Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography

Jose L. Olmos; Suraj Pandey; Jose M. Martin-Garcia; George Calvey; Andrea Katz; Juraj Knoska; Christopher Kupitz; Mark S. Hunter; Mengning Liang; Dominik Oberthuer; Oleksandr Yefanov; Max Wiedorn; Michael Heyman; Mark Holl; Kanupriya Pande; Anton Barty; Mitchell D. Miller; Stephan Stern; Shatabdi Roy-Chowdhury; Jesse Coe; Nirupa Nagaratnam; James Zook; Jacob Verburgt; Tyler Norwood; Ishwor Poudyal; David Xu; Jason Koglin; Matthew H. Seaberg; Yun Zhao; Saša Bajt; Thomas Grant; Valerio Mariani; Garrett Nelson; Ganesh Subramanian; Euiyoung Bae; Raimund Fromme; Russell Fung; Peter Schwander; Matthias Frank; Thomas A. White; Uwe Weierstall; Nadia Zatsepin; John Spence; Petra Fromme; Henry N. Chapman; Lois Pollack; Lee Tremblay; Abbas Ourmazd; George N. Phillips; Marius Schmidt

doi:10.1186/s12915-018-0524-5

Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography

Jose L. Olmos, Suraj Pandey, Jose M. Martin-Garcia, George Calvey, Andrea Katz, Juraj Knoska, Christopher Kupitz, Mark S. Hunter, Mengning Liang, Dominik Oberthuer, Oleksandr Yefanov, Max Wiedorn, Michael Heyman, Mark Holl, Kanupriya Pande, Anton Barty, Mitchell D. Miller, Stephan Stern, Shatabdi Roy-Chowdhury, Jesse CoeNirupa Nagaratnam, James Zook, Jacob Verburgt, Tyler Norwood, Ishwor Poudyal, David Xu, Jason Koglin, Matthew H. Seaberg, Yun Zhao, Saša Bajt, Thomas Grant, Valerio Mariani, Garrett Nelson, Ganesh Subramanian, Euiyoung Bae, Raimund Fromme, Russell Fung, Peter Schwander, Matthias Frank, Thomas A. White, Uwe Weierstall, Nadia Zatsepin, John Spence, Petra Fromme, Henry N. Chapman, Lois Pollack, Lee Tremblay, Abbas Ourmazd, George N. Phillips, Marius Schmidt

Research output: Contribution to journal › Article › peer-review

95 Scopus citations

Abstract

Background: Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases. Results: Here, we demonstrate a general method for capturing enzyme catalysis "in action" by mix-and-inject serial crystallography (MISC). Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis β-lactamase with the third-generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation from 30 ms to 2 s. Conclusions: MISC is a versatile and generally applicable method to investigate reactions of biological macromolecules, some of which are of immense biological significance and might be, in addition, important targets for structure-based drug design. With megahertz X-ray pulse rates expected at the Linac Coherent Light Source II and the European X-ray free-electron laser, multiple, finely spaced time delays can be collected rapidly, allowing a comprehensive description of biomolecular reactions in terms of structure and kinetics from the same set of X-ray data.

Original language	English (US)
Article number	59
Journal	BMC Biology
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s12915-018-0524-5
State	Published - May 31 2018

ASJC Scopus subject areas

Biotechnology
Structural Biology
Ecology, Evolution, Behavior and Systematics
Physiology
Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)
Plant Science
Developmental Biology
Cell Biology

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10.1186/s12915-018-0524-5

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Olmos, J. L., Pandey, S., Martin-Garcia, J. M., Calvey, G., Katz, A., Knoska, J., Kupitz, C., Hunter, M. S., Liang, M., Oberthuer, D., Yefanov, O., Wiedorn, M., Heyman, M., Holl, M., Pande, K., Barty, A., Miller, M. D., Stern, S., Roy-Chowdhury, S., ... Schmidt, M. (2018). Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography. BMC Biology, 16(1), Article 59. https://doi.org/10.1186/s12915-018-0524-5

Olmos, JL, Pandey, S, Martin-Garcia, JM, Calvey, G, Katz, A, Knoska, J, Kupitz, C, Hunter, MS, Liang, M, Oberthuer, D, Yefanov, O, Wiedorn, M, Heyman, M, Holl, M, Pande, K, Barty, A, Miller, MD, Stern, S, Roy-Chowdhury, S, Coe, J, Nagaratnam, N, Zook, J, Verburgt, J, Norwood, T, Poudyal, I, Xu, D, Koglin, J, Seaberg, MH, Zhao, Y, Bajt, S, Grant, T, Mariani, V, Nelson, G, Subramanian, G, Bae, E, Fromme, R, Fung, R, Schwander, P, Frank, M, White, TA, Weierstall, U, Zatsepin, N, Spence, J, Fromme, P, Chapman, HN, Pollack, L, Tremblay, L, Ourmazd, A, Phillips, GN & Schmidt, M 2018, 'Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography', BMC Biology, vol. 16, no. 1, 59. https://doi.org/10.1186/s12915-018-0524-5

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title = "Enzyme intermediates captured {"}on the fly{"} by mix-and-inject serial crystallography",

abstract = "Background: Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases. Results: Here, we demonstrate a general method for capturing enzyme catalysis {"}in action{"} by mix-and-inject serial crystallography (MISC). Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis β-lactamase with the third-generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation from 30 ms to 2 s. Conclusions: MISC is a versatile and generally applicable method to investigate reactions of biological macromolecules, some of which are of immense biological significance and might be, in addition, important targets for structure-based drug design. With megahertz X-ray pulse rates expected at the Linac Coherent Light Source II and the European X-ray free-electron laser, multiple, finely spaced time delays can be collected rapidly, allowing a comprehensive description of biomolecular reactions in terms of structure and kinetics from the same set of X-ray data.",

author = "Olmos, {Jose L.} and Suraj Pandey and Martin-Garcia, {Jose M.} and George Calvey and Andrea Katz and Juraj Knoska and Christopher Kupitz and Hunter, {Mark S.} and Mengning Liang and Dominik Oberthuer and Oleksandr Yefanov and Max Wiedorn and Michael Heyman and Mark Holl and Kanupriya Pande and Anton Barty and Miller, {Mitchell D.} and Stephan Stern and Shatabdi Roy-Chowdhury and Jesse Coe and Nirupa Nagaratnam and James Zook and Jacob Verburgt and Tyler Norwood and Ishwor Poudyal and David Xu and Jason Koglin and Seaberg, {Matthew H.} and Yun Zhao and Sa{\v s}a Bajt and Thomas Grant and Valerio Mariani and Garrett Nelson and Ganesh Subramanian and Euiyoung Bae and Raimund Fromme and Russell Fung and Peter Schwander and Matthias Frank and White, {Thomas A.} and Uwe Weierstall and Nadia Zatsepin and John Spence and Petra Fromme and Chapman, {Henry N.} and Lois Pollack and Lee Tremblay and Abbas Ourmazd and Phillips, {George N.} and Marius Schmidt",

note = "Funding Information: This work was supported by the National Science Foundation (NSF)-Science and Technology Center (STC) 'BioXFEL' through award STC-1231306, and in part by the US Department of Energy, Office of Science, Basic Energy Sciences under contract DE-SC0002164 (to A.O., algorithm design and development) and by the NSF under contract number 1551489 (to A.O., underlying analytical models). Portions of this research were performed at the Linac Coherent Light Source (LCLS). Use of the LCLS, SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Science, Basic Energy Sciences under contract DE-AC02-76SF00515. This material is based upon work supported by the NSF Graduate Research Fellowship Program to J.L.O. under grant no. 1450681. The work was also supported by funds from the National Institutes of Health grants R01 GM117342-01 and R01 GM095583, by funds from the Biodesign Center for Applied Structural Discovery at Arizona State University, and the US Department of Energy through Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344. Part of this work was also supported by program-oriented funds of the Helmholtz Association. Publisher Copyright: {\textcopyright} 2018 Schmidt et al.",

year = "2018",

month = may,

day = "31",

doi = "10.1186/s12915-018-0524-5",

language = "English (US)",

volume = "16",

journal = "BMC Biology",

issn = "1741-7007",

publisher = "BioMed Central",

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TY - JOUR

T1 - Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography

AU - Olmos, Jose L.

AU - Pandey, Suraj

AU - Martin-Garcia, Jose M.

AU - Calvey, George

AU - Katz, Andrea

AU - Knoska, Juraj

AU - Kupitz, Christopher

AU - Hunter, Mark S.

AU - Liang, Mengning

AU - Oberthuer, Dominik

AU - Yefanov, Oleksandr

AU - Wiedorn, Max

AU - Heyman, Michael

AU - Holl, Mark

AU - Pande, Kanupriya

AU - Barty, Anton

AU - Miller, Mitchell D.

AU - Stern, Stephan

AU - Roy-Chowdhury, Shatabdi

AU - Coe, Jesse

AU - Nagaratnam, Nirupa

AU - Zook, James

AU - Verburgt, Jacob

AU - Norwood, Tyler

AU - Poudyal, Ishwor

AU - Xu, David

AU - Koglin, Jason

AU - Seaberg, Matthew H.

AU - Zhao, Yun

AU - Bajt, Saša

AU - Grant, Thomas

AU - Mariani, Valerio

AU - Nelson, Garrett

AU - Subramanian, Ganesh

AU - Bae, Euiyoung

AU - Fromme, Raimund

AU - Fung, Russell

AU - Schwander, Peter

AU - Frank, Matthias

AU - White, Thomas A.

AU - Weierstall, Uwe

AU - Zatsepin, Nadia

AU - Spence, John

AU - Fromme, Petra

AU - Chapman, Henry N.

AU - Pollack, Lois

AU - Tremblay, Lee

AU - Ourmazd, Abbas

AU - Phillips, George N.

AU - Schmidt, Marius

N1 - Funding Information: This work was supported by the National Science Foundation (NSF)-Science and Technology Center (STC) 'BioXFEL' through award STC-1231306, and in part by the US Department of Energy, Office of Science, Basic Energy Sciences under contract DE-SC0002164 (to A.O., algorithm design and development) and by the NSF under contract number 1551489 (to A.O., underlying analytical models). Portions of this research were performed at the Linac Coherent Light Source (LCLS). Use of the LCLS, SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Science, Basic Energy Sciences under contract DE-AC02-76SF00515. This material is based upon work supported by the NSF Graduate Research Fellowship Program to J.L.O. under grant no. 1450681. The work was also supported by funds from the National Institutes of Health grants R01 GM117342-01 and R01 GM095583, by funds from the Biodesign Center for Applied Structural Discovery at Arizona State University, and the US Department of Energy through Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344. Part of this work was also supported by program-oriented funds of the Helmholtz Association. Publisher Copyright: © 2018 Schmidt et al.

PY - 2018/5/31

Y1 - 2018/5/31

N2 - Background: Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases. Results: Here, we demonstrate a general method for capturing enzyme catalysis "in action" by mix-and-inject serial crystallography (MISC). Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis β-lactamase with the third-generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation from 30 ms to 2 s. Conclusions: MISC is a versatile and generally applicable method to investigate reactions of biological macromolecules, some of which are of immense biological significance and might be, in addition, important targets for structure-based drug design. With megahertz X-ray pulse rates expected at the Linac Coherent Light Source II and the European X-ray free-electron laser, multiple, finely spaced time delays can be collected rapidly, allowing a comprehensive description of biomolecular reactions in terms of structure and kinetics from the same set of X-ray data.

AB - Background: Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases. Results: Here, we demonstrate a general method for capturing enzyme catalysis "in action" by mix-and-inject serial crystallography (MISC). Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis β-lactamase with the third-generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation from 30 ms to 2 s. Conclusions: MISC is a versatile and generally applicable method to investigate reactions of biological macromolecules, some of which are of immense biological significance and might be, in addition, important targets for structure-based drug design. With megahertz X-ray pulse rates expected at the Linac Coherent Light Source II and the European X-ray free-electron laser, multiple, finely spaced time delays can be collected rapidly, allowing a comprehensive description of biomolecular reactions in terms of structure and kinetics from the same set of X-ray data.

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JO - BMC Biology

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Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography

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