Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease
Language English Country Netherlands Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
25450173
DOI
10.1016/j.bbagen.2014.10.021
PII: S0304-4165(14)00357-2
Knihovny.cz E-resources
- Keywords
- Cas6 superfamily, Endoribonuclease, Force field, Molecular dynamic simulation, Protein/RNA complex, RNA cleavage,
- MeSH
- CRISPR-Associated Proteins chemistry metabolism MeSH
- Time Factors MeSH
- CRISPR-Cas Systems * MeSH
- Endoribonucleases chemistry metabolism MeSH
- Catalytic Domain MeSH
- Crystallography, X-Ray MeSH
- Clustered Regularly Interspaced Short Palindromic Repeats * MeSH
- Molecular Dynamics Simulation * MeSH
- Protein Binding MeSH
- Binding Sites MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- CRISPR-Associated Proteins MeSH
- Endoribonucleases MeSH
BACKGROUND: Many prokaryotic genomes comprise Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) offering defense against foreign nucleic acids. These immune systems are conditioned by the production of small CRISPR-derived RNAs matured from long RNA precursors. This often requires a Csy4 endoribonuclease cleaving the RNA 3'-end. METHODS: We report extended explicit solvent molecular dynamic (MD) simulations of Csy4/RNA complex in precursor and product states, based on X-ray structures of product and inactivated precursor (55 simulations; ~3.7μs in total). RESULTS: The simulations identify double-protonated His29 and deprotonated terminal phosphate as the likely dominant protonation states consistent with the product structure. We revealed potential substates consistent with Ser148 and His29 acting as the general base and acid, respectively. The Ser148 could be straightforwardly deprotonated through solvent and could without further structural rearrangements deprotonate the nucleophile, contrasting similar studies investigating the general base role of nucleobases in ribozymes. We could not locate geometries consistent with His29 acting as general base. However, we caution that the X-ray structures do not always capture the catalytically active geometries and then the reactive structures may be unreachable by the simulation technique. CONCLUSIONS: We identified potential catalytic arrangement of the Csy4/RNA complex but we also report limitations of the simulation technique. Even for the dominant protonation state we could not achieve full agreement between the simulations and the structural data. GENERAL SIGNIFICANCE: Potential catalytic arrangement of the Csy4/RNA complex is found. Further, we provide unique insights into limitations of simulations of protein/RNA complexes, namely, the influence of the starting experimental structures and force field limitations. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
References provided by Crossref.org
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
