Publications

@article{Bertrand2024,

title = {Structural effects of high laser power densities on an early bacteriorhodopsin photocycle intermediate},

author = {Quentin Bertrand and Przemyslaw Nogly and Eriko Nango and Demet Kekilli and Georgii Khusainov and Antonia Furrer and Daniel James and Florian Dworkowski and Petr Skopintsev and Sandra Mous and Isabelle Martiel and Per B\"{o}rjesson and Giorgia Ortolani and Chia-Ying Huang and Michal Kepa and Dmitry Ozerov and Steffen Br\"{u}nle and Valerie Panneels and Tomoyuki Tanaka and Rie Tanaka and Kensuke Tono and Shigeki Owada and Philip J. M. Johnson and Karol Nass and Gregor Knopp and Claudio Cirelli and Christopher Milne and Gebhard Schertler and So Iwata and Richard Neutze and Tobias Weinert and J\"{o}rg Standfuss},

doi = {10.1038/s41467-024-54422-8},

issn = {2041-1723},

year  = {2024},

date = {2024-12-00},

journal = {Nat Commun},

volume = {15},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractTime-resolved serial crystallography at X-ray Free Electron Lasers offers the opportunity to observe ultrafast photochemical reactions at the atomic level. The technique has yielded exciting molecular insights into various biological processes including light sensing and photochemical energy conversion. However, to achieve sufficient levels of activation within an optically dense crystal, high laser power densities are often used, which has led to an ongoing debate to which extent photodamage may compromise interpretation of the results. Here we compare time-resolved serial crystallographic data of the bacteriorhodopsin K-intermediate collected at laser power densities ranging from 0.04 to 2493 GW/cm2 and follow energy dissipation of the absorbed photons logarithmically from picoseconds to milliseconds. Although the effects of high laser power densities on the overall structure are small, in the upper excitation range we observe significant changes in retinal conformation and increased heating of the functionally critical counterion cluster. We compare light-activation within crystals to that in solution and discuss the impact of the observed changes on bacteriorhodopsin biology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gotthard2024,

title = {Fixed-target pump\textendashprobe SFX: eliminating the scourge of light contamination},

author = {Guillaume Gotthard and Andrea Flores-Ibarra and Melissa Carrillo and Michal W. Kepa and Thomas J. Mason and Dennis P. Stegmann and Bence Olasz and Magdalena Pachota and Florian Dworkowski and Dmitry Ozerov and Bill F. Pedrini and Celestino Padeste and John H. Beale and Przemyslaw Nogly},

doi = {10.1107/s2052252524005591},

issn = {2052-2525},

year  = {2024},

date = {2024-09-00},

urldate = {2024-09-00},

journal = {Int Union Crystallogr J},

volume = {11},

number = {5},

publisher = {International Union of Crystallography (IUCr)},

abstract = {\<jats:p\>X-ray free-electron laser (XFEL) light sources have enabled the rapid growth of time-resolved structural experiments, which provide crucial information on the function of macromolecules and their mechanisms. Here, the aim was to commission the SwissMX fixed-target sample-delivery system at the SwissFEL Cristallina experimental station using the PSI-developed micro-structured polymer (MISP) chip for pump\textendashprobe time-resolved experiments. To characterize the system, crystals of the light-sensitive protein light\textendashoxygen\textendashvoltage domain 1 (LOV1) from \<jats:italic\>Chlamydomonas reinhardtii\</jats:italic\> were used. Using different experimental settings, the accidental illumination, referred to as light contamination, of crystals mounted in wells adjacent to those illuminated by the pump laser was examined. It was crucial to control the light scattering from and through the solid supports otherwise significant contamination occurred. However, the results here show that the opaque MISP chips are suitable for defined pump\textendashprobe studies of a light-sensitive protein. The experiment also probed the sub-millisecond structural dynamics of LOV1 and indicated that at Δ\<jats:italic\>t\</jats:italic\> = 10 µs a covalent thioether bond is established between reactive Cys57 and its flavin mononucleotide cofactor. This experiment validates the crystals to be suitable for in-depth follow-up studies of this still poorly understood signal-transduction mechanism. Importantly, the fixed-target delivery system also permitted a tenfold reduction in protein sample consumption compared with the more common high-viscosity extrusion-based delivery system. This development creates the prospect of an increase in XFEL project throughput for the field.\</jats:p\>},

keywords = {Biochemistry, Biophysics, Chemistry (miscellaneous), General Materials Science, Instrumentation, Structural Biology},

pubstate = {published},

tppubtype = {article}

}

@article{Gotthard2024b,

title = {Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography},

author = {Guillaume Gotthard and Sandra Mous and Tobias Weinert and Raiza Nara Antonelli Maia and Daniel James and Florian Dworkowski and Dardan Gashi and Antonia Furrer and Dmitry Ozerov and Ezequiel Panepucci and Meitian Wang and Gebhard F. X. Schertler and Joachim Heberle and Joerg Standfuss and Przemyslaw Nogly},

doi = {10.1107/s2052252524005608},

issn = {2052-2525},

year  = {2024},

date = {2024-09-00},

urldate = {2024-09-00},

journal = {IUCrJ},

volume = {11},

number = {5},

pages = {792--808},

publisher = {International Union of Crystallography (IUCr)},

abstract = {Light\textendashoxygen\textendashvoltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intracellular signals responsible for various cell behaviors (e.g. phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from Chlamydomonas reinhardtii (CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of CrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Flores-Ibarra2024,

title = {Light-Oxygen-Voltage (LOV)-sensing Domains: Activation Mechanism and Optogenetic Stimulation},

author = {Andrea Flores-Ibarra and Raiza N.A. Maia and Bence Olasz and Jonathan R. Church and Guillaume Gotthard and Igor Schapiro and Joachim Heberle and Przemyslaw Nogly},

doi = {10.1016/j.jmb.2023.168356},

issn = {0022-2836},

year  = {2024},

date = {2024-03-00},

urldate = {2024-03-00},

journal = {Journal of Molecular Biology},

volume = {436},

number = {5},

publisher = {Elsevier BV},

abstract = {The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies.},

keywords = {Biochemistry, Biophysics, Spectroscopy, Structural Biology},

pubstate = {published},

tppubtype = {article}

}

@article{Gruhl2023,

title = {Ultrafast structural changes direct the first molecular events of vision},

author = {Thomas Gruhl and Tobias Weinert and Matthew J. Rodrigues and Christopher J. Milne and Giorgia Ortolani and Karol Nass and Eriko Nango and Saumik Sen and Philip J. M. Johnson and Claudio Cirelli and Antonia Furrer and Sandra Mous and Petr Skopintsev and Daniel James and Florian Dworkowski and Petra Br{a}th and Demet Kekilli and Dmitry Ozerov and Rie Tanaka and Hannah Glover and Camila Bacellar and Steffen Br\"{u}nle and Cecilia M. Casadei and Azeglio D. Diethelm and Dardan Gashi and Guillaume Gotthard and Ramon Guix\`{a}-Gonz\'{a}lez and Yasumasa Joti and Victoria Kabanova and Gregor Knopp and Elena Lesca and Pikyee Ma and Isabelle Martiel and Jonas M\"{u}hle and Shigeki Owada and Filip Pamula and Daniel Sarabi and Oliver Tejero and Ching-Ju Tsai and Niranjan Varma and Anna Wach and S\'{e}bastien Boutet and Kensuke Tono and Przemyslaw Nogly and Xavier Deupi and So Iwata and Richard Neutze and J\"{o}rg Standfuss and Gebhard Schertler and Valerie Panneels},

doi = {10.1038/s41586-023-05863-6},

issn = {1476-4687},

year  = {2023},

date = {2023-03-30},

journal = {Nature},

volume = {615},

number = {7954},

pages = {939--944},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractVision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature3 to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.},

keywords = {Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Mous2022,

title = {Dynamics and mechanism of a light-driven chloride pump},

author = {Sandra Mous and Guillaume Gotthard and David Ehrenberg and Saumik Sen and Tobias Weinert and Philip J. M. Johnson and Daniel James and Karol Nass and Antonia Furrer and Demet Kekilli and Pikyee Ma and Steffen Br\"{u}nle and Cecilia Maria Casadei and Isabelle Martiel and Florian Dworkowski and Dardan Gashi and Petr Skopintsev and Maximilian Wranik and Gregor Knopp and Ezequiel Panepucci and Valerie Panneels and Claudio Cirelli and Dmitry Ozerov and Gebhard F. X. Schertler and Meitian Wang and Chris Milne and Joerg Standfuss and Igor Schapiro and Joachim Heberle and Przemyslaw Nogly},

doi = {10.1126/science.abj6663},

issn = {1095-9203},

year  = {2022},

date = {2022-02-25},

journal = {Science},

volume = {375},

number = {6583},

pages = {845--851},

publisher = {American Association for the Advancement of Science (AAAS)},

abstract = {Chloride transport by microbial rhodopsins is an essential process for which molecular details such as the mechanisms that convert light energy to drive ion pumping and ensure the unidirectionality of the transport have remained elusive. We combined time-resolved serial crystallography with time-resolved spectroscopy and multiscale simulations to elucidate the molecular mechanism of a chloride-pumping rhodopsin and the structural dynamics throughout the transport cycle. We traced transient anion-binding sites, obtained evidence for how light energy is used in the pumping mechanism, and identified steric and electrostatic molecular gates ensuring unidirectional transport. An interaction with the π-electron system of the retinal supports transient chloride ion binding across a major bottleneck in the transport pathway. These results allow us to propose key mechanistic features enabling finely controlled chloride transport across the cell membrane in this light-powered chloride ion pump.},

keywords = {Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Nass2020,

title = {Advances in long-wavelength native phasing at X-ray free-electron lasers},

author = {Karol Nass and Robert Cheng and Laura Vera and Aldo Mozzanica and Sophie Redford and Dmitry Ozerov and Shibom Basu and Daniel James and Gregor Knopp and Claudio Cirelli and Isabelle Martiel and Cecilia Casadei and Tobias Weinert and Przemyslaw Nogly and Petr Skopintsev and Ivan Usov and Filip Leonarski and Tian Geng and Mathieu Rappas and Andrew S. Dor\'{e} and Robert Cooke and Shahrooz Nasrollahi Shirazi and Florian Dworkowski and May Sharpe and Natacha Olieric and Camila Bacellar and Rok Bohinc and Michel O. Steinmetz and Gebhard Schertler and Rafael Abela and Luc Patthey and Bernd Schmitt and Michael Hennig and J\"{o}rg Standfuss and Meitian Wang and Christopher J. Milne},

doi = {10.1107/s2052252520011379},

issn = {2052-2525},

year  = {2020},

date = {2020-11-00},

journal = {Int Union Crystallogr J},

volume = {7},

number = {6},

pages = {965--975},

publisher = {International Union of Crystallography (IUCr)},

abstract = {Long-wavelength pulses from the Swiss X-ray free-electron laser (XFEL) have been used for de novo protein structure determination by native single-wavelength anomalous diffraction (native-SAD) phasing of serial femtosecond crystallography (SFX) data. In this work, sensitive anomalous data-quality indicators and model proteins were used to quantify improvements in native-SAD at XFELs such as utilization of longer wavelengths, careful experimental geometry optimization, and better post-refinement and partiality correction. Compared with studies using shorter wavelengths at other XFELs and older software versions, up to one order of magnitude reduction in the required number of indexed images for native-SAD was achieved, hence lowering sample consumption and beam-time requirements significantly. Improved data quality and higher anomalous signal facilitate so-far underutilized de novo structure determination of challenging proteins at XFELs. Improvements presented in this work can be used in other types of SFX experiments that require accurate measurements of weak signals, for example time-resolved studies.},

keywords = {Biochemistry, Condensed Matter Physics, General Chemistry, General Materials Science},

pubstate = {published},

tppubtype = {article}

}

@article{Magoch2020,

title = {Crystal Structure of Mannose Specific IIA Subunit of Phosphotransferase System from Streptococcus pneumoniae},

author = {Malgorzata Magoch and Przemyslaw Nogly and Przemyslaw Grudnik and Pikyee Ma and Bozena Boczkus and Ana Rute Neves and Margarida Archer and Grzegorz Dubin},

doi = {10.3390/molecules25204633},

issn = {1420-3049},

year  = {2020},

date = {2020-10-00},

journal = {Molecules},

volume = {25},

number = {20},

publisher = {MDPI AG},

abstract = {Streptococcus pneumoniae is a frequent bacterial pathogen of the human respiratory tract causing pneumonia, meningitis and sepsis, a serious healthcare burden in all age groups. S. pneumoniae lacks complete respiratory chain and relies on carbohydrate fermentation for energy generation. One of the essential components for this includes the mannose phosphotransferase system (Man-PTS), which plays a central role in glucose transport and exhibits a broad specificity for a range of hexoses. Importantly, Man-PTS is involved in the global regulation of gene expression for virulence determinants. We herein report the three-dimensional structure of the EIIA domain of S. pneumoniae mannose phosphotransferase system (SpEIIA-Man). Our structure shows a dimeric arrangement of EIIA and reveals a detailed molecular description of the active site. Since PTS transporters are exclusively present in microbes and sugar transporters have already been suggested as valid targets for antistreptococcal antibiotics, our work sets foundation for the future development of antimicrobial strategies against Streptococcus pneumoniae.},

keywords = {Analytical Chemistry, Chemistry (miscellaneous), Drug Discovery, Molecular Medicine, Organic Chemistry, Pharmaceutical Science, Physical and Theoretical Chemistry},

pubstate = {published},

tppubtype = {article}

}

@article{Skopintsev2020,

title = {Femtosecond-to-millisecond structural changes in a light-driven sodium pump},

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

doi = {10.1038/s41586-020-2307-8},

issn = {1476-4687},

year  = {2020},

date = {2020-07-09},

journal = {Nature},

volume = {583},

number = {7815},

pages = {314--318},

publisher = {Springer Science and Business Media LLC},

keywords = {Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Wickstrand2020,

title = {A tool for visualizing protein motions in time-resolved crystallography},

author = {Cecilia Wickstrand and Gergely Katona and Takanori Nakane and Przemyslaw Nogly and Joerg Standfuss and Eriko Nango and Richard Neutze},

doi = {10.1063/1.5126921},

issn = {2329-7778},

year  = {2020},

date = {2020-03-00},

journal = {Structural Dynamics},

volume = {7},

number = {2},

publisher = {AIP Publishing},

keywords = {Condensed Matter Physics, Instrumentation, Radiation, Spectroscopy},

pubstate = {published},

tppubtype = {article}

}

@article{Jaeger2019,

title = {Structural Basis for Allosteric Ligand Recognition in the Human CC Chemokine Receptor 7},

author = {Kathrin Jaeger and Steffen Bruenle and Tobias Weinert and Wolfgang Guba and Jonas Muehle and Takuya Miyazaki and Martin Weber and Antonia Furrer and Noemi Haenggi and Tim Tetaz and Chia-Ying Huang and Daniel Mattle and Jean-Marie Vonach and Alain Gast and Andreas Kuglstatter and Markus G. Rudolph and Przemyslaw Nogly and Joerg Benz and Roger J.P. Dawson and Joerg Standfuss},

doi = {10.1016/j.cell.2019.07.028},

issn = {0092-8674},

year  = {2019},

date = {2019-08-00},

journal = {Cell},

volume = {178},

number = {5},

pages = {1222--1230.e10},

publisher = {Elsevier BV},

keywords = {General Biochemistry, Genetics and Molecular Biology},

pubstate = {published},

tppubtype = {article}

}

@article{Varma2019,

title = {Crystal structure of jumping spider rhodopsin-1 as a light sensitive GPCR},

author = {Niranjan Varma and Eshita Mutt and Jonas M\"{u}hle and Val\'{e}rie Panneels and Akihisa Terakita and Xavier Deupi and Przemyslaw Nogly and Gebhard F. X. Schertler and Elena Lesca},

doi = {10.1073/pnas.1902192116},

issn = {1091-6490},

year  = {2019},

date = {2019-07-16},

journal = {Proc. Natl. Acad. Sci. U.S.A.},

volume = {116},

number = {29},

pages = {14547--14556},

publisher = {Proceedings of the National Academy of Sciences},

abstract = {

            Light-sensitive G protein-coupled receptors (GPCRs)\textemdashrhodopsins\textemdashabsorb photons to isomerize their covalently bound retinal, triggering conformational changes that result in downstream signaling cascades. Monostable rhodopsins release retinal upon isomerization as opposed to the retinal in bistable rhodopsins that “reisomerize” upon absorption of a second photon. Understanding the mechanistic differences between these light-sensitive GPCRs has been hindered by the scarcity of recombinant models of the latter. Here, we reveal the high-resolution crystal structure of a recombinant bistable rhodopsin, jumping spider rhodopsin-1, bound to the inverse agonist 9-

            cis

            retinal. We observe a water-mediated network around the ligand hinting toward the basis of their bistable nature. In contrast to bovine rhodopsin (monostable), the transmembrane bundle of jumping spider rhodopsin-1 as well that of the bistable squid rhodopsin adopts a more “activation-ready” conformation often observed in other nonphotosensitive class A GPCRs. These similarities suggest the role of jumping spider rhodopsin-1 as a potential model system in the study of the structure\textendashfunction relationship of both photosensitive and nonphotosensitive class A GPCRs.

          },

keywords = {Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Weinert2019,

title = {Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography},

author = {Tobias Weinert and Petr Skopintsev and Daniel James and Florian Dworkowski and Ezequiel Panepucci and Demet Kekilli and Antonia Furrer and Steffen Br\"{u}nle and Sandra Mous and Dmitry Ozerov and Przemyslaw Nogly and Meitian Wang and J\"{o}rg Standfuss},

doi = {10.1126/science.aaw8634},

issn = {1095-9203},

year  = {2019},

date = {2019-07-05},

journal = {Science},

volume = {365},

number = {6448},

pages = {61--65},

publisher = {American Association for the Advancement of Science (AAAS)},

abstract = {Refilling the proton pump

          

            Proteins are dynamic. Rearrangements of side chains, secondary structure, and entire domains gate functional transitions on time scales ranging from picoseconds to milliseconds. Weinert

            et al.

            used time-resolved serial crystallography to study large conformational changes in the proton pump bacteriorhodopsin that allow for redistribution of protons during the pumping cycle. They adapted methods used for x-ray free electron lasers to synchrotron x-ray sources. Large loop movements and a chain of water molecules were central to regenerating the starting state of bacteriorhodopsin.

          

          

            Science

            , this issue p.

            61

          },

keywords = {Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Wickstrand2019,

title = {Bacteriorhodopsin: Structural Insights Revealed Using X-Ray Lasers and Synchrotron Radiation},

author = {Cecilia Wickstrand and Przemyslaw Nogly and Eriko Nango and So Iwata and J\"{o}rg Standfuss and Richard Neutze},

doi = {10.1146/annurev-biochem-013118-111327},

issn = {1545-4509},

year  = {2019},

date = {2019-06-20},

journal = {Annu. Rev. Biochem.},

volume = {88},

number = {1},

pages = {59--83},

publisher = {Annual Reviews},

abstract = { Directional transport of protons across an energy transducing membrane\textemdashproton pumping\textemdashis ubiquitous in biology. Bacteriorhodopsin (bR) is a light-driven proton pump that is activated by a buried all- trans retinal chromophore being photoisomerized to a 13- cis conformation. The mechanism by which photoisomerization initiates directional proton transport against a proton concentration gradient has been studied by a myriad of biochemical, biophysical, and structural techniques. X-ray free electron lasers (XFELs) have created new opportunities to probe the structural dynamics of bR at room temperature on timescales from femtoseconds to milliseconds using time-resolved serial femtosecond crystallography (TR-SFX). Wereview these recent developments and highlight where XFEL studies reveal new details concerning the structural mechanism of retinal photoisomerization and proton pumping. We also discuss the extent to which these insights were anticipated by earlier intermediate trapping studies using synchrotron radiation. TR-SFX will open up the field for dynamical studies of other proteins that are not naturally light-sensitive. },

keywords = {Biochemistry},

pubstate = {published},

tppubtype = {article}

}

@article{James2019,

title = {Improving High Viscosity Extrusion of Microcrystals for Time-resolved Serial Femtosecond Crystallography at X-ray Lasers},

author = {Daniel James and Tobias Weinert and Petr Skopintsev and Antonia Furrer and Dardan Gashi and Tomoyuki Tanaka and Eriko Nango and Przemyslaw Nogly and Joerg Standfuss},

doi = {10.3791/59087},

issn = {1940-087X},

year  = {2019},

date = {2019-00-00},

journal = {JoVE},

number = {144},

publisher = {MyJove Corporation},

keywords = {General Biochemistry, General Chemical Engineering, General Immunology and Microbiology, General Neuroscience, Genetics and Molecular Biology},

pubstate = {published},

tppubtype = {article}

}

@article{Tsai2018,

title = {Crystal structure of rhodopsin in complex with a mini-G

            _{o}

            sheds light on the principles of G protein selectivity},

author = {Ching-Ju Tsai and Filip Pamula and Rony Nehm\'{e} and Jonas M\"{u}hle and Tobias Weinert and Tilman Flock and Przemyslaw Nogly and Patricia C. Edwards and Byron Carpenter and Thomas Gruhl and Pikyee Ma and Xavier Deupi and J\"{o}rg Standfuss and Christopher G. Tate and Gebhard F. X. Schertler},

doi = {10.1126/sciadv.aat7052},

issn = {2375-2548},

year  = {2018},

date = {2018-09-07},

journal = {Sci. Adv.},

volume = {4},

number = {9},

publisher = {American Association for the Advancement of Science (AAAS)},

abstract = {

            The structure of the rhodopsin/mini-G

            o

            complex reveals new insights on G protein selectivity.

          },

keywords = {Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Neutze2018,

title = {Time-resolved serial femtosecond crystallography studies at an X-ray free electron laser reveals structural changes in bacteriorhodopsin},

author = {Richard Neutze and Eriko Nango and Tomoyuki Tanaka and Takanori Nakane and So Iwata and Antoine Royant and J\"{o}rg Standfuss and Przemyslaw Nogly and Cecilia Wickstrand},

doi = {10.1016/j.bbabio.2018.09.087},

issn = {0005-2728},

year  = {2018},

date = {2018-09-00},

journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},

volume = {1859},

publisher = {Elsevier BV},

keywords = {Biochemistry, Biophysics, Cell Biology},

pubstate = {published},

tppubtype = {article}

}

@article{Nogly2018,

title = {Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser},

author = {Przemyslaw Nogly and Tobias Weinert and Daniel James and Sergio Carbajo and Dmitry Ozerov and Antonia Furrer and Dardan Gashi and Veniamin Borin and Petr Skopintsev and Kathrin Jaeger and Karol Nass and Petra Br{a}th and Robert Bosman and Jason Koglin and Matthew Seaberg and Thomas Lane and Demet Kekilli and Steffen Br\"{u}nle and Tomoyuki Tanaka and Wenting Wu and Christopher Milne and Thomas White and Anton Barty and Uwe Weierstall and Valerie Panneels and Eriko Nango and So Iwata and Mark Hunter and Igor Schapiro and Gebhard Schertler and Richard Neutze and J\"{o}rg Standfuss},

doi = {10.1126/science.aat0094},

issn = {1095-9203},

year  = {2018},

date = {2018-07-13},

journal = {Science},

volume = {361},

number = {6398},

publisher = {American Association for the Advancement of Science (AAAS)},

keywords = {Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Weinert2017,

title = {Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons},

author = {Tobias Weinert and Natacha Olieric and Robert Cheng and Steffen Br\"{u}nle and Daniel James and Dmitry Ozerov and Dardan Gashi and Laura Vera and May Marsh and Kathrin Jaeger and Florian Dworkowski and Ezequiel Panepucci and Shibom Basu and Petr Skopintsev and Andrew S. Dor\'{e} and Tian Geng and Robert M. Cooke and Mengning Liang and Andrea E. Prota and Valerie Panneels and Przemyslaw Nogly and Ulrich Ermler and Gebhard Schertler and Michael Hennig and Michel O. Steinmetz and Meitian Wang and J\"{o}rg Standfuss},

doi = {10.1038/s41467-017-00630-4},

issn = {2041-1723},

year  = {2017},

date = {2017-12-00},

journal = {Nat Commun},

volume = {8},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractHistorically, room-temperature structure determination was succeeded by cryo-crystallography to mitigate radiation damage. Here, we demonstrate that serial millisecond crystallography at a synchrotron beamline equipped with high-viscosity injector and high frame-rate detector allows typical crystallographic experiments to be performed at room-temperature. Using a crystal scanning approach, we determine the high-resolution structure of the radiation sensitive molybdenum storage protein, demonstrate soaking of the drug colchicine into  tubulin and native sulfur phasing of the human G protein-coupled adenosine receptor. Serial crystallographic data for molecular replacement already converges in 1,000\textendash10,000 diffraction patterns, which we collected in 3 to maximally 82 minutes. Compared with serial data we collected at a free-electron laser, the synchrotron data are of slightly lower resolution, however fewer diffraction patterns are needed for de novo phasing. Overall, the data we collected by room-temperature serial crystallography are of comparable quality to cryo-crystallographic data and can be routinely collected at synchrotrons.},

keywords = {General Biochemistry, General Chemistry, General Physics and Astronomy, Genetics and Molecular Biology, Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Nango2016,

title = {A three-dimensional movie of structural changes in bacteriorhodopsin},

author = {Eriko Nango and Antoine Royant and Minoru Kubo and Takanori Nakane and Cecilia Wickstrand and Tetsunari Kimura and Tomoyuki Tanaka and Kensuke Tono and Changyong Song and Rie Tanaka and Toshi Arima and Ayumi Yamashita and Jun Kobayashi and Toshiaki Hosaka and Eiichi Mizohata and Przemyslaw Nogly and Michihiro Sugahara and Daewoong Nam and Takashi Nomura and Tatsuro Shimamura and Dohyun Im and Takaaki Fujiwara and Yasuaki Yamanaka and Byeonghyun Jeon and Tomohiro Nishizawa and Kazumasa Oda and Masahiro Fukuda and Rebecka Andersson and Petra Br{a}th and Robert Dods and Jan Davidsson and Shigeru Matsuoka and Satoshi Kawatake and Michio Murata and Osamu Nureki and Shigeki Owada and Takashi Kameshima and Takaki Hatsui and Yasumasa Joti and Gebhard Schertler and Makina Yabashi and Ana-Nicoleta Bondar and J\"{o}rg Standfuss and Richard Neutze and So Iwata},

doi = {10.1126/science.aah3497},

issn = {1095-9203},

year  = {2016},

date = {2016-12-23},

journal = {Science},

volume = {354},

number = {6319},

pages = {1552--1557},

publisher = {American Association for the Advancement of Science (AAAS)},

abstract = {Snapshots of bacteriorhodopsin

          

            Bacteriorhodopsin is a membrane protein that harvests the energy content from light to transport protons out of the cell against a transmembrane potential. Nango

            et al.

            used timeresolved serial femtosecond crystallography at an x-ray free electron laser to provide 13 structural snapshots of the conformational changes that occur in the nanoseconds to milliseconds after photoactivation. These changes begin at the active site, propagate toward the extracellular side of the protein, and mediate internal protonation exchanges that achieve proton transport.

          

          

            Science

            , this issue p.

            1552

          },

keywords = {Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Nogly2016b,

title = {Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography},

author = {Przemyslaw Nogly and Valerie Panneels and Garrett Nelson and Cornelius Gati and Tetsunari Kimura and Christopher Milne and Despina Milathianaki and Minoru Kubo and Wenting Wu and Chelsie Conrad and Jesse Coe and Richard Bean and Yun Zhao and Petra Br{a}th and Robert Dods and Rajiv Harimoorthy and Kenneth R. Beyerlein and Jan Rheinberger and Daniel James and Daniel DePonte and Chufeng Li and Leonardo Sala and Garth J. Williams and Mark S. Hunter and Jason E. Koglin and Peter Berntsen and Eriko Nango and So Iwata and Henry N. Chapman and Petra Fromme and Matthias Frank and Rafael Abela and S\'{e}bastien Boutet and Anton Barty and Thomas A. White and Uwe Weierstall and John Spence and Richard Neutze and Gebhard Schertler and J\"{o}rg Standfuss},

doi = {10.1038/ncomms12314},

issn = {2041-1723},

year  = {2016},

date = {2016-11-25},

journal = {Nat Commun},

volume = {7},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractSerial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 r{A} resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.},

keywords = {General Biochemistry, General Chemistry, General Physics and Astronomy, Genetics and Molecular Biology, Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Nogly2016,

title = {Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography},

author = {Przemyslaw Nogly and Valerie Panneels and Garrett Nelson and Cornelius Gati and Tetsunari Kimura and Christopher Milne and Despina Milathianaki and Minoru Kubo and Wenting Wu and Chelsie Conrad and Jesse Coe and Richard Bean and Yun Zhao and Petra Bath and Robert Dods and Rajiv Harimoorthy and Kenneth Beyerlein and Jan Rheinberger and Daniel James and Daniel DePonte and Chufeng Li and Leonardo Sala and Garth Williams and Mark Hunter and Jason E. Koglin and Peter Berntsen and Eriko Nango and So Iwata and Henry Chapman and Petra Fromme and Matthias Frank and Rafael Abela and S\'{e}bastien Boutet and Anton Barty and Thomas A. White and Uwe Weierstall and John Spence and Richard Neutze and Gebhard Schertler and J\"{o}rg Standfuss},

doi = {10.1107/s2053273316099368},

issn = {2053-2733},

year  = {2016},

date = {2016-08-00},

journal = {Acta Cryst Sect A},

volume = {72},

number = {a1},

pages = {s41--s42},

publisher = {International Union of Crystallography (IUCr)},

keywords = {Biochemistry, Condensed Matter Physics, General Materials Science, Inorganic Chemistry, Physical and Theoretical Chemistry, Structural Biology},

pubstate = {published},

tppubtype = {article}

}

@article{pmid27553240,

title = {Serial Millisecond Crystallography of Membrane Proteins},

author = {Kathrin Jaeger and Florian Dworkowski and Przemyslaw Nogly and Christopher Milne and Meitian Wang and Joerg Standfuss},

doi = {10.1007/978-3-319-35072-1_10},

issn = {0065-2598},

year  = {2016},

date = {2016-01-01},

journal = {Adv Exp Med Biol},

volume = {922},

pages = {137--149},

abstract = {Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) is a powerful method to determine high-resolution structures of pharmaceutically relevant membrane proteins. Recently, the technology has been adapted to carry out serial millisecond crystallography (SMX) at synchrotron sources, where beamtime is more abundant. In an injector-based approach, crystals grown in lipidic cubic phase (LCP) or embedded in viscous medium are delivered directly into the unattenuated beam of a microfocus beamline. Pilot experiments show the application of microjet-based SMX for solving the structure of a membrane protein and compatibility of the method with de novo phasing. Planned synchrotron upgrades, faster detectors and software developments will go hand-in-hand with developments at free-electron lasers to provide a powerful methodology for solving structures from microcrystals at room temperature, ligand screening or crystal optimization for time-resolved studies with minimal or no radiation damage.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hofbauer2015,

title = {Stabilization of porcine pancreatic elastase crystals by glutaraldehyde cross-linking},

author = {Stefan Hofbauer and Jos\'{e} A. Brito and Jalmira Mulchande and Przemyslaw Nogly and Miguel Pessanha and Rui Moreira and Margarida Archer},

doi = {10.1107/s2053230x15017045},

issn = {2053-230X},

year  = {2015},

date = {2015-10-00},

journal = {Acta Cryst Sect F},

volume = {71},

number = {10},

pages = {1346--1351},

publisher = {International Union of Crystallography (IUCr)},

abstract = {Elastase is a serine protease from the chymotrypsin family of enzymes with the ability to degrade elastin, an important component of connective tissues. Excessive elastin proteolysis leads to a number of pathological diseases. Porcine pancreatic elastase (PPE) is often used for drug development as a model for human leukocyte elastase (HLE), with which it shares high sequence identity. Crystals of PPE were grown overnight using sodium sulfate and sodium acetate at acidic pH. Cross-linking the crystals with glutaraldehyde was needed to resist the soaking procedure with a diethyl N-(methyl)pyridinyl-substituted oxo-β-lactam inhibitor. Crystals of PPE bound to the inhibitor belonged to the orthorhombic space group P212121, with unit-cell parameters a = 51.0, b = 58.3, c = 74.9 r{A}, and diffracted to 1.8 r{A} resolution using an in-house X-ray source.},

keywords = {Biochemistry, Biophysics, Condensed Matter Physics, Genetics, Structural Biology},

pubstate = {published},

tppubtype = {article}

}

@article{Wu2015,

title = {Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser},

author = {Wenting Wu and Przemyslaw Nogly and Jan Rheinberger and Leonhard M. Kick and Cornelius Gati and Garrett Nelson and Xavier Deupi and J\"{o}rg Standfuss and Gebhard Schertler and Val\'{e}rie Panneels},

doi = {10.1107/s2053230x15009966},

issn = {2053-230X},

year  = {2015},

date = {2015-07-00},

journal = {Acta Cryst Sect F},

volume = {71},

number = {7},

pages = {856--860},

publisher = {International Union of Crystallography (IUCr)},

abstract = {Rhodopsin is a membrane protein from the G protein-coupled receptor family. Together with its ligand retinal, it forms the visual pigment responsible for night vision. In order to perform ultrafast dynamics studies, a time-resolved serial femtosecond crystallography method is required owing to the nonreversible activation of rhodopsin. In such an approach, microcrystals in suspension are delivered into the X-ray pulses of an X-ray free-electron laser (XFEL) after a precise photoactivation delay. Here, a millilitre batch production of high-density microcrystals was developed by four methodical conversion steps starting from known vapour-diffusion crystallization protocols: (i) screening the low-salt crystallization conditions preferred for serial crystallography by vapour diffusion, (ii) optimization of batch crystallization, (iii) testing the crystal size and quality using second-harmonic generation (SHG) imaging and X-ray powder diffraction and (iv) production of millilitres of rhodopsin crystal suspension in batches for serial crystallography tests; these crystals diffracted at an XFEL at the Linac Coherent Light Source using a liquid-jet setup.},

keywords = {Biochemistry, Biophysics, Condensed Matter Physics, Genetics, Structural Biology},

pubstate = {published},

tppubtype = {article}

}

@article{Panneels2015,

title = {Time-resolved structural studies with serial crystallography: A new light on retinal proteins},

author = {Val\'{e}rie Panneels and Wenting Wu and Ching-Ju Tsai and Przemek Nogly and Jan Rheinberger and Kathrin Jaeger and Gregor Cicchetti and Cornelius Gati and Leonhard M. Kick and Leonardo Sala and Guido Capitani and Chris Milne and Celestino Padeste and Bill Pedrini and Xiao-Dan Li and J\"{o}rg Standfuss and Rafael Abela and Gebhard Schertler},

doi = {10.1063/1.4922774},

issn = {2329-7778},

year  = {2015},

date = {2015-07-00},

journal = {Struct. Dyn.},

volume = {2},

number = {4},

publisher = {AIP Publishing},

keywords = {Condensed Matter Physics, Instrumentation, Radiation, Spectroscopy},

pubstate = {published},

tppubtype = {article}

}

@article{pmid25945883,

title = {Light-driven Na(+) pumps as next-generation inhibitory optogenetic tools},

author = {Przemyslaw Nogly and J\"{o}rg Standfuss},

doi = {10.1038/nsmb.3017},

issn = {1545-9985},

year  = {2015},

date = {2015-05-01},

journal = {Nat Struct Mol Biol},

volume = {22},

number = {5},

pages = {351--353},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nogly2015,

title = {Lipidic cubic phase serial millisecond crystallography using synchrotron radiation},

author = {Przemyslaw Nogly and Daniel James and Dingjie Wang and Thomas A. White and Nadia Zatsepin and Anastasya Shilova and Garrett Nelson and Haiguang Liu and Linda Johansson and Michael Heymann and Kathrin Jaeger and Markus Metz and Cecilia Wickstrand and Wenting Wu and Petra Br{a}th and Peter Berntsen and Dominik Oberthuer and Valerie Panneels and Vadim Cherezov and Henry Chapman and Gebhard Schertler and Richard Neutze and John Spence and Isabel Moraes and Manfred Burghammer and Joerg Standfuss and Uwe Weierstall},

doi = {10.1107/s2052252514026487},

issn = {2052-2525},

year  = {2015},

date = {2015-03-00},

journal = {Int Union Crystallogr J},

volume = {2},

number = {2},

pages = {168--176},

publisher = {International Union of Crystallography (IUCr)},

abstract = {Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 r{A}. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway.},

keywords = {Biochemistry, Condensed Matter Physics, General Chemistry, General Materials Science},

pubstate = {published},

tppubtype = {article}

}

@article{Nogly2014,

title = {X-ray structure of a CDP-alcohol phosphatidyltransferase membrane enzyme and insights into its catalytic mechanism},

author = {Przemyslaw Nogly and Ivan Gushchin and Alina Remeeva and Ana M. Esteves and Nuno Borges and Pikyee Ma and Andrii Ishchenko and Sergei Grudinin and Ekaterina Round and Isabel Moraes and Valentin Borshchevskiy and Helena Santos and Valentin Gordeliy and Margarida Archer},

doi = {10.1038/ncomms5169},

issn = {2041-1723},

year  = {2014},

date = {2014-09-22},

journal = {Nat Commun},

volume = {5},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {General Biochemistry, General Chemistry, General Physics and Astronomy, Genetics and Molecular Biology, Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Ma2013,

title = {An Efficient Strategy for Small-Scale Screening and Production of Archaeal Membrane Transport Proteins in Escherichia coli},

author = {Pikyee Ma and Filipa Varela and Malgorzata Magoch and Ana Rita Silva and Ana L\'{u}cia Ros\'{a}rio and Jos\'{e} Brito and T\^{a}nia Filipa Oliveira and Przemyslaw Nogly and Miguel Pessanha and Meike Stelter and Arnulf Kletzin and Peter J. F. Henderson and Margarida Archer},

editor = {Hendrik W. van Veen},

doi = {10.1371/journal.pone.0076913},

issn = {1932-6203},

year  = {2013},

date = {2013-10-07},

journal = {PLoS ONE},

volume = {8},

number = {10},

publisher = {Public Library of Science (PLoS)},

keywords = {Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Nogly2013,

title = {High-resolution structure of an atypical α-phosphoglucomutase related to eukaryotic phosphomannomutases},

author = {Przemyslaw Nogly and Pedro M. Matias and Matteo de Rosa and Rute Castro and Helena Santos and Ana Rute Neves and Margarida Archer},

doi = {10.1107/s0907444913017046},

issn = {0907-4449},

year  = {2013},

date = {2013-10-00},

journal = {Acta Crystallogr D Biol Cryst},

volume = {69},

number = {10},

pages = {2008--2016},

publisher = {International Union of Crystallography (IUCr)},

abstract = {The first structure of a bacterial α-phosphoglucomutase with an overall fold similar to eukaryotic phosphomannomutases is reported. Unlike most α-phosphoglucomutases within the α-D-phosphohexomutase superfamily, it belongs to subclass IIb of the haloacid dehalogenase superfamily (HADSF). It catalyzes the reversible conversion of α-glucose 1-phosphate to glucose 6-phosphate. The crystal structure of α-phosphoglucomutase fromLactococcus lactis(APGM) was determined at 1.5 r{A} resolution and contains a sulfate and a glycerol bound at the enzyme active site that partially mimic the substrate. A dimeric form of APGM is present in the crystal and in solution, an arrangement that may be functionally relevant. The catalytic mechanism of APGM and its strict specificity towards α-glucose 1-phosphate are discussed.},

keywords = {General Medicine, Structural Biology},

pubstate = {published},

tppubtype = {article}

}

@article{Nogly2012,

title = {Production and crystallization of α-phosphoglucomutase from\textit{Lactococcus lactis}},

author = {Przemyslaw Nogly and Rute Castro and Matteo de Rosa and Ana Rute Neves and Helena Santos and Margarida Archer},

doi = {10.1107/s1744309112032629},

issn = {1744-3091},

year  = {2012},

date = {2012-09-00},

journal = {Acta Cryst Sect F},

volume = {68},

number = {9},

pages = {1113--1115},

publisher = {International Union of Crystallography (IUCr)},

keywords = {Biochemistry, Biophysics, Condensed Matter Physics, Genetics, Structural Biology},

pubstate = {published},

tppubtype = {article}

}

@article{Kyzio\l2006,

title = {1,5-Dimethyl-2-nitrimino-1,2-dihydropyridine},

author = {Janusz B. Kyzio\l and Przemys\law Nog\ly and Zdzis\law Daszkiewicz and Jacek Zaleski},

doi = {10.1107/s1600536806045946},

issn = {1600-5368},

year  = {2006},

date = {2006-12-00},

journal = {Acta Cryst E},

volume = {62},

number = {12},

pages = {o5485--o5487},

publisher = {International Union of Crystallography (IUCr)},

keywords = {Condensed Matter Physics, General Chemistry, General Materials Science},

pubstate = {published},

tppubtype = {article}

}