Modeling the DNA-solvent interface

Biopolymers
W R Rudnicki, B Montgomery Pettitt

Abstract

We extend the technique of using perpendicular distribution functions to salt solutions around nucleic acids. Both solute density averaged and nonaveraged reference frames are considered and compared. Using a previous simulation of DNA in salt water of over a nanosecond in duration, the aqueous distribution functions were found to be well coveraged, whereas the salt perpendicular distribution functions were less well determined. Three-dimensional density reconstructions reliably showed the prominent solvation features with transferable functions. The number of solute atom types needed for reconstructions of a given precision was determined in the context of the reference simulation data set with the goal of achieving a required level of reconstruction quality.

Citations

Mar 17, 2011·The Journal of Chemical Physics·Bin Lin, B Montgomery Pettitt
Dec 11, 2013·The Journal of Chemical Physics·Kippi M Dyer, B Montgomery Pettitt
Aug 19, 2011·Langmuir : the ACS Journal of Surfaces and Colloids·Tao WeiIgal Szleifer
Sep 28, 2014·Biochimica Et Biophysica Acta·Gillian C LynchB Montgomery Pettitt
Dec 7, 2000·Biophysical Journal·V A MakarovB M Pettitt
May 4, 2016·Scientific Reports·Paul Boynton, Massimiliano Di Ventra
Aug 19, 2000·Journal of Biomolecular Structure & Dynamics·W R RudnickiB Lesyng
Sep 22, 2015·Journal of Chemical Theory and Computation·Bao Linh Nguyen, B Montgomery Pettitt
May 13, 1998·Biopolymers·V A MakarovB M Pettitt
Feb 27, 1999·Journal of Molecular Biology·M Feig, B M Pettitt
Jun 19, 2002·Accounts of Chemical Research·Vladimir MakarovMichael Feig
Feb 16, 2019·Journal of Chemical Theory and Computation·Shu-Ching Ou, B Montgomery Pettitt
Oct 14, 2000·Annual Review of Physical Chemistry·T E Cheatham, P A Kollman
Sep 8, 2010·Biophysical Journal·Jouko J VirtanenKarl F Freed

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