ArticleProceedings of the National Academy of Sciences of the United States of America2009
Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. 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, 74 citations in OpenAlex.
- DFT Benchmarking for [FeACS omega · 2025Article
- Advancements in bioscavenger mediated detoxification of organophosphorus poisoning.Toxicology research · 2024Review
- Warfare Nerve Agents and Paraoxonase-1 as a Potential Prophylactic Therapy against Intoxication.Protein and peptide letters · 2024Review
- Probing the Suitability of Different CaMolecules (Basel, Switzerland) · 2021Article
- Theoretical Studies on Catalysis Mechanisms of Serum Paraoxonase 1 and Phosphotriesterase Diisopropyl Fluorophosphatase Suggest the Alteration of Substrate Preference from Paraoxonase to DFP.Molecules (Basel, Switzerland) · 2018Article
- Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering.Journal of the American Chemical Society · 2017Article
- Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules.Molecules (Basel, Switzerland) · 2017Review
- Review
- Organophosphate-Hydrolyzing Enzymes as First-Line of Defence Against Nerve Agent-Poisoning: Perspectives and the Road Ahead.The protein journal · 2016Review
- XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement.Acta crystallographica. Section D, Structural biology · 2016Article
- Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP γ-Phosphate.The Journal of biological chemistry · 2015Article
- Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Preliminary time-of-flight neutron diffraction studies of Escherichia coli ABC transport receptor phosphate-binding protein at the Protein Crystallography Station.Acta crystallographica. Section F, Structural biology communications · 2014Article
- Hydrolysis of DFP and the nerve agent (S)-sarin by DFPase proceeds along two different reaction pathways: implications for engineering bioscavengers.The journal of physical chemistry. B · 2014Article
- Seeing the chemistry in biology with neutron crystallography.Physical chemistry chemical physics : PCCP · 2013Article
- Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase.BMC research notes · 2013Article
- Bending stiffness of biological membranes: what can be measured by neutron spin echo?The European physical journal. E, Soft matter · 2013Article
- Catalytic mechanisms for phosphotriesterases.Biochimica et biophysica acta · 2013Review
- Mechanistic Insights into the Hydrolysis of Organophosphorus Compounds by Paraoxonase-1: Exploring the Limits of Substrate Tolerance in a Promiscuous Enzyme.Journal of physical organic chemistry · 2012Article
- Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Hydrogen atoms constitute about half of all atoms in proteins and play a critical role in enzyme mechanisms and macromolecular and solvent structure. Hydrogen atom positions can readily be determined by neutron diffraction, and as such, neutron diffraction is an invaluable tool for elucidating molecular mechanisms. Joint refinement of neutron and X-ray diffraction data can lead to improved models compared with the use of neutron data alone and has now been incorporated into modern, maximum-likelihood based crystallographic refinement programs like CNS. Joint refinement has been applied to neutron and X-ray diffraction data collected on crystals of diisopropyl fluorophosphatase (DFPase), a calcium-dependent phosphotriesterase capable of detoxifying organophosphorus nerve agents. Neutron omit maps reveal a number of important features pertaining to the mechanism of DFPase. Solvent molecule W33, coordinating the catalytic calcium, is a water molecule in a strained coordination environment, and not a hydroxide. The smallest Ca-O-H angle is 53 degrees, well beyond the smallest angles previously observed. Residue Asp-229, is deprotonated, supporting a mechanism involving nucleophilic attack by Asp-229, and excluding water activation by the catalytic calcium. The extended network of hydrogen bonding interactions in the central water filled tunnel of DFPase is revealed, showing that internal solvent molecules form an important, integrated part of the overall structure.
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