ArticleThe journal of physical chemistry. B2017
Pyrophosphate Release in the Protein HIV Reverse Transcriptase.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Slow PPThe Journal of biological chemistry · 2026Article
- Structural basis of deoxynucleotide addition by HIV-1 RT during reverse transcription.Nature communications · 2024Article
- ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics.Journal of chemical theory and computation · 2022Article
- Transient State Kinetics ofBiochemistry · 2022Article
- 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
- The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning.Biochimica et biophysica acta. General subjects · 2020Article
- Steered molecular dynamic simulations of conformational lock of Cu, Zn-superoxide dismutase.Scientific reports · 2019Article
- Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis.The Journal of biological chemistryArticle
- 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
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Authors and funding
3 authors.
Funding
Abstract
Enzymatic reactions usually occur in several steps: a step of substrate binding to the surface of the protein, a step of protein reorganization around the substrate and conduction of a chemical reaction, and a step of product release. The release of inorganic phosphate-PPi-from the matrix of the protein HIV reverse transcriptase is investigated computationally. Atomically detailed simulations with explicit solvent are analyzed to obtain the free energy profile, mean first passage time, and detailed molecular mechanisms of PPi escape. A challenge for the computations is of time scales. The experimental time scale of the process of interest is in milliseconds, and straightforward molecular dynamics simulations are in sub-microseconds. To overcome the time scale gap, we use the algorithm of Milestoning along a reaction coordinate to compute the overall free energy profile and rate. The methods of locally enhanced sampling and steered molecular dynamics determine plausible reaction coordinates. The observed molecular mechanism couples the transfer of the PPi to positively charged lysine side chains that are found on the exit pathway and to an exiting magnesium ion. In accord with experimental findings, the release rate is comparable to the chemical step, allowing for variations in substrate (DNA or RNA template) in which the release becomes rate determining.
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