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  • 1
    Publication Date: 2015-07-23
    Description: G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a approximately 20 degrees rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521999/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521999/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉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, Sebastien -- 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, Jorg -- 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 -- DK071662/DK/NIDDK NIH HHS/ -- EY005216/EY/NEI NIH HHS/ -- EY011500/EY/NEI NIH HHS/ -- GM073197/GM/NIGMS NIH HHS/ -- GM077561/GM/NIGMS NIH HHS/ -- GM095583/GM/NIGMS NIH HHS/ -- GM097463/GM/NIGMS NIH HHS/ -- GM102545/GM/NIGMS NIH HHS/ -- GM103310/GM/NIGMS NIH HHS/ -- GM104212/GM/NIGMS NIH HHS/ -- GM108635/GM/NIGMS NIH HHS/ -- P30EY000331/EY/NEI NIH HHS/ -- P41 GM103310/GM/NIGMS NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073210/GM/NIGMS NIH HHS/ -- R01 DK066202/DK/NIDDK NIH HHS/ -- R01 DK071662/DK/NIDDK NIH HHS/ -- R01 EY011500/EY/NEI NIH HHS/ -- R01 GM087413/GM/NIGMS NIH HHS/ -- R01 GM109955/GM/NIGMS NIH HHS/ -- S10 RR027270/RR/NCRR NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- U54 GM094599/GM/NIGMS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Jul 30;523(7562):561-7. doi: 10.1038/nature14656. Epub 2015 Jul 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA. ; Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA. ; Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA. ; Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany. ; Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA. ; 1] Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA [2] Department of Obstetrics &Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. ; The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, New York 10027, USA. ; Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, USA. ; Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA. ; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada. ; Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, USA. ; Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA. ; 1] Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA [2] BioXFEL, NSF Science and Technology Center, 700 Ellicott Street, Buffalo, New York 14203, USA. ; 1] Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA [2] Department of Physics, Arizona State University, Tempe, Arizona 85287, USA. ; 1] Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA [2] Beijing Computational Science Research Center, Haidian District, Beijing 10084, China. ; 1] Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA [2] Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA. ; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. ; Department of Obstetrics &Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. ; Swiss Light Source at Paul Scherrer Institute, CH-5232 Villigen, Switzerland. ; Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA. ; School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland. ; 1] BioXFEL, NSF Science and Technology Center, 700 Ellicott Street, Buffalo, New York 14203, USA [2] Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois 60637, USA. ; Laboratory of Biomolecular Research at Paul Scherrer Institute, CH-5232 Villigen, Switzerland. ; Department of Biology, Universitat Konstanz, 78457 Konstanz, Germany. ; Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China. ; 1] Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany [2] Centre for Ultrafast Imaging, 22761 Hamburg, Germany. ; 1] Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. ; 1] Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA [2] Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA [3] iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China. ; 1] Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA [2] VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26200343" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arrestin/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Disulfides/chemistry/metabolism ; Humans ; Lasers ; Mice ; Models, Molecular ; Multiprotein Complexes/biosynthesis/chemistry/metabolism ; Protein Binding ; Reproducibility of Results ; Rhodopsin/*chemistry/*metabolism ; Signal Transduction ; X-Rays
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-07-22
    Description: Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 A resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kupitz, Christopher -- Basu, Shibom -- Grotjohann, Ingo -- Fromme, Raimund -- Zatsepin, Nadia A -- Rendek, Kimberly N -- Hunter, Mark S -- Shoeman, Robert L -- White, Thomas A -- Wang, Dingjie -- James, Daniel -- Yang, Jay-How -- Cobb, Danielle E -- Reeder, Brenda -- Sierra, Raymond G -- Liu, Haiguang -- Barty, Anton -- Aquila, Andrew L -- Deponte, Daniel -- Kirian, Richard A -- Bari, Sadia -- Bergkamp, Jesse J -- Beyerlein, Kenneth R -- Bogan, Michael J -- Caleman, Carl -- Chao, Tzu-Chiao -- Conrad, Chelsie E -- Davis, Katherine M -- Fleckenstein, Holger -- Galli, Lorenzo -- Hau-Riege, Stefan P -- Kassemeyer, Stephan -- Laksmono, Hartawan -- Liang, Mengning -- Lomb, Lukas -- Marchesini, Stefano -- Martin, Andrew V -- Messerschmidt, Marc -- Milathianaki, Despina -- Nass, Karol -- Ros, Alexandra -- Roy-Chowdhury, Shatabdi -- Schmidt, Kevin -- Seibert, Marvin -- Steinbrener, Jan -- Stellato, Francesco -- Yan, Lifen -- Yoon, Chunhong -- Moore, Thomas A -- Moore, Ana L -- Pushkar, Yulia -- Williams, Garth J -- Boutet, Sebastien -- Doak, R Bruce -- Weierstall, Uwe -- Frank, Matthias -- Chapman, Henry N -- Spence, John C H -- Fromme, Petra -- 1R01GM095583/GM/NIGMS NIH HHS/ -- R01 GM095583/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Sep 11;513(7517):261-5. doi: 10.1038/nature13453. Epub 2014 Jul 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA [2]. ; Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA. ; Department of Physics, Arizona State University, Tempe, Arizona 85287, USA. ; 1] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA [2] Lawrence Livermore National Laboratory, Livermore, California 94550, USA. ; Max-Planck-Institut fur medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany. ; Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany. ; Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA. ; 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] European XFEL GmbH, Notkestrasse 85, 22607 Hamburg, Germany. ; 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA. ; 1] Department of Physics, Arizona State University, Tempe, Arizona 85287, USA [2] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany. ; 1] Max Planck Advanced Study Group, Center for Free-Electron Laser Science (CFEL), Notkestrasse 85, 22607 Hamburg, Germany [2] Max-Planck-Institut fur Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany. ; 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] Department of Physics and Astronomy, Uppsala University, Regementsvagen 1, SE-752 37 Uppsala, Sweden. ; 1] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA [2] University of Regina, 3737 Wascana Pkwy Regina, Saskatchewan S4S 0A2, Canada. ; Department of Physics, Purdue University, 525 Northwestern Avenue, West Lafayette, Indiana 47907, USA. ; 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany. ; Lawrence Livermore National Laboratory, Livermore, California 94550, USA. ; 1] Max-Planck-Institut fur medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science (CFEL), Notkestrasse 85, 22607 Hamburg, Germany. ; Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. ; 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] Department ARC Centre of Excellence for Coherent X-ray Science, Department of Physics, University of Melbourne, Parkville VIC 3010, Australia. ; Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA. ; 1] Max-Planck-Institut fur medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [3] University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany. ; 1] Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA [2] Uppsala University, Sankt Olofsgatan 10B, 753 12 Uppsala, Sweden. ; 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany [3] Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25043005" target="_blank"〉PubMed〈/a〉
    Keywords: *Crystallography, X-Ray ; Cyanobacteria/*chemistry ; *Models, Molecular ; Photosystem II Protein Complex/*chemistry ; Protein Structure, Tertiary
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2012-06-02
    Description: Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3788707/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3788707/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boutet, Sebastien -- Lomb, Lukas -- Williams, Garth J -- Barends, Thomas R M -- Aquila, Andrew -- Doak, R Bruce -- Weierstall, Uwe -- DePonte, Daniel P -- Steinbrener, Jan -- Shoeman, Robert L -- Messerschmidt, Marc -- Barty, Anton -- White, Thomas A -- Kassemeyer, Stephan -- Kirian, Richard A -- Seibert, M Marvin -- Montanez, Paul A -- Kenney, Chris -- Herbst, Ryan -- Hart, Philip -- Pines, Jack -- Haller, Gunther -- Gruner, Sol M -- Philipp, Hugh T -- Tate, Mark W -- Hromalik, Marianne -- Koerner, Lucas J -- van Bakel, Niels -- Morse, John -- Ghonsalves, Wilfred -- Arnlund, David -- Bogan, Michael J -- Caleman, Carl -- Fromme, Raimund -- Hampton, Christina Y -- Hunter, Mark S -- Johansson, Linda C -- Katona, Gergely -- Kupitz, Christopher -- Liang, Mengning -- Martin, Andrew V -- Nass, Karol -- Redecke, Lars -- Stellato, Francesco -- Timneanu, Nicusor -- Wang, Dingjie -- Zatsepin, Nadia A -- Schafer, Donald -- Defever, James -- Neutze, Richard -- Fromme, Petra -- Spence, John C H -- Chapman, Henry N -- Schlichting, Ilme -- 1R01GM095583/GM/NIGMS NIH HHS/ -- R01 GM095583/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Jul 20;337(6092):362-4. doi: 10.1126/science.1217737. Epub 2012 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA. sboutet@slac.stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22653729" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography, X-Ray/*methods ; Lasers ; Muramidase/chemistry/radiation effects ; *Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2014-12-06
    Description: Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361027/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361027/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tenboer, Jason -- Basu, Shibom -- Zatsepin, Nadia -- Pande, Kanupriya -- Milathianaki, Despina -- Frank, Matthias -- Hunter, Mark -- Boutet, Sebastien -- Williams, Garth J -- Koglin, Jason E -- Oberthuer, Dominik -- Heymann, Michael -- Kupitz, Christopher -- Conrad, Chelsie -- Coe, Jesse -- Roy-Chowdhury, Shatabdi -- Weierstall, Uwe -- James, Daniel -- Wang, Dingjie -- Grant, Thomas -- Barty, Anton -- Yefanov, Oleksandr -- Scales, Jennifer -- Gati, Cornelius -- Seuring, Carolin -- Srajer, Vukica -- Henning, Robert -- Schwander, Peter -- Fromme, Raimund -- Ourmazd, Abbas -- Moffat, Keith -- Van Thor, Jasper J -- Spence, John C H -- Fromme, Petra -- Chapman, Henry N -- Schmidt, Marius -- P41 GM103543/GM/NIGMS NIH HHS/ -- R01GM095583/GM/NIGMS NIH HHS/ -- R24 GM111072/GM/NIGMS NIH HHS/ -- R24GM111072/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Dec 5;346(6214):1242-6. doi: 10.1126/science.1259357.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA. ; Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA. ; Department of Physics, Arizona State University, Tempe, AZ 85287, USA. ; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA. ; Lawrence Livermore National Laboratory, Livermore, CA 94550, USA. ; Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany. ; Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany. ; Hauptman-Woodward Institute, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA. ; Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany. Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany. ; Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA. ; Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA. Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA. ; Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA. ; Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA. m-schmidt@uwm.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25477465" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/*ultrastructure ; Crystallography, X-Ray/*methods ; Photoreceptors, Microbial/chemistry/*ultrastructure ; Protein Conformation ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2012-12-01
    Description: The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction-before-destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3786669/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3786669/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Redecke, Lars -- Nass, Karol -- DePonte, Daniel P -- White, Thomas A -- Rehders, Dirk -- Barty, Anton -- Stellato, Francesco -- Liang, Mengning -- Barends, Thomas R M -- Boutet, Sebastien -- Williams, Garth J -- Messerschmidt, Marc -- Seibert, M Marvin -- Aquila, Andrew -- Arnlund, David -- Bajt, Sasa -- Barth, Torsten -- Bogan, Michael J -- Caleman, Carl -- Chao, Tzu-Chiao -- Doak, R Bruce -- Fleckenstein, Holger -- Frank, Matthias -- Fromme, Raimund -- Galli, Lorenzo -- Grotjohann, Ingo -- Hunter, Mark S -- Johansson, Linda C -- Kassemeyer, Stephan -- Katona, Gergely -- Kirian, Richard A -- Koopmann, Rudolf -- Kupitz, Chris -- Lomb, Lukas -- Martin, Andrew V -- Mogk, Stefan -- Neutze, Richard -- Shoeman, Robert L -- Steinbrener, Jan -- Timneanu, Nicusor -- Wang, Dingjie -- Weierstall, Uwe -- Zatsepin, Nadia A -- Spence, John C H -- Fromme, Petra -- Schlichting, Ilme -- Duszenko, Michael -- Betzel, Christian -- Chapman, Henry N -- 1R01GM095583/GM/NIGMS NIH HHS/ -- R01 GM095583/GM/NIGMS NIH HHS/ -- U54 GM094599/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jan 11;339(6116):227-30. doi: 10.1126/science.1229663. Epub 2012 Nov 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lubeck, at Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23196907" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Cathepsin B/antagonists & inhibitors/*chemistry ; Crystallization ; Crystallography, X-Ray ; Enzyme Precursors/chemistry ; Glycosylation ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protozoan Proteins/antagonists & inhibitors/*chemistry ; Sf9 Cells ; Spodoptera ; Trypanosoma brucei brucei/*enzymology ; X-Rays
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2016-05-07
    Description: A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pande, Kanupriya -- Hutchison, Christopher D M -- Groenhof, Gerrit -- Aquila, Andy -- Robinson, Josef S -- Tenboer, Jason -- Basu, Shibom -- Boutet, Sebastien -- DePonte, Daniel P -- Liang, Mengning -- White, Thomas A -- Zatsepin, Nadia A -- Yefanov, Oleksandr -- Morozov, Dmitry -- Oberthuer, Dominik -- Gati, Cornelius -- Subramanian, Ganesh -- James, Daniel -- Zhao, Yun -- Koralek, Jake -- Brayshaw, Jennifer -- Kupitz, Christopher -- Conrad, Chelsie -- Roy-Chowdhury, Shatabdi -- Coe, Jesse D -- Metz, Markus -- Xavier, Paulraj Lourdu -- Grant, Thomas D -- Koglin, Jason E -- Ketawala, Gihan -- Fromme, Raimund -- Srajer, Vukica -- Henning, Robert -- Spence, John C H -- Ourmazd, Abbas -- Schwander, Peter -- Weierstall, Uwe -- Frank, Matthias -- Fromme, Petra -- Barty, Anton -- Chapman, Henry N -- Moffat, Keith -- van Thor, Jasper J -- Schmidt, Marius -- P41GM103393/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01EY024363/EY/NEI NIH HHS/ -- R01GM095583/GM/NIGMS NIH HHS/ -- R24GM111072/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2016 May 6;352(6286):725-9. doi: 10.1126/science.aad5081. Epub 2016 May 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA. Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. ; Faculty of Natural Sciences, Department of Life Sciences, Imperial College, London SW7 2AZ, UK. ; Nanoscience Center and Department of Chemistry, University of Jyvaskyla, Post Office Box 35, 40014 Jyvaskyla, Finland. ; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA. ; Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA. ; School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA. ; Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. ; Department of Physics, Arizona State University, Tempe, AZ 85287, USA. ; Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. IMPRS-UFAST, Max Planck Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany. ; Hauptman-Woodward Institute, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA. ; Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA. ; Lawrence Livermore National Laboratory, Livermore, CA 94550, USA. ; Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. Center for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany. ; Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA. Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27151871" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2016-02-13
    Description: The three-dimensional structures of macromolecules and their complexes are mainly elucidated by X-ray protein crystallography. A major limitation of this method is access to high-quality crystals, which is necessary to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields information of sufficiently high resolution with which to solve the crystal structure. The observation that crystals with reduced unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks suggests that crystallographic resolution for some macromolecules may be limited not by their heterogeneity, but by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern that is equal to the incoherent sum of diffraction from rigid individual molecular complexes aligned along several discrete crystallographic orientations and that, consequently, contains more information than Bragg peaks alone. Although such continuous diffraction patterns have long been observed--and are of interest as a source of information about the dynamics of proteins--they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5-angstrom limit of measurable Bragg peaks, which allows us to phase the pattern directly. Using the molecular envelope conventionally determined at 4.5 angstroms as a constraint, we obtain a static image of the photosystem II dimer at a resolution of 3.5 angstroms. This result shows that continuous diffraction can be used to overcome what have long been supposed to be the resolution limits of macromolecular crystallography, using a method that exploits commonly encountered imperfect crystals and enables model-free phasing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ayyer, Kartik -- Yefanov, Oleksandr M -- Oberthur, Dominik -- Roy-Chowdhury, Shatabdi -- Galli, Lorenzo -- Mariani, Valerio -- Basu, Shibom -- Coe, Jesse -- Conrad, Chelsie E -- Fromme, Raimund -- Schaffer, Alexander -- Dorner, Katerina -- James, Daniel -- Kupitz, Christopher -- Metz, Markus -- Nelson, Garrett -- Xavier, Paulraj Lourdu -- Beyerlein, Kenneth R -- Schmidt, Marius -- Sarrou, Iosifina -- Spence, John C H -- Weierstall, Uwe -- White, Thomas A -- Yang, Jay-How -- Zhao, Yun -- Liang, Mengning -- Aquila, Andrew -- Hunter, Mark S -- Robinson, Joseph S -- Koglin, Jason E -- Boutet, Sebastien -- Fromme, Petra -- Barty, Anton -- Chapman, Henry N -- P41GM103393/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 GM095583/GM/NIGMS NIH HHS/ -- R01 GM097463/GM/NIGMS NIH HHS/ -- U54 GM094599/GM/NIGMS NIH HHS/ -- England -- Nature. 2016 Feb 11;530(7589):202-6. doi: 10.1038/nature16949.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany. ; Department of Physics, University of Hamburg, 22761 Hamburg, Germany. ; School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA. ; Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA. ; Department of Physics, Arizona State University, Tempe, Arizona 85287, USA. ; Physics Department, University of Wisconsin, Milwaukee, Wisconsin 53211, USA. ; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, GR-70013 Crete, Greece. ; Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC), National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA. ; Centre for Ultrafast Imaging, 22607 Hamburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26863980" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Crystallography, X-Ray/*methods ; Models, Molecular ; Photosystem II Protein Complex/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2013-12-21
    Description: X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. We used an x-ray free-electron laser (XFEL) with individual 50-femtosecond-duration x-ray pulses to minimize radiation damage and obtained a high-resolution room-temperature structure of a human serotonin receptor using sub-10-micrometer microcrystals grown in a membrane mimetic matrix known as lipidic cubic phase. Compared with the structure solved by using traditional microcrystallography from cryo-cooled crystals of about two orders of magnitude larger volume, the room-temperature XFEL structure displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902108/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902108/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Wei -- Wacker, Daniel -- Gati, Cornelius -- Han, Gye Won -- James, Daniel -- Wang, Dingjie -- Nelson, Garrett -- Weierstall, Uwe -- Katritch, Vsevolod -- Barty, Anton -- Zatsepin, Nadia A -- Li, Dianfan -- Messerschmidt, Marc -- Boutet, Sebastien -- Williams, Garth J -- Koglin, Jason E -- Seibert, M Marvin -- Wang, Chong -- Shah, Syed T A -- Basu, Shibom -- Fromme, Raimund -- Kupitz, Christopher -- Rendek, Kimberley N -- Grotjohann, Ingo -- Fromme, Petra -- Kirian, Richard A -- Beyerlein, Kenneth R -- White, Thomas A -- Chapman, Henry N -- Caffrey, Martin -- Spence, John C H -- Stevens, Raymond C -- Cherezov, Vadim -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073210/GM/NIGMS NIH HHS/ -- R01 GM095583/GM/NIGMS NIH HHS/ -- U54 GM094599/GM/NIGMS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 20;342(6165):1521-4. doi: 10.1126/science.1244142.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24357322" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray/*instrumentation/*methods ; Humans ; Lasers ; Protein Conformation ; Receptor, Serotonin, 5-HT2B/chemistry/radiation effects ; Receptors, G-Protein-Coupled/*chemistry/radiation effects ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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