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

Abstract

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.

Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme

“…Nonetheless, RNA is known to exhibit a high degree of conformational heterogeneity, [54][55][56][57] and the active state of ribozymes capable of performing catalysis are often not the most probable ground states in solution. 18,31,32,58 Simulation results presented here support the supposition that there exists a plausible alternative active site structure that positions G42 as the general base, fits the L-platform/L-scaffold framework and has a catalytically relevant occupancy in solution. In this scenario, it is possible that both states are accessible and can contribute to catalysis via different pathways.…”

Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology

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“…Only one simulation (sim 1) has an overall RMSD >2.9 Å from the crystal structure and appears to be somewhat of an outlier. Figure 1D compares atomic fluctuations ( 59 ) ( \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\langle \sigma_i \rangle$\end{document} , averaged for each nucleotide i ) from the solution simulations and derived from the crystallographic data. The fluctuations are generally similar, with the largest discrepancies in the P1 (nucleotides 65–69) and P3 regions where stabilizing crystal contacts (indicated by shading) are not present in solution.…”