Evidence map›Paper›PMID 37723259›Full record

ArticleNature chemistry2023

Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.

Alexander M Wolff, Eriko Nango, Iris D Young, Aaron S Brewster, Minoru Kubo, Takashi Nomura, Michihiro Sugahara, Shigeki Owada, Benjamin A Barad, Kazutaka Ito and 15 more

Open access · hybridAbstract read
In one paragraph

Article in Nature chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.

0numbers the graph read from it
0cells of the map it votes in
54citing papers in PubMed
6.1field-weighted citation impact, top 2% of its field
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

54 citing papers in PubMed, 64 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

25 authors at 13 institutions in 2 countries.

Alexander M WolffDepartment of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA.ORCID 0000-0003-0474-7673
Eriko NangoRIKEN SPring-8 Center, Sayo-gun, Japan. eriko.nango.c4@tohoku.ac.jp.ORCID 0000-0001-9851-7355
Iris D YoungDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
Aaron S BrewsterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0002-0908-7822
Minoru KuboRIKEN SPring-8 Center, Sayo-gun, Japan.ORCID 0000-0002-1470-942X
Takashi NomuraRIKEN SPring-8 Center, Sayo-gun, Japan.
Michihiro SugaharaRIKEN SPring-8 Center, Sayo-gun, Japan.
Shigeki OwadaRIKEN SPring-8 Center, Sayo-gun, Japan.
Benjamin A BaradDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.ORCID 0000-0002-1016-862X
Kazutaka ItoLaboratory for Drug Discovery, Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, Izunokuni-shi, Japan.ORCID 0000-0002-5704-4771
Asmit BhowmickMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0002-6154-6635
Sergio CarbajoSLAC National Accelerator Laboratory, Linac Coherent Light Source, Menlo Park, CA, USA.ORCID 0000-0002-5292-4470
Tomoya HinoDepartment of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan.
James M HoltonMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0002-0596-0137
Dohyun ImDepartment of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Japan.
Lee J O'RiordanMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Tomoyuki TanakaRIKEN SPring-8 Center, Sayo-gun, Japan.
Rie TanakaRIKEN SPring-8 Center, Sayo-gun, Japan.ORCID 0000-0003-1062-4792
Raymond G SierraSLAC National Accelerator Laboratory, Linac Coherent Light Source, Menlo Park, CA, USA.ORCID 0000-0002-6253-8282
Fumiaki YumotoStructural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Japan.
Kensuke TonoRIKEN SPring-8 Center, Sayo-gun, Japan.ORCID 0000-0003-1218-3759
So IwataRIKEN SPring-8 Center, Sayo-gun, Japan.ORCID 0000-0003-1735-2937
Nicholas K SauterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0003-2786-6552
James S FraserDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.ORCID 0000-0002-5080-2859
Michael C ThompsonDepartment of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA. mthompson30@ucmerced.edu.ORCID 0000-0002-6099-2027
Lawrence Berkeley National Laboratory · USKyoto University · JPSPring-8 · JPUniversity of California, Merced · USUniversity of Hyogo · JPAsahi Kasei (Japan) · JPHigh Energy Accelerator Research Organization · JPScripps Institution of Oceanography · USSLAC National Accelerator Laboratory · USTohoku University · JPTottori University · JPUniversity of California, Los Angeles · USUniversity of California, San Francisco · US

Funding

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
Molecular Biophysics Training GrantT32GM149436 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Aashish Manglik · 2023 to 2026
$1.6M
NIGMS NIH HHS R01 GM117126NIGMS NIH HHS T32 GM149436
6 · The paper itself

Abstract

Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

Indexed as

ProteinsCrystallography, X-RayModels, MolecularMolecular ConformationProtein ConformationTemperatureProteins

Identifiers

PMID37723259
PMCPMC10624634
OpenAlexW4386825780

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Registered trials

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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.