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27 results on '"Johnson, Philip J. M."'

1. Influence of pump laser fluence on ultrafast myoglobin structural dynamics

Author

Barends, Thomas R. M., Gorel, Alexander, Bhattacharyya, Swarnendu, Schirò, Giorgio, Bacellar, Camila, Cirelli, Claudio, Colletier, Jacques-Philippe, Foucar, Lutz, Grünbein, Marie Luise, Hartmann, Elisabeth, Hilpert, Mario, Holton, James M., Johnson, Philip J. M., Kloos, Marco, Knopp, Gregor, Marekha, Bogdan, Nass, Karol, Nass Kovacs, Gabriela, Ozerov, Dmitry, Stricker, Miriam, Weik, Martin, Doak, R. Bruce, Shoeman, Robert L., Milne, Christopher J., Huix-Rotllant, Miquel, Cammarata, Marco, and Schlichting, Ilme

Published
2024
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2. A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers

Author

Wranik, Maximilian, Kepa, Michal W., Beale, Emma V., James, Daniel, Bertrand, Quentin, Weinert, Tobias, Furrer, Antonia, Glover, Hannah, Gashi, Dardan, Carrillo, Melissa, Kondo, Yasushi, Stipp, Robin T., Khusainov, Georgii, Nass, Karol, Ozerov, Dmitry, Cirelli, Claudio, Johnson, Philip J. M., Dworkowski, Florian, Beale, John H., Stubbs, Scott, Zamofing, Thierry, Schneider, Marco, Krauskopf, Kristina, Gao, Li, Thorn-Seshold, Oliver, Bostedt, Christoph, Bacellar, Camila, Steinmetz, Michel O., Milne, Christopher, and Standfuss, Jörg

Published
2023
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3. Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography

Author

Wranik, Maximilian, Weinert, Tobias, Slavov, Chavdar, Masini, Tiziana, Furrer, Antonia, Gaillard, Natacha, Gioia, Dario, Ferrarotti, Marco, James, Daniel, Glover, Hannah, Carrillo, Melissa, Kekilli, Demet, Stipp, Robin, Skopintsev, Petr, Brünle, Steffen, Mühlethaler, Tobias, Beale, John, Gashi, Dardan, Nass, Karol, Ozerov, Dmitry, Johnson, Philip J. M., Cirelli, Claudio, Bacellar, Camila, Braun, Markus, Wang, Meitian, Dworkowski, Florian, Milne, Chris, Cavalli, Andrea, Wachtveitl, Josef, Steinmetz, Michel O., and Standfuss, Jörg

Published
2023
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4. Hard X-ray Transient Grating Spectroscopy on Bismuth Germanate

Author

Rouxel, Jeremy R., Fainozzi, Danny, Mankowsky, Roman, Rosner, Benedikt, Seniutinas, Gediminas, Mincigrucci, Riccardo, Catalini, Sara, Foglia, Laura, Cucini, Riccardo, Doring, Florian, Kubec, Adam, Koch, Frieder, Bencivenga, Filippo, Haddad, Andre Al, Gessini, Alessandro, Maznev, Alexei A., Cirelli, Claudio, Gerber, Simon, Pedrini, Bill, Mancini, Giulia F., Razzoli, Elia, Burian, Max, Ueda, Hiroki, Pamfilidis, Georgios, Ferrari, Eugenio, Deng, Yunpei, Mozzanica, Aldo, Johnson, Philip J. M., Ozerov, Dmitry, Izzo, Maria G., Bottari, Cettina, Arrell, Christopher, Divall, Edwin J., Zerdane, Serhane, Sander, Mathias, Knopp, Gregor, Beaud, Paul, Lemke, Henrik T., Milne, Chris J., David, Christian, Torre, Renato, Chergui, Majed, Nelson, Keith A., Masciovecchio, Claudio, Staub, Urs, Patthey, Luc, and Svetina, Cristian

Subjects
Physics - Optics, Condensed Matter - Materials Science
Abstract

Optical-domain Transient Grating (TG) spectroscopy is a versatile background-free four-wave-mixing technique used to probe vibrational, magnetic and electronic degrees of freedom in the time domain. The newly developed coherent X-ray Free Electron Laser sources allow its extension to the X-ray regime. Xrays offer multiple advantages for TG: their large penetration depth allows probing the bulk properties of materials, their element-specificity can address core-excited states, and their short wavelengths create excitation gratings with unprecedented momentum transfer and spatial resolution. We demonstrate for the first time TG excitation in the hard X-ray range at 7.1 keV. In Bismuth Germanate (BGO), the nonresonant TG excitation generates coherent optical phonons detected as a function of time by diffraction of an optical probe pulse. This experiment demonstrates the ability to probe bulk properties of materials and paves the way for ultrafast coherent four-wave-mixing techniques using X-ray probes and involving nanoscale TG spatial periods., Comment: 11 pages, 4 figures

Published
2021
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5. The Speed of Allosteric Signaling Within a Single-Domain Protein

Author

Bozovic, Olga, Ruf, Jeannette, Zanobini, Claudio, Jankovic, Brankica, Buhrke, David, Johnson, Philip J. M., and Hamm, Peter

Subjects
Physics - Biological Physics
Abstract

While much is known about different allosteric regulation mechanisms, the nature of the "allosteric signal", and the timescale on which it propagates, remains elusive. The PDZ3 domain from postsynaptic density-95 protein is a small protein domain with a terminal third alpha helix -- the $\alpha$3-helix, which is known to be allosterically active. By cross-linking the allosteric helix with an azobenzene moiety, we obtained a photocontrollable PDZ3 variant. Photoswitching triggers its allosteric transition, resulting in a change in binding affnity of a peptide to the remote binding pocket. Using time-resolved infrared and UV/Vis spectroscopy, we follow the allosteric signal transduction and reconstruct the timeline in which the allosteric signal propagates through the protein within 200 ns.

Published
2021

6. Ultrafast structural changes direct the first molecular events of vision

Author

Gruhl, Thomas, Weinert, Tobias, Rodrigues, Matthew J., Milne, Christopher J., Ortolani, Giorgia, Nass, Karol, Nango, Eriko, Sen, Saumik, Johnson, Philip J. M., Cirelli, Claudio, Furrer, Antonia, Mous, Sandra, Skopintsev, Petr, James, Daniel, Dworkowski, Florian, Båth, Petra, Kekilli, Demet, Ozerov, Dmitry, Tanaka, Rie, Glover, Hannah, Bacellar, Camila, Brünle, Steffen, Casadei, Cecilia M., Diethelm, Azeglio D., Gashi, Dardan, Gotthard, Guillaume, Guixà-González, Ramon, Joti, Yasumasa, Kabanova, Victoria, Knopp, Gregor, Lesca, Elena, Ma, Pikyee, Martiel, Isabelle, Mühle, Jonas, Owada, Shigeki, Pamula, Filip, Sarabi, Daniel, Tejero, Oliver, Tsai, Ching-Ju, Varma, Niranjan, Wach, Anna, Boutet, Sébastien, Tono, Kensuke, Nogly, Przemyslaw, Deupi, Xavier, Iwata, So, Neutze, Richard, Standfuss, Jörg, Schertler, Gebhard, and Panneels, Valerie

Published
2023
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7. Doming and spin cascade in Ferric Haems: Femtosecond X-ray Absorption and X-ray Emission Studies

Author

Bacellar, Camila, Kinschel, Dominik, Mancini, Giulia F., Ingle, Rebecca A., Rouxel, Jérémy, Cannelli, Oliviero, Cirelli, Claudio, Knopp, Gregor, Szlachetko, Jakub, Lima, Frederico A., Menzi, Samuel, Pamfilidis, Georgios, Kubicek, Katharina, Khakhulin, Dmitry, Gawelda, Wojciech, Rodriguez-Fernandez, Angel, Biednov, Mykola, Bressler, Christian, Arrell, Christopher A., Johnson, Philip J. M., Milne, Christopher, and Chergui, Majed

Subjects
Physics - Chemical Physics
Abstract

The structure-function relationship is at the heart of biology and major protein deformations are correlated to specific functions. In the case of heme proteins, doming is associated with the respiratory function in hemoglobin and myoglobin, while ruffling has been correlated with electron transfer processes, such as in the case of Cytochrome c (Cyt c). The latter has indeed evolved to become an important electron transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe K-edge X-ray absorption near-edge structure (XANES) studies and femtosecond Fe Kalpha and Kbeta X-ray emission spectroscopy (XES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the Iron ion, causing the ferric heme to undergo doming, which we identify for the first time. We also argue that this pattern is common to all ferric haems, raising the question of the biological relevance of doming in such proteins.

Published
2020

8. Enhancement and maximum in the isobaric specific-heat capacity measurements of deeply supercooled water using ultrafast calorimetry

Author

Pathak, Harshad, Späh, Alexander, Esmaeildoost, Niloofar, Sellberg, Jonas A., Kim, Kyung Hwan, Perakis, Fivos, Amann-Winkel, Katrin, Ladd-Parada, Marjorie, Koliyadu, Jayanath, Lane, Thomas J., Yang, Cheolhee, Lemke, Henrik Till, Oggenfuss, Alexander Roland, Johnson, Philip J. M., Deng, Yunpei, Zerdane, Serhane, Mankowsky, Roman, Beaud, Paul, and Nilsson, Anders

Published
2021

9. Correlation of refractive index based and THz streaking arrival time tools for a hard X-ray free-electron laser

Author

Błachucki, Wojciech, primary, Johnson, Philip J. M., additional, Usov, Ivan, additional, Divall, Edwin, additional, Cirelli, Claudio, additional, Knopp, Gregor, additional, Juranić, Pavle, additional, Patthey, Luc, additional, Szlachetko, Jakub, additional, Lemke, Henrik, additional, Milne, Christopher, additional, and Arrell, Christopher, additional

Published
2024
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10. Accessing metal-specific orbital interactions in C–H activation with resonant inelastic X-ray scattering

Author

Banerjee, Ambar, primary, Jay, Raphael M., additional, Leitner, Torsten, additional, Wang, Ru-Pan, additional, Harich, Jessica, additional, Stefanuik, Robert, additional, Coates, Michael R., additional, Beale, Emma V., additional, Kabanova, Victoria, additional, Kahraman, Abdullah, additional, Wach, Anna, additional, Ozerov, Dmitry, additional, Arrell, Christopher, additional, Milne, Christopher, additional, Johnson, Philip J. M., additional, Cirelli, Claudio, additional, Bacellar, Camila, additional, Huse, Nils, additional, Odelius, Michael, additional, and Wernet, Philippe, additional

Published
2024
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11. Spin cascade and doming in ferric hemes : Femtosecond X-ray absorption and X-ray emission studies

Author

Bacellar, Camila, Kinschel, Dominik, Mancini, Giulia F., Ingle, Rebecca A., Rouxel, Jérémy, Cannelli, Oliviero, Cirelli, Claudio, Knopp, Gregor, Szlachetko, Jakub, Lima, Frederico A., Menzi, Samuel, Pamfilidis, Georgios, Kubicek, Katharina, Khakhulin, Dmitry, Gawelda, Wojciech, Rodriguez-Fernandez, Angel, Biednov, Mykola, Bressler, Christian, Arrell, Christopher A., Johnson, Philip J. M., Milne, Christopher J., and Chergui, Majed

Published
2020

12. Femtosecond-to-millisecond structural changes in a light-driven sodium pump

Author

Skopintsev, Petr, Ehrenberg, David, Weinert, Tobias, James, Daniel, Kar, Rajiv K., Johnson, Philip J. M., Ozerov, Dmitry, Furrer, Antonia, Martiel, Isabelle, Dworkowski, Florian, Nass, Karol, Knopp, Gregor, Cirelli, Claudio, Arrell, Christopher, Gashi, Dardan, Mous, Sandra, Wranik, Maximilian, Gruhl, Thomas, Kekilli, Demet, Brünle, Steffen, Deupi, Xavier, Schertler, Gebhard F. X., Benoit, Roger M., Panneels, Valerie, Nogly, Przemyslaw, Schapiro, Igor, Milne, Christopher, Heberle, Joachim, and Standfuss, Jörg

Published
2020
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13. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser

Author

Nass, Karol, primary, Bacellar, Camila, additional, Cirelli, Claudio, additional, Dworkowski, Florian, additional, Gevorkov, Yaroslav, additional, James, Daniel, additional, Johnson, Philip J. M., additional, Kekilli, Demet, additional, Knopp, Gregor, additional, Martiel, Isabelle, additional, Ozerov, Dmitry, additional, Tolstikova, Alexandra, additional, Vera, Laura, additional, Weinert, Tobias, additional, Yefanov, Oleksandr, additional, Standfuss, Jörg, additional, Reiche, Sven, additional, and Milne, Christopher J., additional

Published
2021
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14. Optical second harmonic generation in LiB3O5 modulated by intense femtosecond X-ray pulses

Author

Deng, Yunpei, primary, Zerdane, Serhane, additional, Xie, Xinhua, additional, Divall, Edwin, additional, Johnson, Philip J. M., additional, Arrell, Christopher, additional, Lemke, Henrik Till, additional, Mankowsky, Roman, additional, Oggenfuss, Alex, additional, Svetina, Cristian, additional, Erny, Christian, additional, Cirelli, Claudio, additional, Milne, Christopher, additional, Knopp, Gregor, additional, Beaud, Paul, additional, and Johnson, Steven L., additional

Published
2020
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15. Mixed Potential Energy Surfaces of the Ultrafast Isomerization of Retinal in Bacteriorhodopsin

Author

Prokhorenko Valentyn I., Morizumi Takefumi, Halpin Alexei, Johnson Philip J. M., Ernst Oliver P., and Dwayne Miller R. J.

Subjects
Physics, QC1-999
Abstract

We observe, using electronic two-dimensional photon echo spectroscopy, that the cis and trans potential energy surfaces of the ultrafast isomerization of retinal in bacteriorhodopsin are mixed via the hydrogen out of plane (HOOP) mode.

Published
2013
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16. 2D-IR Spectroscopy of an AHA Labeled Photoswitchable PDZ2 Domain

Author

Stucki-Buchli, Brigitte, Johnson, Philip J M, Bozovic, Olga, Zanobini, Claudio, Koziol, Klemens L, Hamm, Peter, Gulzar, Adnan, Wolf, Steffen, Buchenberg, Sebastian, Stock, Gerhard, University of Zurich, and Hamm, Peter

Subjects
10120 Department of Chemistry, 540 Chemistry, 1606 Physical and Theoretical Chemistry
Published
2017

18. 2D-IR Spectroscopy of an AHA Labeled Photoswitchable PDZ2 Domain

Author

Stucki-Buchli, Brigitte, Johnson, Philip J. M., Bozovic, Olga, Zanobini, Claudio, Koziol, Klemens L., Hamm, Peter, Gulzar, Adnan, Wolf, Steffen, Buchenberg, Sebastian, and Stock, Gerhard

Abstract

We explore the capability of the non-natural amino acid azidohomoalanine (AHA) as an IR label to sense relatively small structural changes in proteins with the help of 2D IR difference spectroscopy. To that end, we AHA-labeled an allosteric protein (the PDZ2 domain from human tyrosine-phosphatase 1E) and furthermore covalently linked it to an azobenzene-derived photoswitch as to mimic its conformational transition upon ligand binding. To determine the strengths and limitations of the AHA label, in total six mutants have been investigated with the label at sites with varying properties. Only one mutant revealed a measurable 2D IR difference signal. In contrast to the commonly observed frequency shifts that report on the degree of solvation, in this case we observe an intensitychange. To understand this spectral response, we performed classical MD simulations, evaluating local contacts of the AHA labels to water molecules and protein side chains and calculating the vibrational frequency on the basis of an electrostatic model. Although these simulations revealed in part significant and complex changes of the number of intraprotein and water contacts upon trans–cisphotoisomerization, they could not provide a clear explanation of why this one label would stick out. Subsequent quantum-chemistry calculations suggest that the response is the result of an electronic interaction involving charge transfer of the azido group with sulfonate groups from the photoswitch. To the best of our knowledge, such an effect has not been described before.

Published
2024
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19. 2D-IR Spectroscopy of an AHA Labeled Photoswitchable PDZ2 Domain

Author

Stucki-Buchli, Brigitte, primary, Johnson, Philip J. M., additional, Bozovic, Olga, additional, Zanobini, Claudio, additional, Koziol, Klemens L., additional, Hamm, Peter, additional, Gulzar, Adnan, additional, Wolf, Steffen, additional, Buchenberg, Sebastian, additional, and Stock, Gerhard, additional

Published
2017
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22. Laser-Limited Signatures of Quantum Coherence

Author

Tempelaar, Roel, primary, Halpin, Alexei, additional, Johnson, Philip J. M., additional, Cai, Jianxin, additional, Murphy, R. Scott, additional, Knoester, Jasper, additional, Miller, R. J. Dwayne, additional, and Jansen, Thomas L. C., additional

Published
2015
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23. Toward single-molecule DNA uptake by Haemophilus influenzae

Author

Johnson, Philip J. M.

Abstract

Haemophilus influenzae is a Gram-negative, non-motile bacterium found in the respiratory tract of higher organisms which is naturally competent; that is, it naturally has the ability to internalise exogenous DNA. The DNA uptake machinery spans two membranes and has been shown to require an asymmetric nine basepair uptake signaling sequence to initiate DNA uptake, but the mechanism is still poorly understood. This thesis presents work toward single molecule DNA uptake experiments involving optical tweezers, including optical tweezer construction and characterization, DNA force-extension relations, plasmid design for single molecule uptake experiments, and efforts to immobilise H. influenzae cells to surfaces of polystyrene beads.

Published
2007

27. Optical second harmonic generation in LiB 3 O 5 modulated by intense femtosecond X-ray pulses.

Author

Deng Y, Zerdane S, Xie X, Divall E, Johnson PJM, Arrell C, Lemke HT, Mankowsky R, Oggenfuss A, Svetina C, Erny C, Cirelli C, Milne C, Knopp G, Beaud P, and Johnson SL

Abstract

Many of the scientific applications for X-ray free-electron lasers seek to exploit the ultrashort pulse durations of intense X-rays to obtain femtosecond time resolution of various processes in a "pump-probe" scheme. One of the limiting factors for such experiments is the timing jitter between the X-rays and ultrashort pulses from more conventional lasers operating at near-optical wavelengths. In this work, we investigate the potential of using X-ray-induced changes in the optical second harmonic generation efficiency of a nonlinear crystal to retrieve single-shot arrival times of X-ray pulses with respect to optical laser pulses. Our experimental results and simulations show changes to the efficiency of the second harmonic generation of 12%, approximately three times larger than the measured changes in the transmission of the 800 nm center-wavelength fundamental pulse. Further experiments showing even larger changes in the transmission of 400 nm center-wavelength pulses show that the mechanism of the second harmonic generation efficiency modulation is mainly the result of X-ray-induced changes in the linear absorption coefficients near 400 nm. We demonstrate and characterize a cross-correlation tool based on this effect in reference to a previously demonstrated method of X-ray/optical cross-correlation.

Published
2020
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