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1. Structural enzymology using X-ray free electron lasers

Author

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

Subjects
Inorganic Chemistry, Chemical Sciences, Physical Sciences, Infectious Diseases, Good Health and Well Being, Physical chemistry, Condensed matter physics, Particle and high energy physics
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.

Published
2017

2. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

Author

Pande, Kanupriya, Hutchison, Christopher DM, Groenhof, Gerrit, Aquila, Andy, Robinson, Josef S, Tenboer, Jason, Basu, Shibom, Boutet, Sébastien, DePonte, Daniel P, Liang, Mengning, White, Thomas A, Zatsepin, Nadia A, Yefanov, Oleksandr, Morozov, Dmitry, Oberthuer, Dominik, Gati, Cornelius, Subramanian, Ganesh, James, Daniel, Zhao, Yun, Koralek, Jake, Brayshaw, Jennifer, Kupitz, Christopher, Conrad, Chelsie, Roy-Chowdhury, Shatabdi, Coe, Jesse D, Metz, Markus, Xavier, Paulraj Lourdu, Grant, Thomas D, Koglin, Jason E, Ketawala, Gihan, Fromme, Raimund, Šrajer, Vukica, Henning, Robert, Spence, John CH, Ourmazd, Abbas, Schwander, Peter, Weierstall, Uwe, Frank, Matthias, Fromme, Petra, Barty, Anton, Chapman, Henry N, Moffat, Keith, van Thor, Jasper J, and Schmidt, Marius

Subjects
Biological Sciences, Chemical Sciences, Theoretical and Computational Chemistry, Bacterial Proteins, Crystallography, Isomerism, Light, Photochemical Processes, Photons, Photoreceptors, Microbial, Protein Conformation, Time Factors, General Science & Technology
Abstract

A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.

Published
2016

3. Protein Energy Landscapes Determined by 5-Dimensional Crystallography

Author

Schmidt, Marius, Srajer, Vukica, Henning, Robert, Ihee, Hyotcherl, Purwar, Namrta, Tenboer, Jason, and Tripathi, Shailesh

Subjects
Physics - Biological Physics, Physics - Chemical Physics, Quantitative Biology - Biomolecules
Abstract

Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be determined from the same set of X-ray data. We demonstrate here how barriers of activation can be determined solely from five-dimensional crystallography [5]. Directly linking molecular structures with barriers of activation between them allows for gaining insight into the structural nature of the barrier. We analyze comprehensive time series of crystal-lographic data at 14 different temperature settings and determine entropy and enthalpy contributions to the barriers of activation. 100 years after the discovery of X-ray scattering, we advance X-ray structure determination to a new frontier, the determination of energy landscapes.

Published
2013

5. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

Author

Tenboer, Jason, Basu, Shibom, Zatsepin, Nadia, Pande, Kanupriya, Milathianaki, Despina, Frank, Matthias, Hunter, Mark, Boutet, Sébastien, Williams, Garth J., Koglin, Jason E., Oberthuer, Dominik, Heymann, Michael, Kupitz, Christopher, Conrad, Chelsie, Coe, Jesse, Roy-Chowdhury, Shatabdi, Weierstall, Uwe, James, Daniel, Wang, Dingjie, Grant, Thomas, Barty, Anton, Yefanov, Oleksandr, Scales, Jennifer, Gati, Cornelius, Seuring, Carolin, Srajer, Vukica, Henning, Robert, Schwander, Peter, Fromme, Raimund, Ourmazd, Abbas, Moffat, Keith, Van Thor, Jasper J., Spence, John C. H., Fromme, Petra, Chapman, Henry N., and Schmidt, Marius

Published
2014

6. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Author

Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Léocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Båth, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojković, Emina A., Schmidt, Marius, and Westenhoff, Sebastian

Published
2016
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7. PROTEIN STRUCTURE: Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

Author

Pande, Kanupriya, Hutchison, Christopher D. M., Groenhof, Gerrit, Aquila, Andy, Robinson, Josef S., Tenboer, Jason, Basu, Shibom, Boutet, Sébastien, DePonte, Daniel P., Liang, Mengning, White, Thomas A., Zatsepin, Nadia A., Yefanov, Oleksandr, Morozov, Dmitry, Oberthuer, Dominik, Gati, Cornelius, Subramanian, Ganesh, James, Daniel, Zhao, Yun, Koralek, Jake, Brayshaw, Jennifer, Kupitz, Christopher, Conrad, Chelsie, Roy-Chowdhury, Shatabdi, Coe, Jesse D., Metz, Markus, Xavier, Paulraj Lourdu, Grant, Thomas D., Koglin, Jason E., Ketawala, Gihan, Fromme, Raimund, Šrajer, Vukica, Henning, Robert, Spence, John C. H., Ourmazd, Abbas, Schwander, Peter, Weierstall, Uwe, Frank, Matthias, Fromme, Petra, Barty, Anton, Chapman, Henry N., Moffat, Keith, van Thor, Jasper J., and Schmidt, Marius

Published
2016
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8. STRUCTURAL BIOLOGY: Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

Author

Tenboer, Jason, Basu, Shibom, Zatsepin, Nadia, Pande, Kanupriya, Milathianaki, Despina, Frank, Matthias, Hunter, Mark, Boutet, Sébastien, Williams, Garth J., Koglin, Jason E., Oberthuer, Dominik, Heymann, Michael, Kupitz, Christopher, Conrad, Chelsie, Coe, Jesse, Roy-Chowdhury, Shatabdi, Weierstall, Uwe, James, Daniel, Wang, Dingjie, Grant, Thomas, Barty, Anton, Yefanov, Oleksandr, Scales, Jennifer, Gati, Cornelius, Seuring, Carolin, Srajer, Vukica, Henning, Robert, Schwander, Peter, Fromme, Raimund, Ourmazd, Abbas, Moffat, Keith, Van Thor, Jasper J., Spence, John C. H., Fromme, Petra, Chapman, Henry N., and Schmidt, Marius

Published
2014
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9. Structural enzymology using X-ray free electron lasers

Author

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

Published
2016
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10. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Author

University of Helsinki, Medicum, Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Leocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Bath, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojkovic, Emina A., Schmidt, Marius, Westenhoff, Sebastian, University of Helsinki, Medicum, Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Leocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Bath, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojkovic, Emina A., Schmidt, Marius, and Westenhoff, Sebastian

Abstract

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 angstrom resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 angstrom resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

Published
2016

13. Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein

Author

van Thor, Jasper J., primary, Warren, Mark M., additional, Lincoln, Craig N., additional, Chollet, Matthieu, additional, Lemke, Henrik Till, additional, Fritz, David M., additional, Schmidt, Marius, additional, Tenboer, Jason, additional, Ren, Zhong, additional, Srajer, Vukica, additional, Moffat, Keith, additional, and Graber, Tim, additional

Published
2014
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16. Room temperature structures beyond 1.5Å by serial femtosecond crystallography.

Author

Schmidt, Marius, Pande, Kanupriya, Basu, Shibom, and Tenboer, Jason

Subjects
FEMTOSECOND lasers, TEMPERATURE effect, CRYSTALLOGRAPHY, CRYSTALLOIDS (Botany), HYDROGEN bonding
Abstract

About 2.5 × 106 snapshots on microcrystals of photoactive yellow protein (PYP) from a recent serial femtosecond crystallographic (SFX) experiment were reanalyzed to maximum resolution. The resolution is pushed to 1.46Å, and a PYP structural model is refined at that resolution. The result is compared to other PYP models determined at atomic resolution around 1Å and better at the synchrotron. By comparing subtleties such as individual isotropic temperature factors and hydrogen bond lengths, we were able to assess the quality of the SFX data at that resolution. We also show that the determination of anisotropic temperature factor ellipsoids starts to become feasible with the SFX data at resolutions better than 1.5Å. [ABSTRACT FROM AUTHOR]

Published
2015
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17. Structural enzymology using X-ray free electron lasers

Author

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

Subjects
3. Good health
Abstract

Structural dynamics 4(4), 044003 (2017). doi:10.1063/1.4972069, 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., Published by AIP Publishing LLC, Melville, NY

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