Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II

Autor: Sierra, RG, Gati, C, Laksmono, H, Dao, EH, Gul, S, Fuller, F, Kern, J, Chatterjee, R, Ibrahim, M, Brewster, AS, Young, ID, Michels-Clark, T, Aquila, A, Liang, M, Hunter, MS, Koglin, JE, Boutet, S, Junco, EA, Hayes, B, Bogan, MJ, Hampton, CY, Puglisi, EV, Sauter, NK, Stan, CA, Zouni, A, Yano, J, Yachandra, VK, Soltis, SM, Puglisi, JD, DeMirci, H

Publikováno v: Sierra, RG; Gati, C; Laksmono, H; Dao, EH; Gul, S; Fuller, F; et al.(2015). Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nature Methods, 13(1), 59-62. doi: 10.1038/nmeth.3667. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/9kp8r8ks

We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______325::0a4f4aba14f2d506ab6bbead63cd745e
http://www.escholarship.org/uc/item/9kp8r8ks

Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography.

Autor: Ertem FB; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey., Guven O; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey., Buyukdag C; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey., Gocenler O; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey., Ayan E; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey., Yuksel B; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey., Gul M; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey., Usta G; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey., Cakılkaya B; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey., Johnson JA; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey., Dao EH; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA., Su Z; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA.; Department of Applied Physics, Stanford University, Stanford, CA, USA., Poitevin F; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA., Yoon CH; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA., Kupitz C; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA., Hayes B; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA., Liang M; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA., Hunter MS; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA., Batyuk A; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA., Sierra RG; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA., Ketawala G; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA., Botha S; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA., Dağ Ç; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.; Koc University, Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research (nSTAR), Istanbul, Turkey.; Koc University Isbank Center for Infectious Diseases (KUISCID), Istanbul, Turkey., DeMirci H; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.; Koc University Isbank Center for Infectious Diseases (KUISCID), Istanbul, Turkey.; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, USA.

Publikováno v: STAR protocols [STAR Protoc] 2022 Jan 24; Vol. 3 (1), pp. 101158. Date of Electronic Publication: 2022 Jan 24 (Print Publication: 2022).

Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing.

Autor: Durdagi S; Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey. Electronic address: serdar.durdagi@bahcesehir.edu.tr., Dağ Ç; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Dogan B; Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey., Yigin M; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Avsar T; Department of Medical Biology, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey., Buyukdag C; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Erol I; Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli 41400, Turkey., Ertem FB; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Calis S; Department of Medical Biology, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Department of Molecular Biology - Genetics and Biotechnology, Istanbul Technical University, Istanbul 34469, Turkey., Yildirim G; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Orhan MD; Department of Medical Biology, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey., Guven O; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Aksoydan B; Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul 34734, Turkey., Destan E; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Sahin K; Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey., Besler SO; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Oktay L; Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey., Shafiei A; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Tolu I; Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey., Ayan E; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Yuksel B; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Peksen AB; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Gocenler O; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Yucel AD; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Can O; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Ozabrahamyan S; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Olkan A; Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; School of Medicine, Bahcesehir University, Istanbul 34734, Turkey., Erdemoglu E; Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Faculty of Medicine, Mersin University, Mersin 33070, Turkey., Aksit F; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Tanisali G; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey., Yefanov OM; Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22607, Germany., Barty A; Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22607, Germany., Tolstikova A; Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22607, Germany., Ketawala GK; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA., Botha S; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA., Dao EH; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA 94025, USA., Hayes B; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Liang M; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Seaberg MH; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Hunter MS; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Batyuk A; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Mariani V; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Su Z; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; Department of Applied Physics, Stanford University, Stanford, CA, USA., Poitevin F; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Yoon CH; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Kupitz C; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Sierra RG; Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Snell EH; Hauptman-Woodward Medical Research Institute, University at Buffalo, 700 Ellicott St, Buffalo, NY, USA; Materials Design and Innovation, SUNY at Buffalo, 700 Ellicott St., Buffalo, NY, USA., DeMirci H; Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA 94025, USA; Koc University Isbank Center for Infectious Diseases (KUISCID), 34450, Istanbul, Turkey. Electronic address: hdemirci@ku.edu.tr.

Publikováno v: Structure (London, England : 1993) [Structure] 2021 Dec 02; Vol. 29 (12), pp. 1382-1396.e6. Date of Electronic Publication: 2021 Aug 16.

Structure of the 30S ribosomal decoding complex at ambient temperature.

Autor: Dao EH; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA., Poitevin F; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA.; Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA., Sierra RG; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA.; Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA., Gati C; Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA.; Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA., Rao Y; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA.; Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA., Ciftci HI; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA., Akşit F; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA., McGurk A; Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA., Obrinski T; Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA., Mgbam P; Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA., Hayes B; Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA., De Lichtenberg C; Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE-901 87 Umeå, Sweden., Pardo-Avila F; Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA., Corsepius N; Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA., Zhang L; Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA., Seaberg MH; Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA., Hunter MS; Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA., Liang M; Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA., Koglin JE; Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA., Wakatsuki S; Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA.; Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA., Demirci H; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA.; Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA.; Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA.

Publikováno v: RNA (New York, N.Y.) [RNA] 2018 Dec; Vol. 24 (12), pp. 1667-1676. Date of Electronic Publication: 2018 Aug 23.

Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin.

Autor: Yoon CH; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., DeMirci H; Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.; Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Sierra RG; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Dao EH; Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.; Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Ahmadi R; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Aksit F; Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Aquila AL; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Batyuk A; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Ciftci H; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Guillet S; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Hayes MJ; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Hayes B; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Lane TJ; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.; Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Liang M; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Lundström U; Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Koglin JE; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Mgbam P; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Rao Y; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Rendahl T; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Rodriguez E; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Zhang L; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Wakatsuki S; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.; Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Boutet S; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA., Holton JM; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.; Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA., Hunter MS; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.

Publikováno v: Scientific data [Sci Data] 2017 Apr 25; Vol. 4, pp. 170055. Date of Electronic Publication: 2017 Apr 25.