ArticleThe journal of physical chemistry. B2010
Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 31 citations in OpenAlex.
- Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Effect of preprocessing and simulation parameters on the performance of molecular docking studies.Journal of molecular modeling · 2023Article
- QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery.Journal of chemical theory and computation · 2023Article
- New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes.Molecules (Basel, Switzerland) · 2021Review
- Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme.ACS catalysis · 2019Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.Journal of chemical theory and computation · 2017Article
- VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.The Journal of chemical physics · 2016Article
- Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions.Chemistry (Weinheim an der Bergstrasse, Germany) · 2014Article
- Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations.Physical chemistry chemical physics : PCCP · 2014Article
- Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation.Current opinion in chemical biology · 2014Review
- Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- The impact of a ligand binding on strand migration in the SAM-I riboswitch.PLoS computational biology · 2013Article
- Mechanism of the bell-shaped profile of ribonuclease a activity: molecular dynamic approach.The protein journal · 2012Article
- Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis.PLoS biology · 2011Article
- An abridged transition state model to derive structure, dynamics, and energy components of DNA polymerase β fidelity.Biochemistry · 2011Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.