University of Chicago Professor and Argonne Joint Appointment Juan de Pablo (MSD) has co-authored a paper in The Journal of Chemical Theory and Computation. The objective of the research is to systematically develop a new, general coarse-grained (CG) model for biologically relevant ions in implicit solvent that is independent of the underlying DNA CG model.
The de Pablo Research Group performs research at the Institute of Molecular Engineering and Argonne that centers on supercomputer simulations to understand and design new materials from scratch and to find applications for them.
Ions are critical to biology, creating potential gradients across cell membranes and acting as active sites for redox chemistry in enzymes. Ions also bind transiently to biological molecules, often modifying their biological activity. This is especially evident in double-stranded DNA (dsDNA), where ions have been implicated in minor groove narrowing,dsDNA toroid formation, and the stabilization of G-quartets. Recently, multivalent ions have been shown to produce heterogeneous dynamics during viral packaging.
We present a general coarse-grained model of sodium, magnesium, spermidine, and chlorine in implicit solvent. The effective potentials between ions are systematically parameterized using a relative entropy coarse-graining approach [Carmichael, S. P. and M. S. Shell, J. Phys. Chem. B, 116, 8383-93 (2012)] that maximizes the information retained in a coarse-grained model.
We describe the local distribution of ions in the vicinity of a recently-published coarse-grained DNA model and demonstrate a dependence of persistence length on ionic strength that differs from that predicted by Odijk-Skolnick-Fixman theory. Consistent with experimental observations, we show that spermidine induces DNA condensation, while magnesium and sodium do not. This model can be used alongside any coarse-grained DNA model that has explicit charges and an accurate reproduction of the excluded volume of dsDNA.
Daniel Mark Hinckley and Juan J. de Pablo, “Coarse-grained Ions for Nucleic Acid Modeling,” The Journal of Chemical Theory and Computation, Just Accepted Manuscript. DOI: 10.1021/acs.jctc.5b00341, Published Online September 29, 2015.