ArticleThe journal of physical chemistry. B2015
Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed.
- Understanding the Fidelity and Specificity of DNA Polymerase I.ACS omega · 2025Article
- Molecular dynamics of the viral life cycle: progress and prospects.Current opinion in virology · 2021Review
- Catalytic Magnesium as a Door Stop for DNA Sliding.The journal of physical chemistry. B · 2021Article
- Structural Mechanism of ω-Currents in a Mutated Kv7.2 Voltage Sensor Domain from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2021Article
- Exploring the Reaction Mechanism of HIV Reverse Transcriptase with a Nucleotide Substrate.The journal of physical chemistry. B · 2020Article
- ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory.Journal of chemical theory and computation · 2020Article
- Insights into DNA polymerase δ's mechanism for accurate DNA replication.Journal of molecular modeling · 2019Article
- New standards for collecting and fitting steady state kinetic data.Beilstein journal of organic chemistry · 2019Review
- Revealing the distinct folding phases of an RNA three-helix junction.Nucleic acids research · 2018Article
- Pyrophosphate Release in the Protein HIV Reverse Transcriptase.The journal of physical chemistry. B · 2017Article
- DNA Polymerase β Cancer-Associated Variant I260M Exhibits Nonspecific Selectivity toward the β-γ Bridging Group of the Incoming dNTP.Biochemistry · 2017Article
- A new general method for simultaneous fitting of temperature and concentration dependence of reaction rates yields kinetic and thermodynamic parameters for HIV reverse transcriptase specificity.The Journal of biological chemistry · 2017Article
- A Change in the Rate-Determining Step of Polymerization by the K289M DNA Polymerase β Cancer-Associated Variant.Biochemistry · 2017Article
- Path-sampling strategies for simulating rare events in biomolecular systems.Current opinion in structural biology · 2017Review
- Rate-limiting Pyrophosphate Release by HIV Reverse Transcriptase Improves Fidelity.The Journal of biological chemistry · 2016Article
- Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β.Proteins · 2016Article
- Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.The Journal of chemical physics · 2016Review
- Induced Fit in the Selection of Correct versus Incorrect Nucleotides by DNA Polymerase β.Biochemistry · 2016Article
- Conformational dynamics during high-fidelity DNA replication and translocation defined using a DNA polymerase with a fluorescent artificial amino acid.The Journal of biological chemistryArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Atomically detailed simulations of HIV RT are performed to investigate the contributions of the conformational transition to the overall rate and specificity of enzyme catalysis. A number of different scenarios are considered within Milestoning theory to provide a more complete picture of the process of opening and closing the enzyme. We consider the open to closed transition in the absence of and with the correct and incorrect substrates. We also consider the free energy profile and the kinetics of the conformational change after the chemistry step in which a new base was added to the DNA, but the DNA was not yet displaced. We partition the free energy along the reaction coordinate and analyze the importance of different protein domains. Strikingly, significant influence on the free energy profile is detected for amino acids far from the active site. The overall long-range impact is about 50 percent of the total. We also illustrate that the overall rate is not necessarily determined by the highest free energy barrier along the reaction path (with respect to the free enzyme and substrate) and that the specificity is not necessarily determined by the same reaction step that determines the rate.
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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.