ArticleProteins2011
Prechemistry versus preorganization in DNA replication fidelity.
Article in Proteins, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
24 citing papers in PubMed, 39 citations in OpenAlex.
- Analyzing the Reaction of Orotidine 5'-Phosphate Decarboxylase as a Way to Examine Some Key Catalytic Proposals.Journal of the American Chemical Society · 2023Article
- Single-molecule Taq DNA polymerase dynamics.Science advances · 2022Article
- Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis.Biomolecules · 2021Review
- Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution.Chemical reviews · 2020Review
- Exploring the Catalytic Mechanism of Cas9 Using Information Inferred from Endonuclease VII.ACS catalysis · 2019Article
- Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction.Nucleic acids research · 2018Article
- Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis.Proteins · 2017Article
- High-Dimensional Mutant and Modular Thermodynamic Cycles, Molecular Switching, and Free Energy Transduction.Annual review of biophysics · 2017Review
- Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis.Structural dynamics (Melville, N.Y.) · 2017Article
- Uniform Free-Energy Profiles of the P-O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ.The journal of physical chemistry. B · 2016Article
- Article
- 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
- The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- On the challenge of exploring the evolutionary trajectory from phosphotriesterase to arylesterase using computer simulations.The journal of physical chemistry. B · 2015Article
- Conformational effects on the pro-S hydrogen abstraction reaction in cyclooxygenase-1: an integrated QM/MM and MD study.Biophysical journal · 2013Article
- Why nature really chose phosphate.Quarterly reviews of biophysics · 2013Review
- Catalytic effects of mutations of distant protein residues in human DNA polymerase β: theory and experiment.Biochemistry · 2012Article
- Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms.Theoretical chemistry accounts · 2012Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The molecular origin of nucleotide insertion catalysis and fidelity of DNA polymerases is explored by means of computational simulations. Special attention is paid to the examination of the validity of proposals that invoke prechemistry effects, checkpoints concepts, and dynamical effects. The simulations reproduce the observed fidelity in Pol β, starting with the relevant observed X-ray structures of the complex with the right (R) and wrong (W) nucleotides. The generation of free energy surfaces for the R and W systems also allowed us to analyze different proposals about the origin of the fidelity and to reach several important conclusions. It is found that the potential of mean force (PMF) obtained by proper sampling does not support QM/MM-based proposals of a large barrier before the prechemistry state. Furthermore, examination of dynamical proposals by the renormalization approach indicates that the motions from open to close configurations do not contribute to catalysis or fidelity. Finally we discuss and analyze the induced fit concept and show that, despite its importance, it does not explain fidelity. That is, the fidelity is apparently due to the change in the preorganization of the chemical site, as a result of the relaxation of the binding site upon binding of the incorrect nucleotide. Finally and importantly, since the issue is the barrier associated with the enzyme-substrate (ES)/DNA complex at the chemical transition state and not the path to this complex formation (unless this path involves rate determining steps), it is also not useful to invoke checkpoints while discussing fidelity.
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What OpenQuestion holds
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.