ArticleThe journal of physical chemistry. B2023
Connecting Conformational Motions to Rapid Dynamics in Human Purine Nucleoside Phosphorylase.
Article in The journal of physical chemistry. B, 2023. 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, 11 citations in OpenAlex.
- Substrate-Specific Differences in Catalytic Strategy and Activity across Ketol-Acid Reductoisomerase Variants.The journal of physical chemistry. B · 2026Article
- The Shaping of Enzymatic Free Energy Barriers through the Creation of Rate-Promoting Vibrations via Inter-Residue Cross-Talk on Multiple Time Scales.The journal of physical chemistry. B · 2025Article
- Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Physics-based modeling in the new era of enzyme engineering.Nature computational science · 2025Review
- The Evolution of the Acylation Mechanism inACS catalysis · 2024Article
- Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity.ACS catalysis · 2024Article
- Myosin-Catalyzed ATP Hydrolysis in the Presence of Disease-Causing Mutations: Mavacamten as a Way to Repair Mechanism.The journal of physical chemistry. B · 2024Article
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Correlation of temperature dependence of hydride kinetic isotope effects with donor-acceptor distances in two solvents of different polarities.Organic & biomolecular chemistry · 2023Article
- Protein Dynamics and Enzymatic Catalysis.The journal of physical chemistry. B · 2023Review
- Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling.Methods in enzymology · 2023Review
- Protein dynamics: The future is bright and complicated!Structural dynamics (Melville, N.Y.) · 2023Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The influence of protein motions on enzyme catalysis remains a topic of active discussion. Protein motions occur across a variety of time scales, from vibrational fluctuations in femtoseconds, to collective motions in milliseconds. There have been numerous studies that show conformational motions may assist in catalysis, protein folding, and substrate specificity. It is also known through transition path sampling studies that rapid promoting vibrations contribute to enzyme catalysis. Human purine nucleoside phosphorylase (PNP) is one enzyme that contains both an important conformational motion and a rapid promoting vibration. The slower motion in this enzyme is associated with a loop motion, that when open allows substrate entry and product release but closes over the active site during catalysis. We examine the differences between an unconstrained PNP structure and a PNP structure with constraints on the loop motion. To investigate possible coupling between the slow and fast protein dynamics, we employed transition path sampling, reaction coordinate identification, electric field calculations, and free energy calculations reported here.
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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.