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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 frommore » the same set of X-ray data.« less

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Science Foundation (NSF)
OSTI Identifier:
1618580
Alternate Identifier(s):
OSTI ID: 1460337
Grant/Contract Number:  
SC0002164; AC02-76SF00515; AC52-07NA27344; AC02-05CH11231
Resource Type:
Published Article
Journal Name:
BMC Biology
Additional Journal Information:
Journal Name: BMC Biology Journal Volume: 16 Journal Issue: 1; Journal ID: ISSN 1741-7007
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Olmos, Jr, Jose L., Pandey, Suraj, Martin-Garcia, Jose M., Calvey, George, Katz, Andrea, Knoska, Juraj, Kupitz, Christopher, Hunter, Mark S., Liang, Mengning, Oberthuer, Dominik, Yefanov, Oleksandr, Wiedorn, Max, Heyman, Michael, Holl, Mark, Pande, Kanupriya, Barty, Anton, Miller, Mitchell D., Stern, Stephan, Roy-Chowdhury, Shatabdi, Coe, Jesse, Nagaratnam, Nirupa, Zook, James, Verburgt, Jacob, Norwood, Tyler, Poudyal, Ishwor, Xu, David, Koglin, Jason, Seaberg, Matthew H., Zhao, Yun, Bajt, Saša, Grant, Thomas, Mariani, Valerio, Nelson, Garrett, Subramanian, Ganesh, Bae, Euiyoung, Fromme, Raimund, Fung, Russell, Schwander, Peter, Frank, Matthias, White, Thomas A., Weierstall, Uwe, Zatsepin, Nadia, Spence, John, Fromme, Petra, Chapman, Henry N., Pollack, Lois, Tremblay, Lee, Ourmazd, Abbas, Phillips, Jr, George N., and Schmidt, Marius. Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography. United Kingdom: N. p., 2018. Web. doi:10.1186/s12915-018-0524-5.
Olmos, Jr, Jose L., Pandey, Suraj, Martin-Garcia, Jose M., Calvey, George, Katz, Andrea, Knoska, Juraj, Kupitz, Christopher, Hunter, Mark S., Liang, Mengning, Oberthuer, Dominik, Yefanov, Oleksandr, Wiedorn, Max, Heyman, Michael, Holl, Mark, Pande, Kanupriya, Barty, Anton, Miller, Mitchell D., Stern, Stephan, Roy-Chowdhury, Shatabdi, Coe, Jesse, Nagaratnam, Nirupa, Zook, James, Verburgt, Jacob, Norwood, Tyler, Poudyal, Ishwor, Xu, David, Koglin, Jason, Seaberg, Matthew H., Zhao, Yun, Bajt, Saša, Grant, Thomas, Mariani, Valerio, Nelson, Garrett, Subramanian, Ganesh, Bae, Euiyoung, Fromme, Raimund, Fung, Russell, Schwander, Peter, Frank, Matthias, White, Thomas A., Weierstall, Uwe, Zatsepin, Nadia, Spence, John, Fromme, Petra, Chapman, Henry N., Pollack, Lois, Tremblay, Lee, Ourmazd, Abbas, Phillips, Jr, George N., & Schmidt, Marius. Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography. United Kingdom. doi:10.1186/s12915-018-0524-5.
Olmos, Jr, Jose L., Pandey, Suraj, Martin-Garcia, Jose M., Calvey, George, Katz, Andrea, Knoska, Juraj, Kupitz, Christopher, Hunter, Mark S., Liang, Mengning, Oberthuer, Dominik, Yefanov, Oleksandr, Wiedorn, Max, Heyman, Michael, Holl, Mark, Pande, Kanupriya, Barty, Anton, Miller, Mitchell D., Stern, Stephan, Roy-Chowdhury, Shatabdi, Coe, Jesse, Nagaratnam, Nirupa, Zook, James, Verburgt, Jacob, Norwood, Tyler, Poudyal, Ishwor, Xu, David, Koglin, Jason, Seaberg, Matthew H., Zhao, Yun, Bajt, Saša, Grant, Thomas, Mariani, Valerio, Nelson, Garrett, Subramanian, Ganesh, Bae, Euiyoung, Fromme, Raimund, Fung, Russell, Schwander, Peter, Frank, Matthias, White, Thomas A., Weierstall, Uwe, Zatsepin, Nadia, Spence, John, Fromme, Petra, Chapman, Henry N., Pollack, Lois, Tremblay, Lee, Ourmazd, Abbas, Phillips, Jr, George N., and Schmidt, Marius. Thu . "Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography". United Kingdom. doi:10.1186/s12915-018-0524-5.
@article{osti_1618580,
title = {Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography},
author = {Olmos, Jr, Jose L. and Pandey, Suraj and Martin-Garcia, Jose M. and Calvey, George and Katz, Andrea and Knoska, Juraj and Kupitz, Christopher and Hunter, Mark S. and Liang, Mengning and Oberthuer, Dominik and Yefanov, Oleksandr and Wiedorn, Max and Heyman, Michael and Holl, Mark and Pande, Kanupriya and Barty, Anton and Miller, Mitchell D. and Stern, Stephan and Roy-Chowdhury, Shatabdi and Coe, Jesse and Nagaratnam, Nirupa and Zook, James and Verburgt, Jacob and Norwood, Tyler and Poudyal, Ishwor and Xu, David and Koglin, Jason and Seaberg, Matthew H. and Zhao, Yun and Bajt, Saša and Grant, Thomas and Mariani, Valerio and Nelson, Garrett and Subramanian, Ganesh and Bae, Euiyoung and Fromme, Raimund and Fung, Russell and Schwander, Peter and Frank, Matthias and White, Thomas A. and Weierstall, Uwe and Zatsepin, Nadia and Spence, John and Fromme, Petra and Chapman, Henry N. and Pollack, Lois and Tremblay, Lee and Ourmazd, Abbas and Phillips, Jr, George N. and Schmidt, Marius},
abstractNote = {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.},
doi = {10.1186/s12915-018-0524-5},
journal = {BMC Biology},
number = 1,
volume = 16,
place = {United Kingdom},
year = {2018},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1186/s12915-018-0524-5

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Cited by: 15 works
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