Open AccessComputation of ionic distributions around charged biomolecular structures: results for right-handed and left-handed DNA.
Author(s) -
Reinhard Klement,
Dikeos Mario Soumpasis,
Thomas M. Jovin
Publication year - 1991
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.88.11.4631
Subject(s) - ionic bonding , dna , macromolecule , ion , chemical physics , conformational isomerism , chemistry , salt (chemistry) , membrane , computation , crystallography , sequence (biology) , biophysics , molecule , biology , computer science , algorithm , biochemistry , organic chemistry
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.