In the last decade and a half, many RNA structures have been solved, helping illuminate their functions. As scientists probe the practical uses of RNA molecules and study ribozymes, catalytic RNAs, as the basis of the “RNA world” hypothesis, development of models that accurately represent reality is paramount. However, many of the deposited models in the PDB have many geometric issues.<br/><br/>While methods like ERRASER work to remove such geometric inaccuracies, the PHENIX/AMBER interface provides advantages over conventional geometric restraints and ERRASER. These include the ability to perform reciprocal space refinement (in contrast to ERRASER’s real space refinement) and the use of molecular mechanics force fields, including electrostatic energy terms, which are of great importance with charged molecules like RNA.<br/><br/>A set of 21 RNA structures ranging in resolution from 1.04 to 3.6 Å was curated to test this interface’s efficacy in nucleic acid structures. The structures were prepared for use with the AMBER forcefields and then refined using conventional restraints and AMBER forcefields in separate refinements. Refinement with AMBER forcefields provided more more physically accurate structures with fewer clashes and better energetics, especially at low resolution. Further work performing 3D-RISM singlepoint calculations of these structures has also been performed to gain a better understanding of the structures and their solvation.

Analyzing RNA crystal structures with the PHENIX/AMBER interface

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.