Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation 1 1Edited by B. Honig

Steered molecular dynamics investigations of protein function

“…Unfortunately, full atomistic simulations of ion channels embedded in a lipid membrane have to account for thousands of atoms and the time scale of the permeation of even one single ion, of approximately 1 s, is inaccessible to molecular dynamics simulations at present. The extraordinary effort to carry out ns simulations, 57,58 or of a single s simulation, 24 underscores the point. The difficulty in simulating the passing of K ϩ or Na ϩ ions through the channel can be overcome by using SMD, which "speeds up" a process.…”

Sequence-specific binding of counterions toB-DNA

“…A recent MD study thus showed that a Na ϩ ion resides (with Ͼ50% occupancy) at the central ApT step of the A 2 T 2 duplex (13,14), a location that is known to have a uniquely low electrostatic potential (13,15). Another MD study found Na ϩ ions (with 5-40% occupancy) at primary solvation sites throughout the minor and major grooves of the same duplex (16). Even Cl Ϫ ions were found to substitute for primary hydration waters in the minor groove (16).…”

Molecular Simulations of DNA Counterion Distributions

“…Such simulations became possible from the second part of 1990s, when a large number of works on MD simulations of DNA, with full-atomic description of solvent and ions, appeared. [64][65][66][67][68][69][70][71] In the majority of these studies, the main interest was in the DNA molecule itself, investigating DNA backbone structure and dynamics, base stacking, phosphate orientation, overall nucleic acid structure, and so on. (For more information on these issues, the reader is referred to recent reviews.…”

“…[70] However, the hydration structure and ion distribution are very similar in AMBER and CHARMM simulations. [71,75] This is because of the fact that these force fields differ mainly by parameters describing intramolecular DNA interactions, whereas parameters describing forces between water, ions, and DNA are almost the same.…”