ArticleScience advances2024
Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography.
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Article in Science advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13citing papers in PubMed
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13 citing papers in PubMed, 15 citations in OpenAlex.
- Multistate Enzyme Design Enables Efficient and Stereoselective Multistep Catalysis.bioRxiv : the preprint server for biology · 2026Article
- Minimized sample consumption for time-resolved serial crystallography applied to the redox cycle of human NQO1.Communications chemistry · 2026Article
- Real-time capture of domain movements during copper amine oxidase catalysis by mix-and-inject serial crystallography.Nature communications · 2025Article
- Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis.Journal of chemical information and modeling · 2025Article
- Semi-automated modeling of reaction states in time-resolved serial femtosecond crystallography using molecular dynamics sampled conformations.Structural dynamics (Melville, N.Y.) · 2025Article
- Preparing for successful protein crystallization experiments.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Advances in microfluidic mixers for time-resolved structural biology with X-rays.Biophysical reviews · 2025Review
- Macromolecular crystallography and biology at the Linac Coherent Light Source.Journal of synchrotron radiation · 2025Article
- X-ray Absorption Spectroscopy of Dilute Metalloenzymes at X-ray Free-Electron Lasers in a Shot-by-Shot Mode.The journal of physical chemistry letters · 2025Article
- Laue-DIALS: Open-source software for polychromatic x-ray diffraction data.Structural dynamics (Melville, N.Y.) · 2024Article
- A snapshot love story: what serial crystallography has done and will do for us.Acta crystallographica. Section D, Structural biology · 2024Review
- Laue-DIALS: open-source software for polychromatic X-ray diffraction data.bioRxiv : the preprint server for biology · 2024Article
- Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
26 authors at 7 institutions in 1 country.
Nathan SmithDepartment of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.ORCID 0000-0003-2785-2345
Medhanjali DasguptaDepartment of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
David C WychComputer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 875405, USA.
Cole DolamoreDepartment of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
Raymond G SierraLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.ORCID 0000-0002-6253-8282
Stella LisovaLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.
Darya Marchany-RiveraStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.ORCID 0000-0001-5462-4562
Aina E CohenStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.ORCID 0000-0003-2414-9427
Sébastien BoutetLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.ORCID 0000-0003-3928-1244
Mark S HunterLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.
Christopher KupitzLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.ORCID 0000-0002-7940-3042
Frédéric PoitevinLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.ORCID 0000-0002-3181-8652
Frank R MossLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.ORCID 0000-0002-6149-6447
David W Mittan-MoreauMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0002-3193-571X
Aaron S BrewsterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0002-0908-7822
Nicholas K SauterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0003-2786-6552
Iris D YoungMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0003-4713-9504
Alexander M WolffDepartment of Chemistry and Biochemistry, University of California, Merced, CA 95340, USA.ORCID 0000-0003-0474-7673
Virendra K TiwariDepartment of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
Nivesh KumarDepartment of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
David B BerkowitzDepartment of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
Ryan G HadtDivision of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Michael C ThompsonDepartment of Chemistry and Biochemistry, University of California, Merced, CA 95340, USA.ORCID 0000-0002-6099-2027
Alec H FollmerDepartment of Chemistry, University of California-Irvine, Irvine, CA 92697, USA.ORCID 0000-0002-6244-6804
Michael E WallComputer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 875405, USA.ORCID 0000-0003-1000-688X
Mark A WilsonDepartment of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.ORCID 0000-0001-6317-900X
SLAC National Accelerator Laboratory · USUniversity of Nebraska–Lincoln · USLawrence Berkeley National Laboratory · USLos Alamos National Laboratory · USUniversity of California, Merced · USCalifornia Institute of Technology · USUniversity of California, Irvine · US
Funding
A Synchrotron Radiation Structural Biology ResourcesP30GM133894 · NIGMS · STANFORD UNIVERSITY · PI Aina E. Cohen, KEITH O HODGSON · 2020 to 2026
$43.3MTargeted mass spectrometry approaches to understand CART processing and recepter interactionsP20GM113126 · NIGMS · UNIVERSITY OF NEBRASKA LINCOLN · PI POWERS, ROBERT · 2016 to 2025
$20.8MStructural Dynamics at LCLSP41GM139687 · NIGMS · STANFORD UNIVERSITY · PI HUNTER, MARK · 2021 to 2025
$7.5MDIALS: New Computational Methods to Enable Challenging Crystallographic ExperimentsR01GM117126 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI SAUTER, NICHOLAS K · 2016 to 2023
$6.1MConfining Metal Complexes within Protein Hosts: Models for Metalloprotein Active SitesR01GM120349 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI BOROVIK, ANDREW S. · 2017 to 2024
$2.4MUnderstanding Geometric and Electronic Structure Contributions to Ground and Excited State Cu- and Ni-Catalyzed Cross-Coupling ReactionsR35GM142595 · NIGMS · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI HADT, RYAN G · 2021 to 2025
$2.1MEXTRAMURAL RES FACILITIES CONSTRC06RR016544 · NCRR · UNIVERSITY OF NEBRASKA LINCOLN · PI PAUL, PREM S · 2001 to 2001
$2.0MHigh-end X-ray Detector System for Femtosecond CrystallographyS10OD023453 · OD · STANFORD UNIVERSITY · PI BOUTET, SEBASTIEN · 2017 to 2017
$1.7MTime-Resolved X-ray Crystallography of Dynamics in Cysteine-Dependent EnzymesR01GM139978 · NIGMS · UNIVERSITY OF NEBRASKA LINCOLN · PI WILSON, MARK A. · 2020 to 2023
$1.2MNCRR NIH HHS C06 RR016544NIGMS NIH HHS P20 GM113126NIGMS NIH HHS P30 GM133894NIGMS NIH HHS P41 GM139687NIGMS NIH HHS R01 GM117126NIGMS NIH HHS R01 GM120349NIGMS NIH HHS R01 GM139978NIGMS NIH HHS R35 GM142595NIH HHS S10 OD023453
Abstract
Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp
Indexed as
Molecular Dynamics SimulationProteinsCatalysisCrystallography, X-RayHydrolasesProtein ConformationHydrolasesProteins
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