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Structural dynamics of 7TM proteins probed by serial femtosecond crystallography

English title Structural dynamics of 7TM proteins probed by serial femtosecond crystallography
Applicant Standfuss Joerg
Number 159558
Funding scheme Project funding (Div. I-III)
Research institution Paul Scherrer Institut
Institution of higher education Paul Scherrer Institute - PSI
Main discipline Biophysics
Start/End 01.05.2015 - 30.04.2018
Approved amount 600'000.00
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All Disciplines (4)

Discipline
Biophysics
Pharmacology, Pharmacy
Structural Research
Molecular Biology

Keywords (9)

visual photoreceptor rhodopsin; seven transmembrane proteins (7TM); retinal binding proteins; serial femtosecond crystallography; light-gated ion channels; light-driven pumps; chemokine receptor; kinetic crystallography; G protein coupled receptors

Lay Summary (German)

Lead
Structural dynamics of 7TM proteins probed by serial femtosecond crystallographyDr Jörg StandfussLaboratory of Biomolecular Research, Paul Scherrer Institut (PSI)
Lay summary

In 2017 wird am Paul Scherrer Institut eine neue Grossforschungsanlage, der Schweizer Freie-Elektronen Laser (SwissFEL), in Betrieb gestellt. Diese Anlage ist ideal um sehr schnell ablaufende biologische Reaktionen in Proteinmolekülen untersuchen zu können. Im gewissen Sinne arbeitet der SwissFEL wie eine Kamera mit der mehrere Schnappschüsse solcher Reaktionen aufgenommen und anschliessend zu einem Film der Reaktion zusammengefügt werden können. Solche Filme werden uns helfen die Wirkungsweise der Proteine besser zu verstehen. Insbesondere für die pharmazeutische Industrie sind Proteine aufgrund ihrer Schlüsselfunktionen ein begehrtes Forschungsobjekt.

In diesem Projekt werden wir die Funktionsweise einer Reihe von Proteinen mittels des SwissFELs und ähnlicher Anlagen in den USA und Japan untersuchen. Unser Fokus liegt dabei auf von Licht aktivierten Proteinen wie dem Lichtsensor Rhodopsin in unserem Auge oder ähnlichen Proteinen die in Bakterien als Lichtsensoren oder zur Photosynthese dienen. Ein weiteres Protein ist ein so genannter Chemokin-Rezeptor der in unserem Immunsystem dafür sorgt dass unsere Abwehrzellen dorthin wandern, wo sie ungeliebte Eindringlinge wie Viren oder Bakterien am effektivsten bekämpfen können. Dieses Teilprojekt wird in enger Zusammenarbeit mit Hoffman La-Roche in Basel betrieben und wird uns helfen das Potential des SwissFELs für die Medikamentenentwicklung zu erforschen.

Direct link to Lay Summary Last update: 08.04.2015

Responsible applicant and co-applicants

Employees

Publications

Publication
Ligand channel in pharmacologically stabilized rhodopsin
Mattle Daniel, Kuhn Bernd, Aebi Johannes, Bedoucha Marc, Kekilli Demet, Grozinger Nathalie, Alker Andre, Rudolph Markus G., Schmid Georg, Schertler Gebhard F. X., Hennig Michael, Standfuss Jörg, Dawson Roger J. P. (2018), Ligand channel in pharmacologically stabilized rhodopsin, in Proceedings of the National Academy of Sciences, 115(14), 3640-3645.
Perspective: Opportunities for ultrafast science at SwissFEL
Abela Rafael, Beaud Paul, van Bokhoven Jeroen A., Chergui Majed, Feurer Thomas, Haase Johannes, Ingold Gerhard, Johnson Steven L., Knopp Gregor, Lemke Henrik, Milne Chris J., Pedrini Bill, Radi Peter, Schertler Gebhard, Standfuss Jörg, Staub Urs, Patthey Luc (2017), Perspective: Opportunities for ultrafast science at SwissFEL, in Structural Dynamics, 4(6), 061602-061602.
Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons.
Weinert Tobias, Olieric Natacha, Cheng Robert, Brünle Steffen, James Daniel, Ozerov Dmitry, Gashi Dardan, Vera Laura, Marsh May, Jaeger Kathrin, Dworkowski Florian, Panepucci Ezequiel, Basu Shibom, Skopintsev Petr, Doré Andrew S, Geng Tian, Cooke Robert M, Liang Mengning, Prota Andrea E, Panneels Valerie, Nogly Przemyslaw, Ermler Ulrich, Schertler Gebhard, Hennig Michael, Steinmetz Michel O, Wang Meitian, Standfuss Jörg (2017), Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons., in Nature communications, 8(1), 542-542.
Structural biology: Signalling under the microscope.
Tsai Ching-Ju, Standfuss Joerg, Glaeser Robert M (2017), Structural biology: Signalling under the microscope., in Nature, 546(7656), 36-37.
Serial crystallography at synchrotrons and X-ray lasers.
Standfuss Jörg, Spence John (2017), Serial crystallography at synchrotrons and X-ray lasers., in IUCrJ, 4(Pt 2), 100-101.
A three-dimensional movie of structural changes in bacteriorhodopsin.
Nango Eriko, Royant Antoine, Kubo Minoru, Nakane Takanori, Wickstrand Cecilia, Kimura Tetsunari, Tanaka Tomoyuki, Tono Kensuke, Song Changyong, Tanaka Rie, Arima Toshi, Yamashita Ayumi, Kobayashi Jun, Hosaka Toshiaki, Mizohata Eiichi, Nogly Przemyslaw, Sugahara Michihiro, Nam Daewoong, Nomura Takashi, Shimamura Tatsuro, Im Dohyun, Fujiwara Takaaki, Yamanaka Yasuaki, Jeon Byeonghyun, Nishizawa Tomohiro, Oda Kazumasa, Fukuda Masahiro, Andersson Rebecka, Båth Petra, Dods Robert, Davidsson Jan, Matsuoka Shigeru, Kawatake Satoshi, Murata Michio, Nureki Osamu, Owada Shigeki, Kameshima Takashi, Hatsui Takaki, Joti Yasumasa, Schertler Gebhard, Yabashi Makina, Bondar Ana-Nicoleta, Standfuss Jörg, Neutze Richard, Iwata So (2017), A three-dimensional movie of structural changes in bacteriorhodopsin., in Science (New York, N.Y.), 354(6319), 1552-1557.
Serial Millisecond Crystallography of Membrane Proteins.
Jaeger Kathrin, Dworkowski Florian, Nogly Przemyslaw, Milne Christopher, Wang Meitian, Standfuss Joerg (2016), Serial Millisecond Crystallography of Membrane Proteins., in n/a (ed.), n/a, n/a, 922, 137-149.
Structural role of the T94I rhodopsin mutation in congenital stationary night blindness.
Singhal Ankita, Guo Ying, Matkovic Milos, Schertler Gebhard, Deupi Xavier, Yan Elsa Cy, Standfuss Joerg (2016), Structural role of the T94I rhodopsin mutation in congenital stationary night blindness., in EMBO reports, 17(10), 1431-1440.
Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography.
Nogly Przemyslaw, Panneels Valerie, Nelson Garrett, Gati Cornelius, Kimura Tetsunari, Milne Christopher, Milathianaki Despina, Kubo Minoru, Wu Wenting, Conrad Chelsie, Coe Jesse, Bean Richard, Zhao Yun, Båth Petra, Dods Robert, Harimoorthy Rajiv, Beyerlein Kenneth R, Rheinberger Jan, James Daniel, DePonte Daniel, Li Chufeng, Sala Leonardo, Williams Garth J, Hunter Mark S, Koglin Jason E, Berntsen Peter, Nango Eriko, Iwata So, Chapman Henry N, Fromme Petra, Frank Matthias, Abela Rafael, Boutet Sébastien, Barty Anton, White Thomas A, Weierstall Uwe, Spence John, Neutze Richard, Schertler Gebhard, Standfuss Jörg (2016), Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography., in Nature communications, 7, 12314-12314.
Functional map of arrestin binding to phosphorylated opsin, with and without agonist.
Peterhans Christian, Lally Ciara C M, Ostermaier Martin K, Sommer Martha E, Standfuss Jörg (2016), Functional map of arrestin binding to phosphorylated opsin, with and without agonist., in Scientific reports, 6, 28686-28686.
Mammalian expression, purification, and crystallization of rhodopsin variants.
Mattle Daniel, Singhal Ankita, Schmid Georg, Dawson Roger, Standfuss Jörg (2015), Mammalian expression, purification, and crystallization of rhodopsin variants., in n/a (ed.), n/a, n/a, 1271, 39-54.
Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser.
Wu Wenting, Nogly Przemyslaw, Rheinberger Jan, Kick Leonhard M, Gati Cornelius, Nelson Garrett, Deupi Xavier, Standfuss Jörg, Schertler Gebhard, Panneels Valérie (2015), Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser., in Acta crystallographica. Section F, Structural biology communications, 71(Pt 7), 856-60.
Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.
Kang Yanyong, Zhou X Edward, Gao Xiang, He Yuanzheng, Liu Wei, Ishchenko Andrii, Barty Anton, White Thomas A, Yefanov Oleksandr, Han Gye Won, Xu Qingping, de Waal Parker W, Ke Jiyuan, Tan M H Eileen, Zhang Chenghai, Moeller Arne, West Graham M, Pascal Bruce D, Van Eps Ned, Caro Lydia N, Vishnivetskiy Sergey A, Lee Regina J, Suino-Powell Kelly M, Gu Xin, Pal Kuntal, Ma Jinming, Zhi Xiaoyong, Boutet Sébastien, Williams Garth J, Messerschmidt Marc, Gati Cornelius, Zatsepin Nadia A, Wang Dingjie, James Daniel, Basu Shibom, Roy-Chowdhury Shatabdi, Conrad Chelsie E, Coe Jesse, Liu Haiguang, Lisova Stella, Kupitz Christopher, Grotjohann Ingo, Fromme Raimund, Jiang Yi, Tan Minjia, Yang Huaiyu, Li Jun, Wang Meitian, Zheng Zhong, Li Dianfan, Howe Nicole, Zhao Yingming, Standfuss Jörg, Diederichs Kay, Dong Yuhui, Potter Clinton S, Carragher Bridget, Caffrey Martin, Jiang Hualiang, Chapman Henry N, Spence John C H, Fromme Petra, Weierstall Uwe, Ernst Oliver P, Katritch Vsevolod, Gurevich Vsevolod V, Griffin Patrick R, Hubbell Wayne L, Stevens Raymond C, Cherezov Vadim, Melcher Karsten, Xu H Eric (2015), Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser., in Nature, 523(7562), 561-7.
Time-resolved structural studies with serial crystallography: A new light on retinal proteins.
Panneels Valérie, Wu Wenting, Tsai Ching-Ju, Nogly Przemek, Rheinberger Jan, Jaeger Kathrin, Cicchetti Gregor, Gati Cornelius, Kick Leonhard M, Sala Leonardo, Capitani Guido, Milne Chris, Padeste Celestino, Pedrini Bill, Li Xiao-Dan, Standfuss Jörg, Abela Rafael, Schertler Gebhard (2015), Time-resolved structural studies with serial crystallography: A new light on retinal proteins., in Structural dynamics (Melville, N.Y.), 2(4), 041718-041718.
Light-driven Na(+) pumps as next-generation inhibitory optogenetic tools.
Nogly Przemyslaw, Standfuss Jörg (2015), Light-driven Na(+) pumps as next-generation inhibitory optogenetic tools., in Nature structural & molecular biology, 22(5), 351-3.
Structural biology. Viral chemokine mimicry.
Standfuss Jörg (2015), Structural biology. Viral chemokine mimicry., in Science (New York, N.Y.), 347(6226), 1071-2.
Lipidic cubic phase serial millisecond crystallography using synchrotron radiation.
Nogly Przemyslaw, James Daniel, Wang Dingjie, White Thomas A, Zatsepin Nadia, Shilova Anastasya, Nelson Garrett, Liu Haiguang, Johansson Linda, Heymann Michael, Jaeger Kathrin, Metz Markus, Wickstrand Cecilia, Wu Wenting, Båth Petra, Berntsen Peter, Oberthuer Dominik, Panneels Valerie, Cherezov Vadim, Chapman Henry, Schertler Gebhard, Neutze Richard, Spence John, Moraes Isabel, Burghammer Manfred, Standfuss Joerg, Weierstall Uwe (2015), Lipidic cubic phase serial millisecond crystallography using synchrotron radiation., in IUCrJ, 2(Pt 2), 168-76.
Retinal isomerization in bacteriorhodopsin captured by a femtosecond X-ray laser
Nogly Przemyslaw, Weinert Tobias, James Daniel, Carbajo Sergio, Ozerov Dmitry, Furrer Antonia, Gashi Dardan, Borin Veniamin, Skopintsev Petr, Jaeger Kathrin, Nass Karol, Bath Petra, Bosman Robert, Koglin Jason, Seaberg Matthew, Lane Thomas, Kekilli Demet, Brünle Steffen, Tanaka Tomoyuki, Wu Wenting, Milne Christopher, White Thomas, Barty Anton, Weierstall Uwe, Panneels Valerie, Nango Eriko, Iwata So, Hunter Mark, Schapiro Igor, Schertler Gebhard, Neutze Richard, Standfuss Joerg, Retinal isomerization in bacteriorhodopsin captured by a femtosecond X-ray laser, in Science, 10.1126.

Collaboration

Group / person Country
Types of collaboration
RIKEN, SACLA Japan (Asia)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Pump-Probe TR-SFX Experiments Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Hepatares Great Britain and Northern Ireland (Europe)
- Publication
- Industry/business/other use-inspired collaboration
Arizona State University, Uwe Weierstall United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
leadXpro Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Industry/business/other use-inspired collaboration
SLAC, LCLS United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Hoffmann-La Roche, Roger Dawson Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Exchange of personnel
- Industry/business/other use-inspired collaboration

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
British Crystallographic Association Meeting Talk given at a conference Time-resolved serial crystallography using synchrotrons and X-ray lasers 26.03.2018 University of Warwick, Great Britain and Northern Ireland Standfuss Joerg;
Gordon Research Conference “Photosensory Receptors and Signal Transduction” Talk given at a conference Excited state structural dynamics of retinal isomerization captured by an x-ray laser 05.02.2018 Il Ciocco, Italy, Italy Standfuss Joerg;
5th Ringberg Workshop on Structural Biology with FELs Talk given at a conference Excited state structural dynamics of retinal isomerization 04.01.2018 Ringberg, Germany Standfuss Joerg;
DFG Roudtable Discussion Photoreceptors Talk given at a conference Time-resolved serial crystallography at synchrotrons and x-ray lasers 08.10.2017 Ringberg, Germany Standfuss Joerg;
Annual Meeting Swiss Society of Crystallography Talk given at a conference Time-resolved serial crystallography at synchrotrons and x-ray lasers 11.09.2017 Geneve, Switzerland Standfuss Joerg;
24th International Union of Crystallography Meeting Talk given at a conference Time-resolved serial crystallography at synchrotrons and x-ray lasers 21.08.2017 Hyderabad, India Standfuss Joerg;
Photonics Workshop Talk given at a conference Time-resolved serial crystallography at synchrotrons and x-ray lasers 11.04.2017 Windisch, Switzerland Standfuss Joerg;
Invited Presentation SACLA Individual talk 10 years of rhodopsin - from crystal structures to lead compounds against retinitis pigmentosa 05.04.2017 SACLA, Japan Standfuss Joerg;
IGER International Symposium on the Physics of Life Talk given at a conference Time-resolved serial crystallography at synchrotrons and x-ray lasers 22.03.2017 Nagoya, Japan Standfuss Joerg;
Rhine-Knee Regional Meeting on Structural Biology Talk given at a conference Time-resolved serial crystallography at synchrotrons and x-ray lasers 28.10.2016 Schöntal, Germany Standfuss Joerg;
16th International Conference on Retinal Proteins Talk given at a conference Time-resolved serial crystallography at synchrotrons and x-ray lasers 02.10.2016 Potsdam, Germany Standfuss Joerg; Skopintsev Peter; James Daniel; Jäger Kathrin; Peterhans Christian;
2nd European Meeting on Phototranstuction Talk given at a conference 10 year of rhodopsin - from crystal structures to lead compounds against retinitis pigmentosa 04.09.2016 Ascona, Switzerland Standfuss Joerg;
Invited presentation at SACLA X-ray laser Japan Individual talk Time-resolved serial crystallography at synchrotrons and x-ray lasers 29.02.2016 Hyogo, Japan Standfuss Joerg;
3rd Annual BioXFEL conference Talk given at a conference Serial crystallography at synchrotrons and x-ray lasers 13.01.2016 San Juan, United States of America Standfuss Joerg;
4th Annual meeting of the GDR3545: GPCRs, from physiology to drugs Talk given at a conference Crystal structures of rhodopsin mutants causing night blindness 04.11.2015 Toulouse, France Standfuss Joerg;
11th Symposium on Trends in Structural Biology Talk given at a conference Serial crystallography 11.10.2015 Zurich, Switzerland Standfuss Joerg;
LCLS Users Meeting Talk given at a conference Time-resolved crystallography using high viscosity injectors 07.10.2015 Stanford University, United States of America Standfuss Joerg;


Self-organised

Title Date Place
30th European Crystallography Meeting - Chair & Organizer Serial crystallography session 04.08.2017 Basel, Switzerland

Knowledge transfer events

Active participation

Title Type of contribution Date Place Persons involved
LEAPS - The League of European Accelerator-based Photon Sources Poster 13.11.2017 Brussels, Belgium Standfuss Joerg;


Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Biologischer Lichtsensor in Aktion gefilmt Film zeigt einen der schnellsten Prozesse in der Biologi Rhaeto-Romanic Switzerland German-speaking Switzerland Western Switzerland 2018
Media relations: print media, online media Scientists Make the First Molecular Movie of a Sensor Widely Used in Nature to Detect and Harvest Li Stanford University International 2018
Media relations: print media, online media From photosynthesis to new compounds for eye diseases SNSF Research in Focus Western Switzerland German-speaking Switzerland Italian-speaking Switzerland International Rhaeto-Romanic Switzerland 2017
Media relations: print media, online media Catching proteins in the act Press release explaining time-resolved crystallography to the general public German-speaking Switzerland Western Switzerland International Italian-speaking Switzerland 2016
Talks/events/exhibitions Representation Bio-SwissFEL: Tag der offenen Tür am Paul Scherrer Institut Italian-speaking Switzerland Western Switzerland International Rhaeto-Romanic Switzerland German-speaking Switzerland 2015

Associated projects

Number Title Start Funding scheme
141235 Structural impact of pathological mutations on the GPCR rhodopsin and its complex with arrestin 01.05.2012 Project funding (Div. I-III)
179351 Tracking the structural dynamics of ligand-protein interactions using X-ray free electron lasers 01.05.2018 Project funding (Div. I-III)
177125 Tunable nanosecond laser for time-resolved serial crystallography at SLS and SwissFEL 01.01.2018 R'EQUIP

Abstract

This proposal addresses one of the major promises of X-ray free electron laser (X-FEL) technology: to advance structural biology from the determination of molecular snapshots to molecular movies. Together structural and dynamic information will provide unique insights into the function of proteins as principal building blocks of our biology.We suggest studying the structural dynamics of several members from the seven transmembrane helix (7TM) class of proteins. 7TM proteins are found in organisms ranging from archaea to humans and are adapted to fulfill a wide range of biological functions. Located in the cellular membrane, most 7TM proteins act as pumps or channels to allow passage of ions, or as transducers of biological signals. The latter has important implications for pharmacology, as the largest family of 7TM proteins, G protein-coupled receptors (GPCRs), includes about 30% of all human drug targets. We will initially focus on retinal binding 7TM proteins, as they can be activated with a flash of laser light. As the classical model to study the family of 7TM proteins, bacteriorhodopsin (bR) is ideal to establish the technology. As example of a light-gated ion channel we will probe the structural dynamics of channelrhodopsin. The study of this retinal binding 7TM protein has important optogenetic applications in probing of neural circuits with millisecond precision. In a next step we will extent our studies to the visual photoreceptor rhodopsin as member of the GPCR class of 7TM proteins. Our previous studies have shown how perturbation of rhodopsin activation leads to the development of severe retinopathy. Understanding the dynamics of this process will provide crucial information on the development of hereditary blindness. Finally, we will study the human chemokine receptor CCR7, as an example for a non-retinal binding 7TM protein. Activation of CCR7 regulates the migration of memory T cells and stimulates dendritic cell maturation in inflammatory responses. We will investigate these proteins using time-resolved serial femtosecond crystallography (TR-SFX). We have several reasons to prefer serial crystallography over other methods to study protein intermediates like freeze-trapping or Laue crystallography. The highly brilliant pulses of an X-FEL allow collecting high-resolution data from nano- to micrometer sized crystals that can be homogenously activated. X-FELs allow the investigation of dynamics from the femto- to millisecond range and are less dependent on strongly diffracting crystals with low mosaic spreads. Furthermore, the use of lipidic cubic phases (LCP) for crystal growth and delivery has significantly reduced the amount of protein needed for serial crystallographic experiments. Importantly, data collection using highly brilliant femtosecond laser pulses allows to outrun radiation damage and determine membrane protein structures at previously unprecedented spatial and temporal resolution. The Paul Scherrer Institute (PSI) provides an ideal research environment for this project with access to well-equipped laboratory space, robotic crystallization facilities and the Swiss Light Source (SLS) synchrotron. The proposed project will further benefit from the developing X-FEL community around the Swiss Free Electron Laser (SwissFEL) currently under construction at the PSI. Only by starting now will we be able to establish X-FEL related research in Switzerland in time for completion of the extraordinary resource SwissFEL.
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