Brownian dynamics simulations of ion atmospheres around polyalanine and B-DNA: Effects of biomolecular dielectric

• Published in: Biopolymers 2003-10, Vol.70 (3), p.391-402
• Main Authors: Cerutti, David S., Wong, Chung F., McCammon, J. Andrew
• Format: Article
• Language: English
• Subjects: Algorithms; Brownian dynamics simulation; Computer Simulation; continuum solvent model; dielectric boundary; DNA - chemistry; Electrochemistry; explicit ions; ion atmosphere; Ions - chemistry; Models, Chemical; Peptides - chemistry; Poisson equation; polyalanine; Protein Structure, Secondary
• ISSN: 0006-3525; 1097-0282
• DOI: 10.1002/bip.10498

We have extended an earlier Brownian dynamics simulation algorithm for simulating the structural dynamics of ions around biomolecules to accommodate dielectric inhomogeneity. The electrostatic environment of a biomolecule immersed in water was obtained by numerically solving the Poisson equation with the biomolecule treated as a low dielectric region and the solvent treated as a high dielectric region. Instead of using the mean‐field type approximations of ion interactions as in the Poisson–Boltzmann model, the ions were treated explicitly by allowing them to evolve dynamically under the electrostatic field of the biomolecule. This model thus accounts for ion–ion correlations and the finite‐size effects of the ions. For a 13‐residue α‐helical polyalanine and a 12‐base‐pair bp B‐form DNA, we found that the choice of the dielectric constant of the biomolecule has much larger effects on the mean ionic structure around the biomolecule than on the fluctuational and dynamical properties of the ions surrounding the biomolecule. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 391–402, 2003