Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation

The Journal of Physical Chemistry B vol. 123  p. 4611-4624  DOI: 10.1021/acs.jpcb.8b11923
PMID/PMCID: PMC6614744 Published: 2019-04-19 

Şölen Ekesan [ ] , Darrin M. York [ ]

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Crystal simulations provide useful tools, along with solution simulations, to test nucleic acid force fields, but should be interpreted with care owing to the difficulty of establishing the environmental conditions needed to reproduce experimental crystal packing. These challenges underscore the need to construct proper protocols for carrying out crystal simulations and analyzing results to identify the origin of deviations from crystallographic data. Toward this end, we introduce a novel framework for B-factor decomposition into additive intramolecular, rotational, and translational atomic fluctuation components and partitioning of each of these components into individual asymmetric unit and lattice contributions. We apply the framework to a benchmark set of A-DNA, Z-DNA, and B-DNA double helix systems of various chain lengths. Overall, the intramolecular deviations from the crystal were quite small (≤1.0 Å), suggesting high accuracy of the force field, whereas crystal packing was not well reproduced. The present work establishes a framework to conduct and analyze crystal simulations that ultimately take on issues of crystal packing and can provide insight into nucleic acid force fields.