Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography
18 pags, 11 figs, 5 tabs
| Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2021 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/258729 |
| Acceso en línea: | http://hdl.handle.net/10261/258729 https://api.elsevier.com/content/abstract/scopus_id/85118931472 |
| Access Level: | acceso abierto |
| Palabra clave: | European X-ray Free-Electron Laser X-ray crystallography Antibiotic resistance Ceftriaxone Drug discovery Enzyme kinetics Enzyme mechanisms Irreversible inhibition Megahertz pulse-repetition rate Mix-and-inject serial crystallography Protein structure determination Serial femtosecond crystallography Substrate diffusion in crystals Sulbactam β-lactamases |
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oai:digital.csic.es:10261/258729 |
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España |
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| dc.title.none.fl_str_mv |
Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography |
| title |
Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography |
| spellingShingle |
Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography Pandey, Suraj European X-ray Free-Electron Laser X-ray crystallography Antibiotic resistance Ceftriaxone Drug discovery Enzyme kinetics Enzyme mechanisms Irreversible inhibition Megahertz pulse-repetition rate Mix-and-inject serial crystallography Protein structure determination Serial femtosecond crystallography Substrate diffusion in crystals Sulbactam β-lactamases |
| title_short |
Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography |
| title_full |
Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography |
| title_fullStr |
Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography |
| title_full_unstemmed |
Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography |
| title_sort |
Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography |
| dc.creator.none.fl_str_mv |
Pandey, Suraj Calvey, George Katz, Andrea M. Malla, Tek Narsingh Koua, Faisal H. M. Martín-García, José M. Poudyal, Ishwor Yang, Jay-How Vakili, Mohammad Yefanov, Oleksandr Zielinski, Kara A. Bajt, Sasa Awel, Salah Doerner, Katarina Frank, Matthias Gelisio, Luca Jernigan, Rebecca Kirkwood, Henry Kloos, Marco Koliyadu, Jayanath Mariani, Valerio Miller, Mitchell D. Mills, Grant Nelson, Garrett Olmos, Jose L. Sadri, Alireza Sato, Tokushi Tolstikova, Alexandra Xu, Weijun Ourmazd, Abbas Spence, John C. H. Schwander, Peter Barty, Anton Chapman, Henry N. Fromme, Petra Mancuso, Adrian P. Phillips, George N. Bean, Richard Pollack, Lois Schmidt, Marius |
| author |
Pandey, Suraj |
| author_facet |
Pandey, Suraj Calvey, George Katz, Andrea M. Malla, Tek Narsingh Koua, Faisal H. M. Martín-García, José M. Poudyal, Ishwor Yang, Jay-How Vakili, Mohammad Yefanov, Oleksandr Zielinski, Kara A. Bajt, Sasa Awel, Salah Doerner, Katarina Frank, Matthias Gelisio, Luca Jernigan, Rebecca Kirkwood, Henry Kloos, Marco Koliyadu, Jayanath Mariani, Valerio Miller, Mitchell D. Mills, Grant Nelson, Garrett Olmos, Jose L. Sadri, Alireza Sato, Tokushi Tolstikova, Alexandra Xu, Weijun Ourmazd, Abbas Spence, John C. H. Schwander, Peter Barty, Anton Chapman, Henry N. Fromme, Petra Mancuso, Adrian P. Phillips, George N. Bean, Richard Pollack, Lois Schmidt, Marius |
| author_role |
author |
| author2 |
Calvey, George Katz, Andrea M. Malla, Tek Narsingh Koua, Faisal H. M. Martín-García, José M. Poudyal, Ishwor Yang, Jay-How Vakili, Mohammad Yefanov, Oleksandr Zielinski, Kara A. Bajt, Sasa Awel, Salah Doerner, Katarina Frank, Matthias Gelisio, Luca Jernigan, Rebecca Kirkwood, Henry Kloos, Marco Koliyadu, Jayanath Mariani, Valerio Miller, Mitchell D. Mills, Grant Nelson, Garrett Olmos, Jose L. Sadri, Alireza Sato, Tokushi Tolstikova, Alexandra Xu, Weijun Ourmazd, Abbas Spence, John C. H. Schwander, Peter Barty, Anton Chapman, Henry N. Fromme, Petra Mancuso, Adrian P. Phillips, George N. Bean, Richard Pollack, Lois Schmidt, Marius |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
National Science Foundation (US) Department of Energy (US) National Institutes of Health (US) Lawrence Livermore National Laboratory German Research Foundation European Commission European Research Council Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] |
| dc.subject.none.fl_str_mv |
European X-ray Free-Electron Laser X-ray crystallography Antibiotic resistance Ceftriaxone Drug discovery Enzyme kinetics Enzyme mechanisms Irreversible inhibition Megahertz pulse-repetition rate Mix-and-inject serial crystallography Protein structure determination Serial femtosecond crystallography Substrate diffusion in crystals Sulbactam β-lactamases |
| topic |
European X-ray Free-Electron Laser X-ray crystallography Antibiotic resistance Ceftriaxone Drug discovery Enzyme kinetics Enzyme mechanisms Irreversible inhibition Megahertz pulse-repetition rate Mix-and-inject serial crystallography Protein structure determination Serial femtosecond crystallography Substrate diffusion in crystals Sulbactam β-lactamases |
| description |
18 pags, 11 figs, 5 tabs |
| publishDate |
2021 |
| dc.date.none.fl_str_mv |
2021 2022 2022 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article http://purl.org/coar/resource_type/c_6501 Publisher's version info:eu-repo/semantics/publishedVersion |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10261/258729 https://api.elsevier.com/content/abstract/scopus_id/85118931472 |
| url |
http://hdl.handle.net/10261/258729 https://api.elsevier.com/content/abstract/scopus_id/85118931472 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
#PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/EC/H2020/637295 info:eu-repo/grantAgreement/EC/FP7/609920 IUCrJ https://doi.org/10.1107/S2052252521008125 Sí |
| dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess |
| eu_rights_str_mv |
openAccess |
| dc.publisher.none.fl_str_mv |
International Union of Crystallography |
| publisher.none.fl_str_mv |
International Union of Crystallography |
| dc.source.none.fl_str_mv |
reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC instname:Consejo Superior de Investigaciones Científicas (CSIC) |
| instname_str |
Consejo Superior de Investigaciones Científicas (CSIC) |
| reponame_str |
DIGITAL.CSIC. Repositorio Institucional del CSIC |
| collection |
DIGITAL.CSIC. Repositorio Institucional del CSIC |
| repository.name.fl_str_mv |
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| repository.mail.fl_str_mv |
|
| _version_ |
1869421490656509952 |
| spelling |
Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallographyPandey, SurajCalvey, GeorgeKatz, Andrea M.Malla, Tek NarsinghKoua, Faisal H. M.Martín-García, José M.Poudyal, IshworYang, Jay-HowVakili, MohammadYefanov, OleksandrZielinski, Kara A.Bajt, SasaAwel, SalahDoerner, KatarinaFrank, MatthiasGelisio, LucaJernigan, RebeccaKirkwood, HenryKloos, MarcoKoliyadu, JayanathMariani, ValerioMiller, Mitchell D.Mills, GrantNelson, GarrettOlmos, Jose L.Sadri, AlirezaSato, TokushiTolstikova, AlexandraXu, WeijunOurmazd, AbbasSpence, John C. H.Schwander, PeterBarty, AntonChapman, Henry N.Fromme, PetraMancuso, Adrian P.Phillips, George N.Bean, RichardPollack, LoisSchmidt, MariusEuropean X-ray Free-Electron LaserX-ray crystallographyAntibiotic resistanceCeftriaxoneDrug discoveryEnzyme kineticsEnzyme mechanismsIrreversible inhibitionMegahertz pulse-repetition rateMix-and-inject serial crystallographyProtein structure determinationSerial femtosecond crystallographySubstrate diffusion in crystalsSulbactamβ-lactamases18 pags, 11 figs, 5 tabsHere, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase of the enzymatic cycle is observed with near-atomic resolution using the most advanced X-ray source currently available: the European XFEL (EuXFEL). The high repetition rate of the EuXFEL combined with our mix-and-inject technology enables the initial phase of ceftriaxone binding to the Mycobacterium tuberculosis β-lactamase to be followed using time-resolved crystallography in real time. It is shown how a diffusion coefficient in enzyme crystals can be derived directly from the X-ray data, enabling the determination of ligand and enzyme-ligand concentrations at any position in the crystal volume as a function of time. In addition, the structure of the irreversible inhibitor sulbactam bound to the enzyme at a 66 ms time delay after mixing is described. This demonstrates that the EuXFEL can be used as an important tool for biomedically relevant research.This work was supported by the National Science Foundation Science and Technology Center 'BioXFEL' through award STC-1231306, and in part by the US Department of Energy, Office of Science, Basic Energy Sciences under contract DESC0002164 (AO, algorithm design and development) and by the National Science Foundation under contract Nos. 1551489 (AO, underlying analytical models) and DBI-2029533 (AO, functional conformations). This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. 1450681 to JLO. The work was also supported by funds from the National Institutes of Health grant R01 GM117342-0404. Funding and support are also acknowledged from the National Institutes of Health grant R01 GM095583, from the Biodesign Center for Applied Structural Discovery at ASU, from National Science Foundation award No. 1565180 and the US Department of Energy through Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344. KAZ was supported by the Cornell Molecular Biophysics Training Program (NIH T32-GM008267). This work was also supported by the Cluster of Excellence 'CUI: Advanced Imaging of Matter' of the Deutsche Forschungsgemeinschaft (DFG), EXC 2056, project ID 390715994. CFEL is supported by the Gottfried Wilhelm Leibniz Program of the DFG, the 'X-probe' project funded by the European Union 2020 Research and Innovation Program under Marie Sklodowska-Curie grant agreement 637295, the European Research Council, 'Frontiers in Attosecond X-ray Science: Imaging and Spectroscopy (AXSIS)', ERC-2013-SyG 609920, and the Human Frontiers Science Program grant RGP0010 2017. This work is also supported by the AXSIS project funded by the European Research Council under the European Union Seventh Framework Program (FP/2007-2013)/ERC Grant Agreement No. 609920.Peer reviewedInternational Union of CrystallographyNational Science Foundation (US)Department of Energy (US)National Institutes of Health (US)Lawrence Livermore National LaboratoryGerman Research FoundationEuropean CommissionEuropean Research CouncilConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202220222021info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/258729https://api.elsevier.com/content/abstract/scopus_id/85118931472reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/637295info:eu-repo/grantAgreement/EC/FP7/609920IUCrJhttps://doi.org/10.1107/S2052252521008125Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2587292026-05-22T06:33:51Z |
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15,811543 |