Paper Citing NAMD - Abstract
Savelyev, Alexey; MacKerell, Alexander D., Jr.
Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li+, Na+, K+, and Rb+ via Water-Mediated Hydrogen Bonding
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4473-4485, SEP 2015
Recently, we reported the differential impact of the monovalent cations Li+, Na+, K+, and Rb+ on DNA conformational properties. These were identified from variations in the calculated solution-state X-ray DNA spectra as a function of the ion type in solvation buffer in MD simulations using our recently developed polarizable force field based on the classical Drude oscillator. Changes in the DNA structure were found to mainly involve variations in the minor groove width. Because minor groove dimensions vary significantly in protein DNA complexes and have been shown to play a critical role in both specific and nonspecific DNA readout, understanding the origins of the observed differential DNA modulation by the first-group monovalent ions is of great biological importance. In the present study, we show that the primary microscopic mechanism for the phenomenon is the formation of water-mediated hydrogen bonds between solvated cations located inside the minor groove and simultaneously to two DNA strands, a process whose intensity and impact on DNA structure depends on both the type of ion and the DNA sequence. Additionally, it is shown that the formation of such ion-DNA hydrogen bond complexes appreciably modulates the conformation of the backbone by increasing the population of the BIT substate. Notably, the differential impact of the ions on DNA conformational behavior is only predicted by the Drude polarizable model for DNA with virtually no effect observed from MD simulations utilizing the additive CHARNIM36 model. Analysis of dipole moments of the water shows the Drude SWM4 model to possess high sensitivity to changes in the local environment, which indicates the important role of electronic polarization in the salt-dependent conformational properties. This also suggests that inclusion of polarization effects is required to model even relatively simple biological systems, such as DNA, in various ionic solutions.
