Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease

• Published in: Biochimica et biophysica acta Vol. 1850; no. 5; pp. 1072 - 1090
• Main Authors: Estarellas, Carolina, Otyepka, Michal, Koča, Jaroslav, Banáš, Pavel, Krepl, Miroslav, Šponer, Jiří
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.05.2015
• Subjects: Binding Sites; Cas6 superfamily; Catalytic Domain; Clustered Regularly Interspaced Short Palindromic Repeats; CRISPR-Associated Proteins - chemistry; CRISPR-Associated Proteins - metabolism; CRISPR-Cas Systems; Crystallography, X-Ray; Endoribonuclease; Endoribonucleases - chemistry; Endoribonucleases - metabolism; Force field; genome; immune system; Molecular dynamic simulation; molecular dynamics; Molecular Dynamics Simulation; phosphates; Protein Binding; Protein/RNA complex; RNA cleavage; RNA precursors; solvents; Time Factors; X-radiation; Force field; Molecular dynamic simulation; Cas6 superfamily; RNA cleavage; Endoribonuclease; Protein/RNA complex
• ISSN: 0304-4165; 0006-3002; 1872-8006
• DOI: 10.1016/j.bbagen.2014.10.021

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. 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). 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. 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. 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. [Display omitted] •Extensive MD simulations of Csy4/RNA endonuclease product and precursor were done.•Atomistic structure consistent with His29/Ser148 general acid/base role is reported.•The dominant protonation states of the product X-ray structure are predicted.•Limitations of the simulation methodology are illustrated and discussed.