ArticleThe journal of physical chemistry. B2010
Conformational dynamics in human purine nucleoside phosphorylase with reactants and transition-state analogues.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 26 citations in OpenAlex.
- Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations.Journal of computer-aided molecular design · 2021Article
- A Biophysical Perspective on Enzyme Catalysis.Biochemistry · 2019Article
- Enzymatic Transition States and Drug Design.Chemical reviews · 2018Review
- Intracellular rebinding of transition-state analogues provides extendedThe Journal of biological chemistry · 2017Article
- Heat Capacity Changes for Transition-State Analogue Binding and Catalysis with Human 5'-Methylthioadenosine Phosphorylase.ACS chemical biology · 2017Article
- Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics.Journal of the American Chemical Society · 2016Article
- Transition States and transition state analogue interactions with enzymes.Accounts of chemical research · 2015Article
- The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.Nature communications · 2015Article
- Conformational freedom in tight binding enzymatic transition-state analogues.The journal of physical chemistry. B · 2013Article
- Catalytic site conformations in human PNP by 19F-NMR and crystallography.Chemistry & biology · 2013Article
- Transition States, analogues, and drug development.ACS chemical biology · 2013Review
- Mass Modulation of Protein Dynamics Associated with Barrier Crossing in Purine Nucleoside Phosphorylase.The journal of physical chemistry letters · 2012Article
- Density functional study on the derivatives of purine.Journal of molecular modeling · 2012Article
- Investigation of catalytic loop structure, dynamics, and function relationship of Yersinia protein tyrosine phosphatase by temperature-jump relaxation spectroscopy and X-ray structural determination.The journal of physical chemistry. B · 2012Article
- Femtosecond dynamics coupled to chemical barrier crossing in a Born-Oppenheimer enzyme.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Arsenate and phosphate as nucleophiles at the transition states of human purine nucleoside phosphorylase.Biochemistry · 2011Article
- Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes.Annual review of biochemistry · 2011Review
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Dynamic motions of human purine nucleoside phosphorylase (hPNP) in complex with transition-state analogues and reactants were studied using 10 ns explicit solvent molecular dynamics simulations. hPNP is a homotrimer that catalyzes the phosphorolysis of purine 6-oxynucleosides. The ternary complex of hPNP includes the binding of a ligand and phosphate to the active site. Molecular dynamics simulations were performed on the ternary complex of six ligands including the picomolar transition-state analogues, Immucillin-H (K(d) = 56 pM), DADMe-Immucillin-H (K(d) = 8.5 pM), DATMe-Immucillin-H (K(d) = 8.6 pM), SerMe-Immucillin-H (K(d) = 5.2 pM), the substrate inosine, and a complex containing only phosphate. Protein-inhibitor complexes of the late transition-state inhibitors, DADMe-Imm-H and DATMe-Imm-H, are inflexible. Despite the structural similarity of SerMe-Imm-H and DATMe-Imm-H, the protein complex of SerMe-Imm-H is flexible, and the inhibitor is highly mobile within the active sites. All inhibitors exhibit an increased number of nonbonding interactions in the active site relative to the substrate inosine. Water density within the catalytic site is lower for DADMe-ImmH, DATMe-Imm-H, and SerMe-Imm-H than that for the substrate inosine. Tight binding of the picomolar inhibitors results from increased interactions within the active site and a reduction in the number of water molecules organized within the catalytic site relative to the substrate inosine.
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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.