Computation of ionic distributions around charged biomolecular structures: results for right-handed and left-handed DNA.
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.
Klement
R
R
Max-Planck-Institute für Biophysikalische Chemie, Göttingen, Federal Republic of Germany.
Soumpasis
D M
DM
Jovin
T M
TM
D004247:DNA / Q000737:chemistry*; D004573:Electrolytes; D008433:Mathematics; D008958:Models, Molecular; D008962:Models, Theoretical; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry
D004573:Electrolytes; D012313:RNA; D004247:DNA