Evidence map›Paper›PMID 37645800›Full record

ArticlebioRxiv : the preprint server for biology2023

Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography.

Nathan Smith, Medhanjali Dasgupta, David C Wych, Cole Dolamore, Raymond G Sierra, Stella Lisova, Darya Marchany-Rivera, Aina E Cohen, Sébastien Boutet, Mark S Hunter and 15 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 3 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

25 authors at 7 institutions in 1 country.

Nathan SmithDepartment of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588.
Medhanjali DasguptaDepartment of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588.
David C WychComputer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 875405.
Cole DolamoreDepartment of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588.
Raymond G SierraLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.
Stella LisovaLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.
Darya Marchany-RiveraStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.
Aina E CohenStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.
Sébastien BoutetLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.
Mark S HunterLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.
Christopher KupitzLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.
Frédéric PoitevinLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.
Frank R MossLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.
Aaron S BrewsterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Nicholas K SauterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Iris D YoungMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Alexander M WolffDepartment of Chemistry and Biochemistry, University of California, Merced, CA, 93540.
Virendra K TiwariDepartment of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588.
Nivesh KumarDepartment of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588.
David B BerkowitzDepartment of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588.
Ryan G HadtDivision of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA USA.
Michael C ThompsonDepartment of Chemistry and Biochemistry, University of California, Merced, CA, 93540.
Alec H FollmerDepartment of Chemistry, University of California-Irvine, Irvine, CA 92697.
Michael E WallComputer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 875405.
Mark A WilsonDepartment of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588.
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
$43.3M
Targeted mass spectrometry approaches to understand CART processing and recepter interactionsP20GM113126 · NIGMS · UNIVERSITY OF NEBRASKA LINCOLN · PI POWERS, ROBERT · 2016 to 2025
$20.8M
Structural Dynamics at LCLSP41GM139687 · NIGMS · STANFORD UNIVERSITY · PI HUNTER, MARK · 2021 to 2025
$7.5M
DIALS: New Computational Methods to Enable Challenging Crystallographic ExperimentsR01GM117126 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI SAUTER, NICHOLAS K · 2016 to 2023
$6.1M
Confining Metal Complexes within Protein Hosts: Models for Metalloprotein Active SitesR01GM120349 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI BOROVIK, ANDREW S. · 2017 to 2024
$2.4M
Understanding 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
$2.1M
EXTRAMURAL RES FACILITIES CONSTRC06RR016544 · NCRR · UNIVERSITY OF NEBRASKA LINCOLN · PI PAUL, PREM S · 2001 to 2001
$2.0M
Time-Resolved X-ray Crystallography of Dynamics in Cysteine-Dependent EnzymesR01GM139978 · NIGMS · UNIVERSITY OF NEBRASKA LINCOLN · PI WILSON, MARK A. · 2020 to 2023
$1.2M
NCRR 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 GM142595
6 · The paper itself

Abstract

Enzymes populate ensembles of structures with intrinsically different catalytic proficiencies that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL) to observe catalysis in a designed mutant (G150T) 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 catalytic intermediate selects for catalytically competent substates. A prior proposal for active site cysteine charge-coupled conformational changes in ICH is validated by determining structures of the enzyme over a range of pH values. A combination of large molecular dynamics simulations of the enzyme in crystallo and time-resolved electron density maps shows that ionization of the general acid Asp17 during catalysis causes additional conformational changes that propagate across the dimer interface, connecting the two active sites. These ionization-linked changes in the ICH conformational ensemble permit water to enter the active site in a location that is poised for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

Indexed as

enzyme dynamicsisonitrileserial crystallographyx-ray free electron laser

Identifiers

PMID37645800
PMCPMC10462001
OpenAlexW4386031146

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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Registered trials

None linked

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.