Structural enzymology using X-ray free electron lasers

Christopher Kupitz; Jose L. Olmos; Mark Holl; Lee Tremblay; Kanupriya Pande; Suraj Pandey; Dominik Oberthür; Mark Hunter; Mengning Liang; Andrew Aquila; Jason Tenboer; George Calvey; Andrea Katz; Yujie Chen; Max O. Wiedorn; Juraj Knoska; Alke Meents; Valerio Majriani; Tyler Norwood; Ishwor Poudyal; Thomas Grant; Mitchell D. Miller; Weijun Xu; Aleksandra Tolstikova; Andrew Morgan; Markus Metz; Jose Martin-Gracia; James D. Zook; Shatabdi Roy-Chowdhury; Jesse Coe; Nirupa Nagaratnam; Domingo Meza; Raimund Fromme; Shibom Basu; Matthias Frank; Thomas White; Anton Barty; Sasa Bajt; Oleksandr Yefanov; Henry N. Chapman; Nadia Zatsepin; Garrett Nelson; Uwe Weierstall; John Spence; Peter Schwander; Lois Pollack; Petra Fromme; Abbas Ourmazd; George N. Phillips; Marius Schmidt

doi:10.1063/1.4972069

Structural enzymology using X-ray free electron lasers

Christopher Kupitz, Jose L. Olmos, Mark Holl, Lee Tremblay, Kanupriya Pande, Suraj Pandey, Dominik Oberthür, Mark Hunter, Mengning Liang, Andrew Aquila, Jason Tenboer, George Calvey, Andrea Katz, Yujie Chen, Max O. Wiedorn, Juraj Knoska, Alke Meents, Valerio Majriani, Tyler Norwood, Ishwor PoudyalThomas Grant, Mitchell D. Miller, Weijun Xu, Aleksandra Tolstikova, Andrew Morgan, Markus Metz, Jose Martin-Gracia, James D. Zook, Shatabdi Roy-Chowdhury, Jesse Coe, Nirupa Nagaratnam, Domingo Meza, Raimund Fromme, Shibom Basu, Matthias Frank, Thomas White, Anton Barty, Sasa Bajt, Oleksandr Yefanov, Henry N. Chapman, Nadia Zatsepin, Garrett Nelson, Uwe Weierstall, John Spence, Peter Schwander, Lois Pollack, Petra Fromme, Abbas Ourmazd, George N. Phillips, Marius Schmidt

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

82 Scopus citations

Abstract

Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated. Here, we demonstrate that MISC is feasible at an X-ray free electron laser by studying the reaction of M. tuberculosis ß-lactamase microcrystals with ceftriaxone antibiotic solution. Electron density maps of the apo-ß-lactamase and of the ceftriaxone bound form were obtained at 2.8 Å and 2.4 Å resolution, respectively. These results pave the way to study cyclic and non-cyclic reactions and represent a new field of time-resolved structural dynamics for numerous substrate-triggered biological reactions.

Original language	English (US)
Article number	044003
Journal	Structural Dynamics
Volume	4
Issue number	4
DOIs	https://doi.org/10.1063/1.4972069
State	Published - Jul 1 2017

ASJC Scopus subject areas

Radiation
Instrumentation
Condensed Matter Physics
Spectroscopy

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10.1063/1.4972069

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Kupitz, C., Olmos, J. L., Holl, M., Tremblay, L., Pande, K., Pandey, S., Oberthür, D., Hunter, M., Liang, M., Aquila, A., Tenboer, J., Calvey, G., Katz, A., Chen, Y., Wiedorn, M. O., Knoska, J., Meents, A., Majriani, V., Norwood, T., ... Schmidt, M. (2017). Structural enzymology using X-ray free electron lasers. Structural Dynamics, 4(4), Article 044003. https://doi.org/10.1063/1.4972069

Kupitz, C, Olmos, JL, Holl, M, Tremblay, L, Pande, K, Pandey, S, Oberthür, D, Hunter, M, Liang, M, Aquila, A, Tenboer, J, Calvey, G, Katz, A, Chen, Y, Wiedorn, MO, Knoska, J, Meents, A, Majriani, V, Norwood, T, Poudyal, I, Grant, T, Miller, MD, Xu, W, Tolstikova, A, Morgan, A, Metz, M, Martin-Gracia, J, Zook, JD, Roy-Chowdhury, S, Coe, J, Nagaratnam, N, Meza, D, Fromme, R, Basu, S, Frank, M, White, T, Barty, A, Bajt, S, Yefanov, O, Chapman, HN, Zatsepin, N, Nelson, G, Weierstall, U, Spence, J, Schwander, P, Pollack, L, Fromme, P, Ourmazd, A, Phillips, GN & Schmidt, M 2017, 'Structural enzymology using X-ray free electron lasers', Structural Dynamics, vol. 4, no. 4, 044003. https://doi.org/10.1063/1.4972069

@article{2799937b58fc4ec09d25b2458360bbb5,

title = "Structural enzymology using X-ray free electron lasers",

abstract = "Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated. Here, we demonstrate that MISC is feasible at an X-ray free electron laser by studying the reaction of M. tuberculosis {\ss}-lactamase microcrystals with ceftriaxone antibiotic solution. Electron density maps of the apo-{\ss}-lactamase and of the ceftriaxone bound form were obtained at 2.8 {\AA} and 2.4 {\AA} resolution, respectively. These results pave the way to study cyclic and non-cyclic reactions and represent a new field of time-resolved structural dynamics for numerous substrate-triggered biological reactions.",

author = "Christopher Kupitz and Olmos, {Jose L.} and Mark Holl and Lee Tremblay and Kanupriya Pande and Suraj Pandey and Dominik Oberth{\"u}r and Mark Hunter and Mengning Liang and Andrew Aquila and Jason Tenboer and George Calvey and Andrea Katz and Yujie Chen and Wiedorn, {Max O.} and Juraj Knoska and Alke Meents and Valerio Majriani and Tyler Norwood and Ishwor Poudyal and Thomas Grant and Miller, {Mitchell D.} and Weijun Xu and Aleksandra Tolstikova and Andrew Morgan and Markus Metz and Jose Martin-Gracia and Zook, {James D.} and Shatabdi Roy-Chowdhury and Jesse Coe and Nirupa Nagaratnam and Domingo Meza and Raimund Fromme and Shibom Basu and Matthias Frank and Thomas White and Anton Barty and Sasa Bajt and Oleksandr Yefanov and Chapman, {Henry N.} and Nadia Zatsepin and Garrett Nelson and Uwe Weierstall and John Spence and Peter Schwander and Lois Pollack and Petra Fromme and Abbas Ourmazd and Phillips, {George N.} and Marius Schmidt",

note = "Funding Information: This work was supported by NSF-STC {"}BioXFEL{"} (STC-1231306) and NIH Grant Nos. GM098248 and GM109456 (Phillips for sample preparation) as well as NIH Grant No. GM095583 (to P.F. and members of her team). This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program to J.L.O. under Grant No. 1450681. A.O. was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award No. DE-SC0002164 (algorithm design and development), and by the U.S. National Science Foundation under Award Nos. STC 1231306 (joint initiation and design of experiment) and 1551489 (underlying analytical models). Use of the Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. Part of this work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and M.F. was supported by LLNL Lab-Directed Research and Development Project No. 012-ERD-031. G.N. was supported by NIH Award No. GM097463. Parts of the sample injector used at LCLS for this research was funded by the National Institutes of Health, P41GM103393, formerly P41RR001209. Support is acknowledged from the Biodesign Center for Applied Structural Discovery at ASU, the Helmholtz Association Virtual Institute Dynamic Pathways and the BMBF through Project Nos. 05K13GUK and 05K14CHA. M.M. is supported by the European Union under the programme FP7-PEOPLE-2012-ITN Nanomem, Grant No. 317079. We thank C. Conrad for helpful discussions. Publisher Copyright: {\textcopyright} 2016 Author(s).",

year = "2017",

month = jul,

day = "1",

doi = "10.1063/1.4972069",

language = "English (US)",

volume = "4",

journal = "Structural Dynamics",

issn = "2329-7778",

publisher = "AAPM - American Association of Physicists in Medicine",

number = "4",

}

TY - JOUR

T1 - Structural enzymology using X-ray free electron lasers

AU - Kupitz, Christopher

AU - Olmos, Jose L.

AU - Holl, Mark

AU - Tremblay, Lee

AU - Pande, Kanupriya

AU - Pandey, Suraj

AU - Oberthür, Dominik

AU - Hunter, Mark

AU - Liang, Mengning

AU - Aquila, Andrew

AU - Tenboer, Jason

AU - Calvey, George

AU - Katz, Andrea

AU - Chen, Yujie

AU - Wiedorn, Max O.

AU - Knoska, Juraj

AU - Meents, Alke

AU - Majriani, Valerio

AU - Norwood, Tyler

AU - Poudyal, Ishwor

AU - Grant, Thomas

AU - Miller, Mitchell D.

AU - Xu, Weijun

AU - Tolstikova, Aleksandra

AU - Morgan, Andrew

AU - Metz, Markus

AU - Martin-Gracia, Jose

AU - Zook, James D.

AU - Roy-Chowdhury, Shatabdi

AU - Coe, Jesse

AU - Nagaratnam, Nirupa

AU - Meza, Domingo

AU - Fromme, Raimund

AU - Basu, Shibom

AU - Frank, Matthias

AU - White, Thomas

AU - Barty, Anton

AU - Bajt, Sasa

AU - Yefanov, Oleksandr

AU - Chapman, Henry N.

AU - Zatsepin, Nadia

AU - Nelson, Garrett

AU - Weierstall, Uwe

AU - Spence, John

AU - Schwander, Peter

AU - Pollack, Lois

AU - Fromme, Petra

AU - Ourmazd, Abbas

AU - Phillips, George N.

AU - Schmidt, Marius

N1 - Funding Information: This work was supported by NSF-STC "BioXFEL" (STC-1231306) and NIH Grant Nos. GM098248 and GM109456 (Phillips for sample preparation) as well as NIH Grant No. GM095583 (to P.F. and members of her team). This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program to J.L.O. under Grant No. 1450681. A.O. was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award No. DE-SC0002164 (algorithm design and development), and by the U.S. National Science Foundation under Award Nos. STC 1231306 (joint initiation and design of experiment) and 1551489 (underlying analytical models). Use of the Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. Part of this work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and M.F. was supported by LLNL Lab-Directed Research and Development Project No. 012-ERD-031. G.N. was supported by NIH Award No. GM097463. Parts of the sample injector used at LCLS for this research was funded by the National Institutes of Health, P41GM103393, formerly P41RR001209. Support is acknowledged from the Biodesign Center for Applied Structural Discovery at ASU, the Helmholtz Association Virtual Institute Dynamic Pathways and the BMBF through Project Nos. 05K13GUK and 05K14CHA. M.M. is supported by the European Union under the programme FP7-PEOPLE-2012-ITN Nanomem, Grant No. 317079. We thank C. Conrad for helpful discussions. Publisher Copyright: © 2016 Author(s).

PY - 2017/7/1

Y1 - 2017/7/1

N2 - Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated. Here, we demonstrate that MISC is feasible at an X-ray free electron laser by studying the reaction of M. tuberculosis ß-lactamase microcrystals with ceftriaxone antibiotic solution. Electron density maps of the apo-ß-lactamase and of the ceftriaxone bound form were obtained at 2.8 Å and 2.4 Å resolution, respectively. These results pave the way to study cyclic and non-cyclic reactions and represent a new field of time-resolved structural dynamics for numerous substrate-triggered biological reactions.

AB - Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated. Here, we demonstrate that MISC is feasible at an X-ray free electron laser by studying the reaction of M. tuberculosis ß-lactamase microcrystals with ceftriaxone antibiotic solution. Electron density maps of the apo-ß-lactamase and of the ceftriaxone bound form were obtained at 2.8 Å and 2.4 Å resolution, respectively. These results pave the way to study cyclic and non-cyclic reactions and represent a new field of time-resolved structural dynamics for numerous substrate-triggered biological reactions.

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U2 - 10.1063/1.4972069

DO - 10.1063/1.4972069

M3 - Article

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SN - 2329-7778

VL - 4

JO - Structural Dynamics

JF - Structural Dynamics

IS - 4

M1 - 044003

ER -

Structural enzymology using X-ray free electron lasers

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