ArticleJournal of the American Chemical Society2013
Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 86 citations in OpenAlex.
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- Force fields matter in DNA polProtein science : a publication of the Protein Society · 2026Article
- Structures of an engineered phospholipase D with specificity for secondary alcohol transphosphatidylation: insights into plasticity of substrate binding and activation.The Biochemical journal · 2021Article
- Differences in the Nature of the Phosphoryl Transfer Transition State in Protein Phosphatase 1 and Alkaline Phosphatase: Insights from QM Cluster Models.The journal of physical chemistry. B · 2020Article
- Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Non-Conventional Metal Ion Cofactor Requirement of Dinoflagellate Alkaline Phosphatase and Translational Regulation by Phosphorus Limitation.Microorganisms · 2019Article
- Transition-State Interactions in a Promiscuous Enzyme: Sulfate and Phosphate Monoester Hydrolysis by Pseudomonas aeruginosa Arylsulfatase.Biochemistry · 2019Article
- Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase.Molecules (Basel, Switzerland) · 2018Article
- Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations.Methods in enzymology · 2018Article
- Water is an active matrix of life for cell and molecular biology.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin.Biochemistry · 2017Article
- Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects.Journal of the American Chemical Society · 2016Article
- Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.Journal of the American Chemical Society · 2016Article
- Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer.Biochemistry · 2016Review
- Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.Chemical reviews · 2016Review
- QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes.Methods in enzymology · 2016Article
- DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters.Journal of chemical theory and computation · 2015Article
- Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily.Journal of the American Chemical Society · 2015Article
- Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications.The journal of physical chemistry. B · 2015Article
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 2015Article
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2 authors at 1 institution in 1 country.
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Abstract
The first step for the hydrolysis of a phosphate monoester (pNPP(2-)) in enzymes of the alkaline phosphatase (AP) superfamily, R166S AP and wild-type NPP, is studied using QM/MM simulations based on an approximate density functional theory (SCC-DFTBPR) and a recently introduced QM/MM interaction Hamiltonian. The calculations suggest that similar loose transition states are involved in both enzymes, despite the fact that phosphate monoesters are the cognate substrates for AP but promiscuous substrates for NPP. The computed loose transition states are clearly different from the more synchronous ones previously calculated for diester reactions in the same AP enzymes. Therefore, our results explicitly support the proposal that AP enzymes are able to recognize and stabilize different types of transition states in a single active site. Analysis of the structural features of computed transition states indicates that the plastic nature of the bimetallic site plays a minor role in accommodating multiple types of transition states and that the high degree of solvent accessibility of the AP active site also contributes to its ability to stabilize diverse transition-state structures without the need of causing large structural distortions of the bimetallic motif. The binding mode of the leaving group in the transition state highlights that vanadate may not always be an ideal transition state analog for loose phosphoryl transfer transition states.
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