ArticleJournal of the American Chemical Society2016
Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics.
Article in Journal of the American Chemical Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 51 citations in OpenAlex.
- Substrate-Specific Differences in Catalytic Strategy and Activity across Ketol-Acid Reductoisomerase Variants.The journal of physical chemistry. B · 2026Article
- Cancer-associated TRF1 mutations alter PARP1 interaction dynamics: an in silico study.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Article
- Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity.ACS catalysis · 2024Article
- Structural, Spectroscopic, and Computational Insights from Canavanine-Bound and Two Catalytically Compromised Variants of the Ethylene-Forming Enzyme.Biochemistry · 2024Article
- Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH.Chemical science · 2024Article
- Protein Dynamics and Enzymatic Catalysis.The journal of physical chemistry. B · 2023Review
- Connecting Conformational Motions to Rapid Dynamics in Human Purine Nucleoside Phosphorylase.The journal of physical chemistry. B · 2023Article
- Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling.Methods in enzymology · 2023Review
- Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.Journal of chemical theory and computation · 2022Review
- Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions.Molecules (Basel, Switzerland) · 2022Review
- Article
- Transition Path Sampling Based Calculations of Free Energies for Enzymatic Reactions: The Case of Human Methionine Adenosyl Transferase andThe journal of physical chemistry. B · 2022Article
- Hydride Transfer Mechanism of Enzymatic Sugar Nucleotide C2 Epimerization Probed with a Loose-Fit CDP-Glucose Substrate.ACS catalysis · 2022Article
- Method for Identifying Common Features in Reactive Trajectories of a Transition Path Sampling Ensemble.Journal of chemical theory and computation · 2022Article
- Identification of Thermal Conduits That Link the Protein-Water Interface to the Active Site Loop and Catalytic Base in Enolase.Journal of the American Chemical Society · 2021Article
- Protein Mass-Modulated Effects in Alkaline Phosphatase.Biochemistry · 2021Article
- Role of Protein Motions in Catalysis by Formate Dehydrogenase.The journal of physical chemistry. B · 2020Article
- Multiple Reaction Pathways in the Morphinone Reductase-Catalyzed Hydride Transfer Reaction.ACS omega · 2020Article
- Optimization of the Turnover in Artificial Enzymes via Directed Evolution Results in the Coupling of Protein Dynamics to Chemistry.Journal of the American Chemical Society · 2019Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The relevance of sub-picosecond protein motions to the catalytic event remains a topic of debate. Heavy enzymes (isotopically substituted) provide an experimental tool for bond-vibrational links to enzyme catalysis. A recent transition path sampling study with heavy purine nucleoside phosphorylase (PNP) characterized the experimentally observed mass-dependent slowing of barrier crossing (Antoniou, D.; Ge, X.; Schramm, V. L.; Schwartz, S. D. J. Phys. Chem. Lett. 2012, 3, 3538). Here we computationally identify second-sphere amino acid residues predicted to influence the freedom of the catalytic site vibrational modes linked to heavy enzyme effects in PNP. We mutated heavy and light PNPs to increase the catalytic site vibrational freedom. Enzymatic barrier-crossing rates were converted from mass-dependent to mass-independent as a result of the mutations. The mutagenic uncoupling of femtosecond motions between catalytic site groups and reactants decreased transition state barrier crossing by 2 orders of magnitude, an indication of the femtosecond dynamic contributions to catalysis.
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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.