12):2801-23. DOI: 10.1002/bip.360231208. View

Arnott S, Hukins D . Optimised parameters for A-DNA and B-DNA. Biochem Biophys Res Commun. 1972; 47(6):1504-9. DOI: 10.1016/0006-291X(72)90243-4. View

Soumpasis D . Statistical mechanics of the B----Z transition of DNA: contribution of diffuse ionic interactions. Proc Natl Acad Sci U S A. 1984; 81(16):5116-20. PMC: 391648. DOI: 10.1073/pnas.81.16.5116. View

Record Jr M, Mazur S, Melancon P, Roe J, Shaner S, Unger L . Double helical DNA: conformations, physical properties, and interactions with ligands. Annu Rev Biochem. 1981; 50:997-1024. DOI: 10.1146/annurev.bi.50.070181.005025. View

10.

Clementi E, Corongiu G . Simulations of the solvent structure for macromolecules. III. Determination of the Na+ counter ion structure. Biopolymers. 1982; 21(4):763-77. DOI: 10.1002/bip.360210404. View

11.

Wang A, QUIGLEY G, Kolpak F, van der Marel G, VAN Boom J, Rich A . Left-handed double helical DNA: variations in the backbone conformation. Science. 1981; 211(4478):171-6. DOI: 10.1126/science.7444458. View

12.

Drew H, Takano T, Tanaka S, Itakura K, DICKERSON R . High-salt d(CpGpCpG), a left-handed Z' DNA double helix. Nature. 1980; 286(5773):567-73. DOI: 10.1038/286567a0. View

13.

Record Jr M, Anderson C, Lohman T . Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q Rev Biophys. 1978; 11(2):103-78. DOI: 10.1017/s003358350000202x. View

14.

Klement R, Soumpasis D, Kitzing E, Jovin T . Inclusion of ionic interactions in force field calculations of charged biomolecules--DNA structural transitions. Biopolymers. 1990; 29(6-7):1089-103. DOI: 10.1002/bip.360290620. View