ArticleProceedings of the National Academy of Sciences of the United States of America2011
Dynamics and dissipation in enzyme catalysis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed.
- MixPI: Mixed-time slicing path integral software for quantized molecular dynamics simulations.The Journal of chemical physics · 2026Article
- Computational Method for the Detection of Communication Pathways in Enzymes that Correlate with Experimentally Defined Thermal Activation Networks.The journal of physical chemistry letters · 2026Article
- Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy.The Journal of chemical physics · 2023Article
- Alternate Strategies to Induce Dynamically Modulated Transient Transcription Machineries.ACS nano · 2023Article
- A multi-layered computational structural genomics approach enhances domain-specific interpretation of Kleefstra syndrome variants in EHMT1.Computational and structural biotechnology journal · 2023Article
- Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations.Structural dynamics (Melville, N.Y.) · 2021Article
- Catalytic Principles from Natural Enzymes and Translational Design Strategies for Synthetic Catalysts.ACS central science · 2021Review
- Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins.Frontiers in molecular biosciences · 2021Article
- The physical origin of rate promoting vibrations in enzymes revealed by structural rigidity.Scientific reports · 2020Article
- Quantifying the limits of transition state theory in enzymatic catalysis.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Molecular Basis for K63-Linked Ubiquitination Processes in Double-Strand DNA Break Repair: A Focus on Kinetics and Dynamics.Journal of molecular biology · 2017Review
- The role of the MetThe Journal of biological chemistry · 2017Article
- Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease.Journal of the American Chemical Society · 2016Article
- Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.The Journal of chemical physics · 2016Review
- Minimization of dynamic effects in the evolution of dihydrofolate reductase.Chemical science · 2016Article
- Ligand-Dependent Conformational Dynamics of Dihydrofolate Reductase.Biochemistry · 2016Article
- Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase.Angewandte Chemie (International ed. in English) · 2015Article
- Role of dynamics in enzyme catalysis: substantial versus semantic controversies.Accounts of chemical research · 2015Review
- Evolution alters the enzymatic reaction coordinate of dihydrofolate reductase.The journal of physical chemistry. B · 2015Article
- The enzymatic reaction catalyzed by lactate dehydrogenase exhibits one dominant reaction path.Chemical physics · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We use quantized molecular dynamics simulations to characterize the role of enzyme vibrations in facilitating dihydrofolate reductase hydride transfer. By sampling the full ensemble of reactive trajectories, we are able to quantify and distinguish between statistical and dynamical correlations in the enzyme motion. We demonstrate the existence of nonequilibrium dynamical coupling between protein residues and the hydride tunneling reaction, and we characterize the spatial and temporal extent of these dynamical effects. Unlike statistical correlations, which give rise to nanometer-scale coupling between distal protein residues and the intrinsic reaction, dynamical correlations vanish at distances beyond 4-6 Å from the transferring hydride. This work finds a minimal role for nonlocal vibrational dynamics in enzyme catalysis, and it supports a model in which nanometer-scale protein fluctuations statistically modulate--or gate--the barrier for the intrinsic reaction.
Indexed as
Identifiers
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.