Advanced XFEL and Synchrotron based Probes of Protein Structure and Dynamics

Project Information

X-probe

Grant agreement ID: 637295

DOI

10.3030/637295

Project closed

EC signature date 27 October 2014

Start date 1 January 2015

End date 31 December 2018

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 2 331 284,76

EU contribution

€ 2 331 284,76

Coordinated by

UNIVERSITA DEGLI STUDI DI ROMA LA SAPIENZA
Italy

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (8)

Micro crystals of light sensitive proteins

Growth of micro-crystals of light sensitive proteins suitable for serial femtosecond crystallography studies at X-FELs.

Publish novel structural insights

Frontier studies on time-resolved diffraction and WAXS studies of light-sensitive proteins at XFELS

Publish time-resolved diffraction/WAXS

Papers reporting results on protein structural dynamics

Short pulsed facility

Commissioning of a short-pulsed X-ray facility at MAXIV in Lund

Mid-term Dissemination and exploitation plan

Update a shared plan for dissemination and exploitation of results

Final Dissemination and exploitation plan

A shared plan for dissemination and exploitation of results

Crystallization of light sensitive proteins

Crystallization of large crystals of light sensitive proteins suitable for Laue diffraction

WAXS software suite

Develop software to analyze time-resolved WAXS data incorporating molecular dynamics simulations

Websites, patent fillings, videos etc. (1)

Website

Information to the public and scientific and industrial community

Demonstrators, pilots, prototypes (2)

New tools for nano-crystallography

Develop and market new tools for sample handling and sample preparation for XFEL sources

Software packages for analysing X-ray diffraction

Develop software for processing, merging and scaling X-ray diffraction data from thousands of images

Other (1)

International Final Conference

International conference open to external participants on X-probe results

Publications

Peer reviewed articles (26)

Growing Protein Crystals with Distinct Dimensions Using Automated Crystallization Coupled with <em>In Situ</em> Dynamic Light Scattering

Author(s): Daniela Baitan, Robin Schubert, Arne Meyer, Karsten Dierks, Markus Perbandt, Christian Betzel
Published in: Journal of Visualized Experiments, Issue 138, 2018, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/57070

Structural basis for selective inhibition of antibacterial target MraY, a membrane-bound enzyme involved in peptidoglycan synthesis

Author(s): Jenny Hering, Elin Dunevall, Margareta Ek, Gisela Brändén
Published in: Drug Discovery Today, Issue 23/7, 2018, Page(s) 1426-1435, ISSN 1359-6446
Publisher: Elsevier BV
DOI: 10.1016/j.drudis.2018.05.020

Engineered ferritin for lanthanide binding

Author(s): Lorenzo Calisti, Matilde Cardoso Trabuco, Alberto Boffi, Claudia Testi, Linda Celeste Montemiglio, Amédée des Georges, Irene Benni, Andrea Ilari, Bartłomiej Taciak, Maciej Białasek, Tomasz Rygiel, Magdalena Król, Paola Baiocco, Alessandra Bonamore
Published in: PLOS ONE, Issue 13/8, 2018, Page(s) e0201859, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0201859

Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser

Author(s): Przemyslaw Nogly, Tobias Weinert, Daniel James, Sergio Carbajo, Dmitry Ozerov, Antonia Furrer, Dardan Gashi, Veniamin Borin, Petr Skopintsev, Kathrin Jaeger, Karol Nass, Petra Båth, Robert Bosman, Jason Koglin, Matthew Seaberg, Thomas Lane, Demet Kekilli, Steffen Brünle, Tomoyuki Tanaka, Wenting Wu, Christopher Milne, Thomas White, Anton Barty, Uwe Weierstall, Valerie Panneels, Eriko Nango, So I
Published in: Science, 2018, Page(s) eaat0094, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aat0094

FemtoMAX – an X-ray beamline for structural dynamics at the short-pulse facility of MAX IV

Author(s): Henrik Enquist, Andrius Jurgilaitis, Amelie Jarnac, Åsa U. J. Bengtsson, Matthias Burza, Francesca Curbis, Christian Disch, J. Carl Ekström, Maher Harb, Lennart Isaksson, Marija Kotur, David Kroon, Filip Lindau, Erik Mansten, Jesper Nygaard, Anna I. H. Persson, Van Thai Pham, Michael Rissi, Sara Thorin, Chien-Ming Tu, Erik Wallén, Xiaocui Wang, Sverker Werin, Jörgen Larsson
Published in: Journal of Synchrotron Radiation, Issue 25/2, 2018, Page(s) 570-579, ISSN 1600-5775
Publisher: Wiley-Blackwell on behalf of the International Union of Crystallography
DOI: 10.1107/S1600577517017660

Communication: Demonstration of a 20 ps X-ray switch based on a photoacoustic transducer

Author(s): A. Jarnac, Xiaocui Wang, Å. U. J. Bengtsson, J. C. Ekström, H. Enquist, A. Jurgilaitis, D. Kroon, A. I. H. Persson, V.-T. Pham, C. M. Tu, J. Larsson
Published in: Structural Dynamics, Issue 4/5, 2017, Page(s) 051102, ISSN 2329-7778
Publisher: AIP publishing
DOI: 10.1063/1.4993730

Substrate-induced conformational change in cytochrome P450 OleP

Author(s): Giacomo Parisi, Linda Celeste Montemiglio, Alessandro Giuffrè, Alberto Macone, Antonella Scaglione, Gabriele Cerutti, Cécile Exertier, Carmelinda Savino, Beatrice Vallone
Published in: The FASEB Journal, Issue 33/2, 2019, Page(s) 1787-1800, ISSN 0892-6638
Publisher: Federation of American Societies for Experimental Biology
DOI: 10.1096/fj.201800450RR

Probing Transient Photoinduced Charge Transfer in Prussian Blue Analogues with Time-Resolved XANES and Optical Spectroscopy

Author(s): Serhane Zerdane, Marco Cammarata, Lodovico Balducci, Roman Bertoni, Laure Catala, Sandra Mazerat, Talal Mallah, Martin N. Pedersen, Michael Wulff, Kosuke Nakagawa, Hiroko Tokoro, Shin-ichi Ohkoshi, Eric Collet
Published in: European Journal of Inorganic Chemistry, Issue 2018/3-4, 2018, Page(s) 272-277, ISSN 1434-1948
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/ejic.201700657

Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin

Author(s): Giovanni Chillemi, Massimiliano Anselmi, Nico Sanna, Cristiano Padrin, Lodovico Balducci, Marco Cammarata, Elisabetta Pace, Majed Chergui, Maurizio Benfatto
Published in: Structural Dynamics, Issue 5/5, 2018, Page(s) 054101, ISSN 2329-7778
Publisher: American Crystallographic Association, Inc.
DOI: 10.1063/1.5031806

Serial femtosecond crystallography structure of cytochrome c oxidase at room temperature

Author(s): Rebecka Andersson, Cecilia Safari, Robert Dods, Eriko Nango, Rie Tanaka, Ayumi Yamashita, Takanori Nakane, Kensuke Tono, Yasumasa Joti, Petra Båth, Elin Dunevall, Robert Bosman, Osamu Nureki, So Iwata, Richard Neutze, Gisela Brändén
Published in: Scientific Reports, Issue 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-04817-z

Initial metal–metal bond breakage detected by fs X-ray scattering in the photolysis of Ru 3 (CO) 12 in cyclohexane at 400 nm

Author(s): Q. Y. Kong, M. G. Laursen, K. Haldrup, K. S. Kjær, D. Khakhulin, E. Biasin, T. B. van Driel, M. Wulff, V. Kabanova, R. Vuilleumier, S. Bratos, M. M. Nielsen, K. J. Gaffney, T. C. Weng, M. H. J. Koch
Published in: Photochemical & Photobiological Sciences, Issue 18/2, 2019, Page(s) 319-327, ISSN 1474-905X
Publisher: Royal Society of Chemistry
DOI: 10.1039/c8pp00420j

Megahertz serial crystallography

Author(s): Max O. Wiedorn, Dominik Oberthür, Richard Bean, Robin Schubert, Nadine Werner, Brian Abbey, Martin Aepfelbacher, Luigi Adriano, Aschkan Allahgholi, Nasser Al-Qudami, Jakob Andreasson, Steve Aplin, Salah Awel, Kartik Ayyer, Saša Bajt, Imrich Barák, Sadia Bari, Johan Bielecki, Sabine Botha, Djelloul Boukhelef, Wolfgang Brehm, Sandor Brockhauser, Igor Cheviakov, Matthew A. Coleman, Francisco Cruz-
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-06156-7

Double-flow focused liquid injector for efficient serial femtosecond crystallography

Author(s): Dominik Oberthuer, Juraj Knoška, Max O. Wiedorn, Kenneth R. Beyerlein, David A. Bushnell, Elena G. Kovaleva, Michael Heymann, Lars Gumprecht, Richard A. Kirian, Anton Barty, Valerio Mariani, Aleksandra Tolstikova, Luigi Adriano, Salah Awel, Miriam Barthelmess, Katerina Dörner, P. Lourdu Xavier, Oleksandr Yefanov, Daniel R. James, Garrett Nelson, Dingjie Wang, George Calvey, Yujie Chen, Andrea Sc
Published in: Scientific Reports, Issue 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep44628

Pink-beam serial crystallography

Author(s): A. Meents, M. O. Wiedorn, V. Srajer, R. Henning, I. Sarrou, J. Bergtholdt, M. Barthelmess, P. Y. A. Reinke, D. Dierksmeyer, A. Tolstikova, S. Schaible, M. Messerschmidt, C. M. Ogata, D. J. Kissick, M. H. Taft, D. J. Manstein, J. Lieske, D. Oberthuer, R. F. Fischetti, H. N. Chapman
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-017-01417-3

Recent developments in CrystFEL

Author(s): Thomas A. White, Valerio Mariani, Wolfgang Brehm, Oleksandr Yefanov, Anton Barty, Kenneth R. Beyerlein, Fedor Chervinskii, Lorenzo Galli, Cornelius Gati, Takanori Nakane, Alexandra Tolstikova, Keitaro Yamashita, Chun Hong Yoon, Kay Diederichs, Henry N. Chapman
Published in: Journal of Applied Crystallography, Issue 49/2, 2016, Page(s) 680-689, ISSN 1600-5767
Publisher: IUCr
DOI: 10.1107/s1600576716004751

Excimer based fluorescent pyrene–ferritin conjugate for protein oligomerization studies and imaging in living cells

Author(s): Irene Benni, Matilde Cardoso Trabuco, Enrico Di Stasio, Alessandro Arcovito, Alberto Boffi, Francesco Malatesta, Alessandra Bonamore, Simone De Panfilis, Valeria de Turris, Paola Baiocco
Published in: RSC Advances, Issue 8/23, 2018, Page(s) 12815-12822, ISSN 2046-2069
Publisher: Royal Society of Chemistry
DOI: 10.1039/c8ra00210j

Probing bulky ligand entry in engineered archaeal ferritins

Author(s): Lorenzo Calisti, Irene Benni, Matilde Cardoso Trabuco, Paola Baiocco, Barbara Ruzicka, Alberto Boffi, Elisabetta Falvo, Francesco Malatesta, Alessandra Bonamore
Published in: Biochimica et Biophysica Acta (BBA) - General Subjects, Issue 1861/2, 2017, Page(s) 450-456, ISSN 0304-4165
Publisher: Elsevier BV
DOI: 10.1016/j.bbagen.2016.10.007

Structural basis for selectivity and diversity in angiotensin II receptors

Author(s): Haitao Zhang, Gye Won Han, Alexander Batyuk, Andrii Ishchenko, Kate L. White, Nilkanth Patel, Anastasiia Sadybekov, Beata Zamlynny, Michael T. Rudd, Kaspar Hollenstein, Alexandra Tolstikova, Thomas A. White, Mark S. Hunter, Uwe Weierstall, Wei Liu, Kerim Babaoglu, Eric L. Moore, Ryan D. Katz, Jennifer M. Shipman, Margarita Garcia-Calvo, Sujata Sharma, Payal Sheth, Stephen M. Soisson, Raymond C. St
Published in: Nature, Issue 544/7650, 2017, Page(s) 327-332, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature22035

Real-Time Observation of Protein Dense Liquid Cluster Evolution during Nucleation in Protein Crystallization

Author(s): Robin Schubert, Arne Meyer, Daniela Baitan, Karsten Dierks, Markus Perbandt, Christian Betzel
Published in: Crystal Growth & Design, Issue 17/3, 2017, Page(s) 954-958, ISSN 1528-7483
Publisher: American Chemical Society
DOI: 10.1021/acs.cgd.6b01826

Proximal and distal control for ligand binding in neuroglobin: role of the CD loop and evidence for His64 gating

Author(s): Cécile Exertier, Lisa Milazzo, Ida Freda, Linda Celeste Montemiglio, Antonella Scaglione, Gabriele Cerutti, Giacomo Parisi, Massimiliano Anselmi, Giulietta Smulevich, Carmelinda Savino, Beatrice Vallone
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-41780-3

Humanized archaeal ferritin as a tool for cell targeted delivery

Author(s): de Turris V., Cardoso Trabuco M., Peruzzi G., Boffi A., Testi C., Vallone B., Montemiglio L.C., des Georges A., Calisti L., Benni I., Bonamore A. and Baiocco P.
Published in: nanoscale, 2017, ISSN 2040-3364
Publisher: Royal Society of Chemistry
DOI: 10.5281/zenodo.2527178

Probing bulky ligand entry in engineered archaeal ferritins

Author(s): Calisti L., Benni I., Cardoso Trabuco M., Baiocco P., Ruzicka B., Boffi A., Falvo E., Malatesta F. and Bonamore A.
Published in: Biochim Biophys Acta, 2017, ISSN 0304-4165
Publisher: Elsevier BV
DOI: 10.5281/zenodo.2528583

Studies of electron diffusion in photo-excited Ni using time-resolved X-ray diffraction

Author(s): A. I. H. Persson, A. Jarnac, Xiaocui Wang, H. Enquist, A. Jurgilaitis, J. Larsson
Published in: Applied Physics Letters, Issue 109/20, 2016, Page(s) 203115, ISSN 0003-6951
Publisher: American Institute of Physics
DOI: 10.1063/1.4967470

MraY–antibiotic complex reveals details of tunicamycin mode of action

Author(s): Jonna K Hakulinen, Jenny Hering, Gisela Brändén, Hongming Chen, Arjan Snijder, Margareta Ek, Patrik Johansson
Published in: Nature Chemical Biology, Issue 13/3, 2017, Page(s) 265-267, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/nchembio.2270

The Two-Photon Reversible Reaction of the Bistable Jumping Spider Rhodopsin-1

Author(s): David Ehrenberg, Niranjan Varma, Xavier Deupi, Mitsumasa Koyanagi, Akihisa Terakita, Gebhard F.X. Schertler, Joachim Heberle, Elena Lesca
Published in: Biophysical Journal, Issue 116/7, 2019, Page(s) 1248-1258, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2019.02.025

Generation of a large compressive strain wave in graphite by ultrashort-pulse laser irradiation

Author(s): Xiaocui Wang, A. Jarnac, J. C. Ekström, Å. U. J. Bengtsson, F. Dorchies, H. Enquist, A. Jurgilaitis, M. N. Pedersen, C.-M. Tu, M. Wulff, J. Larsson
Published in: Structural Dynamics, Issue 6/2, 2019, Page(s) 024501, ISSN 2329-7778
Publisher: amarican crystallographic association
DOI: 10.1063/1.5089291