1
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Huang X, Zhang C, Shang X, Chen Y, Xiao Q, Wei Z, Wang G, Zhen X, Xu G, Min J, Shen S, Liu Y. The NTE domain of PTENα/β promotes cancer progression by interacting with WDR5 via its SSSRRSS motif. Cell Death Dis 2024; 15:335. [PMID: 38744853 PMCID: PMC11094138 DOI: 10.1038/s41419-024-06714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024]
Abstract
PTENα/β, two variants of PTEN, play a key role in promoting tumor growth by interacting with WDR5 through their N-terminal extensions (NTEs). This interaction facilitates the recruitment of the SET1/MLL methyltransferase complex, resulting in histone H3K4 trimethylation and upregulation of oncogenes such as NOTCH3, which in turn promotes tumor growth. However, the molecular mechanism underlying this interaction has remained elusive. In this study, we determined the first crystal structure of PTENα-NTE in complex with WDR5, which reveals that PTENα utilizes a unique binding motif of a sequence SSSRRSS found in the NTE domain of PTENα/β to specifically bind to the WIN site of WDR5. Disruption of this interaction significantly impedes cell proliferation and tumor growth, highlighting the potential of the WIN site inhibitors of WDR5 as a way of therapeutic intervention of the PTENα/β associated cancers. These findings not only shed light on the important role of the PTENα/β-WDR5 interaction in carcinogenesis, but also present a promising avenue for developing cancer treatments that target this pathway.
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Affiliation(s)
- Xiaolei Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Cheng Zhang
- Institute of Aging & Tissue Regeneration, Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), 200127, Shanghai, China
| | - Xinci Shang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Yichang Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Qin Xiao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Zhengguo Wei
- School of Biology and Basic Medical Science, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Guanghui Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Xuechu Zhen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, 430079, Wuhan, Hubei, China
| | - Shaoming Shen
- Institute of Aging & Tissue Regeneration, Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), 200127, Shanghai, China.
| | - Yanli Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China.
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2
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Cellini A, Shankar MK, Nimmrich A, Hunt LA, Monrroy L, Mutisya J, Furrer A, Beale EV, Carrillo M, Malla TN, Maj P, Vrhovac L, Dworkowski F, Cirelli C, Johnson PJM, Ozerov D, Stojković EA, Hammarström L, Bacellar C, Standfuss J, Maj M, Schmidt M, Weinert T, Ihalainen JA, Wahlgren WY, Westenhoff S. Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography. Nat Chem 2024; 16:624-632. [PMID: 38225270 PMCID: PMC10997514 DOI: 10.1038/s41557-023-01413-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 11/28/2023] [Indexed: 01/17/2024]
Abstract
Charge-transfer reactions in proteins are important for life, such as in photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report the structural changes that take place while electrons transfer along a chain of four conserved tryptophans in the Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at a key asparagine, at a conserved salt bridge, and by rearrangements of nearby water molecules. We detect charge-induced structural changes close to the second tryptophan from 1 ps to 20 ps, identifying a nearby methionine as an active participant in the redox chain, and from 20 ps around the fourth tryptophan. The photolyase undergoes highly directed and carefully timed adaptations of its structure. This questions the validity of the linear solvent response approximation in Marcus theory and indicates that evolution has optimized fast protein fluctuations for optimal charge transfer.
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Madan Kumar Shankar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Leigh Anna Hunt
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Leonardo Monrroy
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jennifer Mutisya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Piotr Maj
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Lidija Vrhovac
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | | | - Emina A Stojković
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Leif Hammarström
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | - Michał Maj
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | - Janne A Ihalainen
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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3
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Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK. Author Correction: Structural evidence for intermediates during O 2 formation in photosystem II. Nature 2024; 626:E12. [PMID: 38291188 PMCID: PMC10866699 DOI: 10.1038/s41586-024-07099-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Affiliation(s)
- Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rana Hussein
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mohamed Ibrahim
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Margaret D Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mun Hon Cheah
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Thomas Fransson
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Corey J Kaminsky
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Julia Gätcke
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Stephanie Haupt
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isabela I Nangca
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen M Keable
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Orkun Aydin
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Leland B Gee
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Daniel W Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fikret Mamedov
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Holger Dobbek
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Athina Zouni
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden.
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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4
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Barends TRM, Gorel A, Bhattacharyya S, Schirò G, Bacellar C, Cirelli C, Colletier JP, Foucar L, Grünbein ML, Hartmann E, Hilpert M, Holton JM, Johnson PJM, Kloos M, Knopp G, Marekha B, Nass K, Nass Kovacs G, Ozerov D, Stricker M, Weik M, Doak RB, Shoeman RL, Milne CJ, Huix-Rotllant M, Cammarata M, Schlichting I. Influence of pump laser fluence on ultrafast myoglobin structural dynamics. Nature 2024; 626:905-911. [PMID: 38355794 PMCID: PMC10881388 DOI: 10.1038/s41586-024-07032-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
High-intensity femtosecond pulses from an X-ray free-electron laser enable pump-probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer1,2. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore3-17. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern18,19 whether this experimental approach20 allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions18,19. Here we describe ultrafast pump-probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe-CO bond distance (predicted by recent quantum wavepacket dynamics21) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump-probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump-probe experiments20 such that mechanistically relevant insight emerges.
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Affiliation(s)
| | - Alexander Gorel
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | | | | | - Lutz Foucar
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | | | - Mario Hilpert
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | | | - Bogdan Marekha
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, Lyon, France
| | - Karol Nass
- Paul Scherrer Institute, Villigen, Switzerland
| | | | | | | | - Martin Weik
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Heidelberg, Germany
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5
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Lv M, Zhou W, Hao Y, Li F, Zhang H, Yao X, Shi Y, Zhang L. Structural insights into the specific recognition of mitochondrial ribosome-binding factor hsRBFA and 12 S rRNA by methyltransferase METTL15. Cell Discov 2024; 10:11. [PMID: 38291322 PMCID: PMC10828496 DOI: 10.1038/s41421-023-00634-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 12/02/2023] [Indexed: 02/01/2024] Open
Abstract
Mitochondrial rRNA modifications are essential for mitoribosome assembly and its proper function. The m4C methyltransferase METTL15 maintains mitochondrial homeostasis by catalyzing m4C839 located in 12 S rRNA helix 44 (h44). This modification is essential to fine-tuning the ribosomal decoding center and increasing decoding fidelity according to studies of a conserved site in Escherichia coli. Here, we reported a series of crystal structures of human METTL15-hsRBFA-h44-SAM analog, METTL15-hsRBFA-SAM, METTL15-SAM and apo METTL15. The structures presented specific interactions of METTL15 with different substrates and revealed that hsRBFA recruits METTL15 to mitochondrial small subunit for further modification instead of 12 S rRNA. Finally, we found that METTL15 deficiency caused increased reactive oxygen species, decreased membrane potential and altered cellular metabolic state. Knocking down METTL15 caused an elevated lactate secretion and increased levels of histone H4K12-lactylation and H3K9-lactylation. METTL15 might be a suitable model to study the regulation between mitochondrial metabolism and histone lactylation.
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Affiliation(s)
- Mengqi Lv
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Wanwan Zhou
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yijie Hao
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Fudong Li
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Huafeng Zhang
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xuebiao Yao
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yunyu Shi
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Liang Zhang
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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6
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Nannenga BL. A new approach for serial electron diffraction data collection. IUCrJ 2024; 11:7-8. [PMID: 38131390 PMCID: PMC10833380 DOI: 10.1107/s2052252523010953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
This commentary describes a novel method for serial electron diffraction data collection in electron crystallography, utilizing a scanning transmission electron microscope to rapidly obtain patterns with low radiation dose. This approach, demonstrated with zeolite samples, has the potential to provide highly automated and rapid structures from nanocrystalline materials.
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Affiliation(s)
- Brent L. Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ USA
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7
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Hogan-Lamarre P, Luo Y, Bücker R, Miller RJD, Zou X. STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials. IUCrJ 2024; 11:62-72. [PMID: 38038991 PMCID: PMC10833385 DOI: 10.1107/s2052252523009661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25.
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Affiliation(s)
- Pascal Hogan-Lamarre
- Department of Physics, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Yi Luo
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106, Sweden
| | - Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - R. J. Dwayne Miller
- Department of Physics, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Chemistry, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106, Sweden
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8
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Hutchison CDM, Baxter JM, Fitzpatrick A, Dorlhiac G, Fadini A, Perrett S, Maghlaoui K, Lefèvre SB, Cordon-Preciado V, Ferreira JL, Chukhutsina VU, Garratt D, Barnard J, Galinis G, Glencross F, Morgan RM, Stockton S, Taylor B, Yuan L, Romei MG, Lin CY, Marangos JP, Schmidt M, Chatrchyan V, Buckup T, Morozov D, Park J, Park S, Eom I, Kim M, Jang D, Choi H, Hyun H, Park G, Nango E, Tanaka R, Owada S, Tono K, DePonte DP, Carbajo S, Seaberg M, Aquila A, Boutet S, Barty A, Iwata S, Boxer SG, Groenhof G, van Thor JJ. Optical control of ultrafast structural dynamics in a fluorescent protein. Nat Chem 2023; 15:1607-1615. [PMID: 37563326 PMCID: PMC10624617 DOI: 10.1038/s41557-023-01275-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/12/2023] [Indexed: 08/12/2023]
Abstract
The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.
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Affiliation(s)
| | - James M Baxter
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Ann Fitzpatrick
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Gabriel Dorlhiac
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Alisia Fadini
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Samuel Perrett
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Karim Maghlaoui
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Salomé Bodet Lefèvre
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Violeta Cordon-Preciado
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Josie L Ferreira
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Volha U Chukhutsina
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Douglas Garratt
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Jonathan Barnard
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Gediminas Galinis
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Flo Glencross
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Rhodri M Morgan
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Sian Stockton
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Ben Taylor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Letong Yuan
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jon P Marangos
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Viktoria Chatrchyan
- Physikalisch Chemisches Institut, Ruprecht-Karls Universität Heidelberg, Heidelberg, Germany
| | - Tiago Buckup
- Physikalisch Chemisches Institut, Ruprecht-Karls Universität Heidelberg, Heidelberg, Germany
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Jaehyun Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
- Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea
| | - Sehan Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Intae Eom
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Minseok Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Dogeun Jang
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Hyeongi Choi
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - HyoJung Hyun
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Gisu Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Eriko Nango
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan
| | - Daniel P DePonte
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sergio Carbajo
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Matt Seaberg
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Andrew Aquila
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sebastien Boutet
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - So Iwata
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Jasper J van Thor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK.
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9
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Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia JM, Mariani V, Pandey S, Poudyal I, Sierra RG, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman HN, Stojkovic EA, Batyuk A, Boutet S, Phillips GN, Pollack L, Schmidt M. Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam. Nat Commun 2023; 14:5507. [PMID: 37679343 PMCID: PMC10485065 DOI: 10.1038/s41467-023-41246-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/27/2023] [Indexed: 09/09/2023] Open
Abstract
For decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in atomic detail (between 2.2 and 2.7 Å resolution) by room-temperature, time-resolved crystallography with millisecond time-resolution (with timepoints between 3 ms and 700 ms) how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating, cooperativity, induced fit, and conformational selection all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme noncovalently before reacting to a trans-enamine. This was made possible in part by the application of singular value decomposition to the MISC data using a program that remains functional even if unit cell parameters change up to 3 Å during the reaction.
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Affiliation(s)
- Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Kara Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Luis Aldama
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Sasa Bajt
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Denisse Feliz
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Brendon Hayes
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark Hunter
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christopher Kupitz
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Stella Lisova
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Jose Manuel Martin-Garcia
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | - Valerio Mariani
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ishwor Poudyal
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Raymond G Sierra
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Chung Hong Yoon
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Abbas Ourmazd
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, 20 Arizona State University, Tempe, AZ, USA
| | - Peter Schwander
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Anton Barty
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Emina A Stojkovic
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Alexander Batyuk
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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10
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Morse PT, Pérez-Mejías G, Wan J, Turner AA, Márquez I, Kalpage HA, Vaishnav A, Zurek MP, Huettemann PP, Kim K, Arroum T, De la Rosa MA, Chowdhury DD, Lee I, Brunzelle JS, Sanderson TH, Malek MH, Meierhofer D, Edwards BFP, Díaz-Moreno I, Hüttemann M. Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle. Nat Commun 2023; 14:4166. [PMID: 37443314 PMCID: PMC10345088 DOI: 10.1038/s41467-023-39820-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Skeletal muscle is more resilient to ischemia-reperfusion injury than other organs. Tissue specific post-translational modifications of cytochrome c (Cytc) are involved in ischemia-reperfusion injury by regulating mitochondrial respiration and apoptosis. Here, we describe an acetylation site of Cytc, lysine 39 (K39), which was mapped in ischemic porcine skeletal muscle and removed by sirtuin5 in vitro. Using purified protein and cellular double knockout models, we show that K39 acetylation and acetylmimetic K39Q replacement increases cytochrome c oxidase (COX) activity and ROS scavenging while inhibiting apoptosis via decreased binding to Apaf-1, caspase cleavage and activity, and cardiolipin peroxidase activity. These results are discussed with X-ray crystallography structures of K39 acetylated (1.50 Å) and acetylmimetic K39Q Cytc (1.36 Å) and NMR dynamics. We propose that K39 acetylation is an adaptive response that controls electron transport chain flux, allowing skeletal muscle to meet heightened energy demand while simultaneously providing the tissue with robust resilience to ischemia-reperfusion injury.
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Affiliation(s)
- Paul T Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Alice A Turner
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Inmaculada Márquez
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Hasini A Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Matthew P Zurek
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Philipp P Huettemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Katherine Kim
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Dipanwita Dutta Chowdhury
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do 31116, Republic of Korea
| | - Joseph S Brunzelle
- Life Sciences Collaborative Access Team, Northwestern University, Center for Synchrotron Research, Argonne, IL, 60439, USA
| | - Thomas H Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Moh H Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Brian F P Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain.
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA.
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11
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Keown JR, Crawshaw AD, Trincao J, Carrique L, Gildea RJ, Horrell S, Warren AJ, Axford D, Owen R, Evans G, Bézier A, Metcalf P, Grimes JM. Atomic structure of a nudivirus occlusion body protein determined from a 70-year-old crystal sample. Nat Commun 2023; 14:4160. [PMID: 37443157 PMCID: PMC10345106 DOI: 10.1038/s41467-023-39819-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Infectious protein crystals are an essential part of the viral lifecycle for double-stranded DNA Baculoviridae and double-stranded RNA cypoviruses. These viral protein crystals, termed occlusion bodies or polyhedra, are dense protein assemblies that form a crystalline array, encasing newly formed virions. Here, using X-ray crystallography we determine the structure of a polyhedrin from Nudiviridae. This double-stranded DNA virus family is a sister-group to the baculoviruses, whose members were thought to lack occlusion bodies. The 70-year-old sample contains a well-ordered lattice formed by a predominantly α-helical building block that assembles into a dense, highly interconnected protein crystal. The lattice is maintained by extensive hydrophobic and electrostatic interactions, disulfide bonds, and domain switching. The resulting lattice is resistant to most environmental stresses. Comparison of this structure to baculovirus or cypovirus polyhedra shows a distinct protein structure, crystal space group, and unit cell dimensions, however, all polyhedra utilise common principles of occlusion body assembly.
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Affiliation(s)
- Jeremy R Keown
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Adam D Crawshaw
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Jose Trincao
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Loïc Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Richard J Gildea
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Sam Horrell
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Anna J Warren
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Danny Axford
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Robin Owen
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
- Rosalind Franklin Institute, Harwell Campus, Didcot, UK
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR7261 CNRS-Université de Tours, Tours, France
| | - Peter Metcalf
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
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12
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Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK. Structural evidence for intermediates during O 2 formation in photosystem II. Nature 2023; 617:629-636. [PMID: 37138085 PMCID: PMC10191843 DOI: 10.1038/s41586-023-06038-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/31/2023] [Indexed: 05/05/2023]
Abstract
In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O-O bond formation chemistry1-3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok's photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok's water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4-6, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1-Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.
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Affiliation(s)
- Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rana Hussein
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mohamed Ibrahim
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Margaret D Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mun Hon Cheah
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Thomas Fransson
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Corey J Kaminsky
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Julia Gätcke
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Stephanie Haupt
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isabela I Nangca
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen M Keable
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Orkun Aydin
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Leland B Gee
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Daniel W Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fikret Mamedov
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Holger Dobbek
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Athina Zouni
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden.
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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13
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Kilim O, Mentes A, Pál B, Csabai I, Gellért Á. SARS-CoV-2 receptor-binding domain deep mutational AlphaFold2 structures. Sci Data 2023; 10:134. [PMID: 36918581 PMCID: PMC10013278 DOI: 10.1038/s41597-023-02035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
Leveraging recent advances in computational modeling of proteins with AlphaFold2 (AF2) we provide a complete curated data set of all single mutations from each of the 7 main SARS-CoV-2 lineages spike protein receptor binding domain (RBD) resulting in 3819X7 = 26733 PDB structures. We visualize the generated structures and show that AF2 pLDDT values are correlated with state-of-the-art disorder approximations, implying some internal protein dynamics are also captured by the model. Joint increasing mutational coverage of both structural and phenotype data coupled with advances in machine learning can be leveraged to accelerate virology research, specifically future variant prediction. We hope this data release can offer assistance into further understanding of the local and global mutational landscape of SARS-CoV-2 as well as provide insight into the biological understanding that 3D structure acts as a bridge between protein genotype and phenotype.
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Affiliation(s)
- Oz Kilim
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Anikó Mentes
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Balázs Pál
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
- Wigner Research Centre for Physics, 1121, Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Ákos Gellért
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary.
- Veterinary Medical Research Institute, Eötvös Loránd Research Network, 1581, Budapest, P.O. box 18, Hungary.
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14
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Hu J, Jiang W, Zuo J, Shi D, Chen X, Yang X, Zhang W, Ma L, Liu Z, Xing Q. Structural basis of bacterial effector protein azurin targeting tumor suppressor p53 and inhibiting its ubiquitination. Commun Biol 2023; 6:59. [PMID: 36650277 PMCID: PMC9845241 DOI: 10.1038/s42003-023-04458-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Tumor suppressor p53 prevents tumorigenesis by promoting cell cycle arrest and apoptosis through transcriptional regulation. Dysfunction of p53 occurs frequently in human cancers. Thus, p53 becomes one of the most promising targets for anticancer treatment. A bacterial effector protein azurin triggers tumor suppression by stabilizing p53 and elevating its basal level. However, the structural and mechanistic basis of azurin-mediated tumor suppression remains elusive. Here we report the atomic details of azurin-mediated p53 stabilization by combining X-ray crystallography with nuclear magnetic resonance. Structural and mutagenic analysis reveals that the p28 region of azurin, which corresponds to a therapeutic peptide, significantly contributes to p53 binding. This binding stabilizes p53 by disrupting COP1-mediated p53 ubiquitination and degradation. Using the structure-based design, we obtain several affinity-enhancing mutants that enable amplifying the effect of azurin-induced apoptosis. Our findings highlight how the structure of the azurin-p53 complex can be leveraged to design azurin derivatives for cancer therapy.
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Affiliation(s)
- Jianjian Hu
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wenxue Jiang
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, 430074 China
| | - Jiaqi Zuo
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Dujuan Shi
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, 430074 China
| | - Xiaoqi Chen
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, 430074 China
| | - Xiao Yang
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, 430074 China
| | - Wenhui Zhang
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lixin Ma
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, 430074 China
| | - Zhu Liu
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, 430074 China
| | - Qiong Xing
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, 430074 China
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15
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Chung S, Kang MS, Alimbetov DS, Mun GI, Yunn NO, Kim Y, Kim BG, Wie M, Lee EA, Ra JS, Oh JM, Lee D, Lee K, Kim J, Han SH, Kim KT, Chung WK, Nam KH, Park J, Lee B, Kim S, Zhao W, Ryu SH, Lee YS, Myung K, Cho Y. Regulation of BRCA1 stability through the tandem UBX domains of isoleucyl-tRNA synthetase 1. Nat Commun 2022; 13:6732. [PMID: 36347866 DOI: 10.1038/s41467-022-34612-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) have evolved to acquire various additional domains. These domains allow ARSs to communicate with other cellular proteins in order to promote non-translational functions. Vertebrate cytoplasmic isoleucyl-tRNA synthetases (IARS1s) have an uncharacterized unique domain, UNE-I. Here, we present the crystal structure of the chicken IARS1 UNE-I complexed with glutamyl-tRNA synthetase 1 (EARS1). UNE-I consists of tandem ubiquitin regulatory X (UBX) domains that interact with a distinct hairpin loop on EARS1 and protect its neighboring proteins in the multi-synthetase complex from degradation. Phosphomimetic mutation of the two serine residues in the hairpin loop releases IARS1 from the complex. IARS1 interacts with BRCA1 in the nucleus, regulates its stability by inhibiting ubiquitylation via the UBX domains, and controls DNA repair function.
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16
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Ayan E, Yuksel B, Destan E, Ertem FB, Yildirim G, Eren M, Yefanov OM, Barty A, Tolstikova A, Ketawala GK, Botha S, Dao EH, Hayes B, Liang M, Seaberg MH, Hunter MS, Batyuk A, Mariani V, Su Z, Poitevin F, Yoon CH, Kupitz C, Cohen A, Doukov T, Sierra RG, Dağ Ç, DeMirci H. Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature. Commun Biol 2022; 5:73. [PMID: 35058563 PMCID: PMC8776744 DOI: 10.1038/s42003-021-02903-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/28/2021] [Indexed: 11/11/2022] Open
Abstract
Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.
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Affiliation(s)
- Esra Ayan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Busra Yuksel
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Ebru Destan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Fatma Betul Ertem
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Gunseli Yildirim
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Meryem Eren
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | | | - Anton Barty
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Gihan K Ketawala
- 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
| | - Sabine Botha
- 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
| | - E Han Dao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Matthew H Seaberg
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Valerio Mariani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Zhen Su
- 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, 94305, USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Aina Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Çağdaş Dağ
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research, Koc University, 34450, Istanbul, Turkey
- Koc University Isbank Center for Infectious Diseases (KUISCID), 34010, Istanbul, Turkey
| | - Hasan DeMirci
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey.
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, 94025, USA.
- Koc University Isbank Center for Infectious Diseases (KUISCID), 34010, Istanbul, Turkey.
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17
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Xu H, Wang B, Zhao TN, Liang ZT, Peng TB, Song XH, Wu JJ, Wang YC, Su XD. Structure-based analyses of neutralization antibodies interacting with naturally occurring SARS-CoV-2 RBD variants. Cell Res 2021; 31:1126-9. [PMID: 34480123 DOI: 10.1038/s41422-021-00554-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/24/2021] [Indexed: 02/07/2023] Open
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18
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Clabbers MTB, Holmes S, Muusse TW, Vajjhala PR, Thygesen SJ, Malde AK, Hunter DJB, Croll TI, Flueckiger L, Nanson JD, Rahaman MH, Aquila A, Hunter MS, Liang M, Yoon CH, Zhao J, Zatsepin NA, Abbey B, Sierecki E, Gambin Y, Stacey KJ, Darmanin C, Kobe B, Xu H, Ve T. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Nat Commun 2021; 12:2578. [PMID: 33972532 PMCID: PMC8110528 DOI: 10.1038/s41467-021-22590-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/18/2021] [Indexed: 02/03/2023] Open
Abstract
MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.
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Affiliation(s)
- Max T B Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, USA
| | - Susannah Holmes
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Timothy W Muusse
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Parimala R Vajjhala
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sara J Thygesen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alpeshkumar K Malde
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia
| | - Dominic J B Hunter
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Leonie Flueckiger
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Md Habibur Rahaman
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jingjing Zhao
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Nadia A Zatsepin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Brian Abbey
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Yann Gambin
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Katryn J Stacey
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Connie Darmanin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia.
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19
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Grünbein ML, Gorel A, Foucar L, Carbajo S, Colocho W, Gilevich S, Hartmann E, Hilpert M, Hunter M, Kloos M, Koglin JE, Lane TJ, Lewandowski J, Lutman A, Nass K, Nass Kovacs G, Roome CM, Sheppard J, Shoeman RL, Stricker M, van Driel T, Vetter S, Doak RB, Boutet S, Aquila A, Decker FJ, Barends TRM, Stan CA, Schlichting I. Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet. Nat Commun 2021; 12:1672. [PMID: 33723266 PMCID: PMC7960726 DOI: 10.1038/s41467-021-21819-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
X-ray free-electron lasers (XFELs) enable obtaining novel insights in structural biology. The recently available MHz repetition rate XFELs allow full data sets to be collected in shorter time and can also decrease sample consumption. However, the microsecond spacing of MHz XFEL pulses raises new challenges, including possible sample damage induced by shock waves that are launched by preceding pulses in the sample-carrying jet. We explored this matter with an X-ray-pump/X-ray-probe experiment employing haemoglobin microcrystals transported via a liquid jet into the XFEL beam. Diffraction data were collected using a shock-wave-free single-pulse scheme as well as the dual-pulse pump-probe scheme. The latter, relative to the former, reveals significant degradation of crystal hit rate, diffraction resolution and data quality. Crystal structures extracted from the two data sets also differ. Since our pump-probe attributes were chosen to emulate EuXFEL operation at its 4.5 MHz maximum pulse rate, this prompts concern about such data collection.
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Affiliation(s)
- Marie Luise Grünbein
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Alexander Gorel
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Lutz Foucar
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Sergio Carbajo
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - William Colocho
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Sasha Gilevich
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Elisabeth Hartmann
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Mario Hilpert
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Mark Hunter
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Marco Kloos
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany ,grid.434729.f0000 0004 0590 2900Present Address: European XFEL GmbH, Schenefeld, Germany
| | - Jason E. Koglin
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA ,grid.148313.c0000 0004 0428 3079Present Address: Los Alamos National Laboratory, Los Alamos, NM USA
| | - Thomas J. Lane
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA ,grid.466493.a0000 0004 0390 1787Present Address: Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - Jim Lewandowski
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Alberto Lutman
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Karol Nass
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany ,grid.5991.40000 0001 1090 7501Present Address: Paul Scherrer Institut, Villigen, Switzerland
| | - Gabriela Nass Kovacs
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Christopher M. Roome
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - John Sheppard
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Robert L. Shoeman
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Miriam Stricker
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany ,grid.4991.50000 0004 1936 8948Present Address: Department of Statistics, University of Oxford, Oxford, UK
| | - Tim van Driel
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Sharon Vetter
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - R. Bruce Doak
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Sébastien Boutet
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Andrew Aquila
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Franz Josef Decker
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Thomas R. M. Barends
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Claudiu Andrei Stan
- grid.430387.b0000 0004 1936 8796Department of Physics, Rutgers University Newark, Newark, NJ USA
| | - Ilme Schlichting
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
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20
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Fu Z, Huang B, Tang J, Liu S, Liu M, Ye Y, Liu Z, Xiong Y, Zhu W, Cao D, Li J, Niu X, Zhou H, Zhao YJ, Zhang G, Huang H. The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery. Nat Commun 2021; 12:488. [PMID: 33473130 PMCID: PMC7817691 DOI: 10.1038/s41467-020-20718-8] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/16/2020] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is the pathogen responsible for the COVID-19 pandemic. The SARS-CoV-2 papain-like cysteine protease (PLpro) has been implicated in playing important roles in virus maturation, dysregulation of host inflammation, and antiviral immune responses. The multiple functions of PLpro render it a promising drug target. Therefore, we screened a library of approved drugs and also examined available inhibitors against PLpro. Inhibitor GRL0617 showed a promising in vitro IC50 of 2.1 μM and an effective antiviral inhibition in cell-based assays. The co-crystal structure of SARS-CoV-2 PLproC111S in complex with GRL0617 indicates that GRL0617 is a non-covalent inhibitor and it resides in the ubiquitin-specific proteases (USP) domain of PLpro. NMR data indicate that GRL0617 blocks the binding of ISG15 C-terminus to PLpro. Using truncated ISG15 mutants, we show that the C-terminus of ISG15 plays a dominant role in binding PLpro. Structural analysis reveals that the ISG15 C-terminus binding pocket in PLpro contributes a disproportionately large portion of binding energy, thus this pocket is a hot spot for antiviral drug discovery targeting PLpro.
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Affiliation(s)
- Ziyang Fu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Bin Huang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Jinle Tang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Shuyan Liu
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Ming Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yuxin Ye
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Zhihong Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yuxian Xiong
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wenning Zhu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Dan Cao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Jihui Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China
| | - Huan Zhou
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Yong Juan Zhao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China.
| | - Hao Huang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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21
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Ikuta T, Shihoya W, Sugiura M, Yoshida K, Watari M, Tokano T, Yamashita K, Katayama K, Tsunoda SP, Uchihashi T, Kandori H, Nureki O. Structural insights into the mechanism of rhodopsin phosphodiesterase. Nat Commun 2020; 11:5605. [PMID: 33154353 PMCID: PMC7644710 DOI: 10.1038/s41467-020-19376-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
Rhodopsin phosphodiesterase (Rh-PDE) is an enzyme rhodopsin belonging to a recently discovered class of microbial rhodopsins with light-dependent enzymatic activity. Rh-PDE consists of the N-terminal rhodopsin domain and C-terminal phosphodiesterase (PDE) domain, connected by 76-residue linker, and hydrolyzes both cAMP and cGMP in a light-dependent manner. Thus, Rh-PDE has potential for the optogenetic manipulation of cyclic nucleotide concentrations, as a complementary tool to rhodopsin guanylyl cyclase and photosensitive adenylyl cyclase. Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The crystal structure of the rhodopsin domain at 2.6 Å resolution revealed a new topology of rhodopsins, with 8 TMs including the N-terminal extra TM, TM0. Mutational analyses demonstrated that TM0 plays a crucial role in the enzymatic photoactivity. We further solved the crystal structures of the rhodopsin domain (3.5 Å) and PDE domain (2.1 Å) with their connecting linkers, which showed a rough sketch of the full-length Rh-PDE. Integrating these structures, we proposed a model of full-length Rh-PDE, based on the HS-AFM observations and computational modeling of the linker region. These findings provide insight into the photoactivation mechanisms of other 8-TM enzyme rhodopsins and expand the definition of rhodopsins.
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Affiliation(s)
- Tatsuya Ikuta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Kazuho Yoshida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Masahito Watari
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Takaya Tokano
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan.
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
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22
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Fu L, Ye F, Feng Y, Yu F, Wang Q, Wu Y, Zhao C, Sun H, Huang B, Niu P, Song H, Shi Y, Li X, Tan W, Qi J, Gao GF. Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease. Nat Commun 2020; 11:4417. [PMID: 32887884 PMCID: PMC7474075 DOI: 10.1038/s41467-020-18233-x] [Citation(s) in RCA: 334] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/22/2020] [Indexed: 01/08/2023] Open
Abstract
COVID-19 was declared a pandemic on March 11 by WHO, due to its great threat to global public health. The coronavirus main protease (Mpro, also called 3CLpro) is essential for processing and maturation of the viral polyprotein, therefore recognized as an attractive drug target. Here we show that a clinically approved anti-HCV drug, Boceprevir, and a pre-clinical inhibitor against feline infectious peritonitis (corona) virus (FIPV), GC376, both efficaciously inhibit SARS-CoV-2 in Vero cells by targeting Mpro. Moreover, combined application of GC376 with Remdesivir, a nucleotide analogue that inhibits viral RNA dependent RNA polymerase (RdRp), results in sterilizing additive effect. Further structural analysis reveals binding of both inhibitors to the catalytically active side of SARS-CoV-2 protease Mpro as main mechanism of inhibition. Our findings may provide critical information for the optimization and design of more potent inhibitors against the emerging SARS-CoV-2 virus.
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Affiliation(s)
- Lifeng Fu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, 100101, Beijing, China
| | - Fei Ye
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control & Prevention, Chinese Center for Disease Control and Prevention, China CDC, 102206, Beijing, China
| | - Yong Feng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Feng Yu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201204, Shanghai, China
| | - Qisheng Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201204, Shanghai, China
| | - Yan Wu
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, 100069, Beijing, China
| | - Cheng Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Huan Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Baoying Huang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control & Prevention, Chinese Center for Disease Control and Prevention, China CDC, 102206, Beijing, China
| | - Peihua Niu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control & Prevention, Chinese Center for Disease Control and Prevention, China CDC, 102206, Beijing, China
| | - Hao Song
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, 100101, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xuebing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control & Prevention, Chinese Center for Disease Control and Prevention, China CDC, 102206, Beijing, China.
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
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23
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Gallagher-Jones M, Bustillo KC, Ophus C, Richards LS, Ciston J, Lee S, Minor AM, Rodriguez JA. Atomic structures determined from digitally defined nanocrystalline regions. IUCrJ 2020; 7:490-499. [PMID: 32431832 PMCID: PMC7201287 DOI: 10.1107/s2052252520004030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/22/2020] [Indexed: 06/11/2023]
Abstract
Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based ab initio solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography.
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Affiliation(s)
- Marcus Gallagher-Jones
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Karen C. Bustillo
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
| | - Colin Ophus
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
| | - Logan S. Richards
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Jim Ciston
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Andrew M. Minor
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
- Department of Materials Science and Engineering, University of California, Berkeley, California, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
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24
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Bücker R, Hogan-Lamarre P, Mehrabi P, Schulz EC, Bultema LA, Gevorkov Y, Brehm W, Yefanov O, Oberthür D, Kassier GH, Dwayne Miller RJ. Serial protein crystallography in an electron microscope. Nat Commun 2020; 11:996. [PMID: 32081905 PMCID: PMC7035385 DOI: 10.1038/s41467-020-14793-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/27/2020] [Indexed: 12/16/2022] Open
Abstract
Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample delivery techniques are required. On the other hand, rotation electron diffraction (MicroED) has shown great potential as an alternative means for protein nano-crystallography. Here, we present a method for serial electron diffraction of protein nanocrystals combining the benefits of both approaches. In a scanning transmission electron microscope, crystals randomly dispersed on a sample grid are automatically mapped, and a diffraction pattern at fixed orientation is recorded from each at a high acquisition rate. Dose fractionation ensures minimal radiation damage effects. We demonstrate the method by solving the structure of granulovirus occlusion bodies and lysozyme to resolutions of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation.
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Affiliation(s)
- Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Pascal Hogan-Lamarre
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Eike C Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lindsey A Bultema
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Vision Systems, Hamburg University of Technology, Harburger Schlossstrasse 20, 21079, Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Günther H Kassier
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - R J Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany.
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.
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25
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Khakurel KP, Angelov B, Andreasson J. Macromolecular Nanocrystal Structural Analysis with Electron and X-Rays: A Comparative Review. Molecules 2019; 24:E3490. [PMID: 31561479 PMCID: PMC6804143 DOI: 10.3390/molecules24193490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 01/10/2023] Open
Abstract
Crystallography has long been the unrivaled method that can provide the atomistic structural models of macromolecules, using either X-rays or electrons as probes. The methodology has gone through several revolutionary periods, driven by the development of new sources, detectors, and other instrumentation. Novel sources of both X-ray and electrons are constantly emerging. The increase in brightness of these sources, complemented by the advanced detection techniques, has relaxed the traditionally strict need for large, high quality, crystals. Recent reports suggest high-quality diffraction datasets from crystals as small as a few hundreds of nanometers can be routinely obtained. This has resulted in the genesis of a new field of macromolecular nanocrystal crystallography. Here we will make a brief comparative review of this growing field focusing on the use of X-rays and electrons sources.
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Affiliation(s)
- Krishna P Khakurel
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
| | - Borislav Angelov
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
| | - Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
- Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
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26
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Stevenson HP, Lin G, Barnes CO, Sutkeviciute I, Krzysiak T, Weiss SC, Reynolds S, Wu Y, Nagarajan V, Makhov AM, Lawrence R, Lamm E, Clark L, Gardella TJ, Hogue BG, Ogata CM, Ahn J, Gronenborn AM, Conway JF, Vilardaga JP, Cohen AE, Calero G. Transmission electron microscopy for the evaluation and optimization of crystal growth. Acta Crystallogr D Struct Biol 2016; 72:603-15. [PMID: 27139624 PMCID: PMC4854312 DOI: 10.1107/s2059798316001546] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/25/2016] [Indexed: 11/10/2022] Open
Abstract
The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that the presence of well ordered lattices with higher order Bragg spots, revealed by Fourier analysis of TEM images, is a good predictor of diffraction-quality crystals. Moreover, the use of TEM allowed (i) comparison of lattice quality among crystals from different conditions in crystallization screens; (ii) the detection of crystal pathologies that could contribute to poor X-ray diffraction, including crystal lattice defects, anisotropic diffraction and crystal contamination by heavy protein aggregates and nanocrystal nuclei; (iii) the qualitative estimation of crystal solvent content to explore the effect of lattice dehydration on diffraction and (iv) the selection of high-quality crystal fragments for microseeding experiments to generate reproducibly larger sized crystals. Applications to X-ray free-electron laser (XFEL) and micro-electron diffraction (microED) experiments are also discussed.
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Affiliation(s)
- Hilary P Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Christopher O Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Ieva Sutkeviciute
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, M240 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Troy Krzysiak
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Simon C Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Shelley Reynolds
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Ying Wu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | | | - Alexander M Makhov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Robert Lawrence
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287, USA
| | - Emily Lamm
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Lisa Clark
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Timothy J Gardella
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Brenda G Hogue
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287, USA
| | - Craig M Ogata
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 60439, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - James F Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jean Pierre Vilardaga
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, M240 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
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27
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Boutet S, Foucar L, Barends TRM, Botha S, Doak RB, Koglin JE, Messerschmidt M, Nass K, Schlichting I, Seibert MM, Shoeman RL, Williams GJ. Characterization and use of the spent beam for serial operation of LCLS. J Synchrotron Radiat 2015; 22:634-43. [PMID: 25931079 PMCID: PMC4416680 DOI: 10.1107/s1600577515004002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/26/2015] [Indexed: 05/30/2023]
Abstract
X-ray free-electron laser sources such as the Linac Coherent Light Source offer very exciting possibilities for unique research. However, beam time at such facilities is very limited and in high demand. This has led to significant efforts towards beam multiplexing of various forms. One such effort involves re-using the so-called spent beam that passes through the hole in an area detector after a weak interaction with a primary sample. This beam can be refocused into a secondary interaction region and used for a second, independent experiment operating in series. The beam profile of this refocused beam was characterized for a particular experimental geometry at the Coherent X-ray Imaging instrument at LCLS. A demonstration of this multiplexing capability was performed with two simultaneous serial femtosecond crystallography experiments, both yielding interpretable data of sufficient quality to produce electron density maps.
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Affiliation(s)
- Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas R. M. Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Sabine Botha
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R. Bruce Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jason E. Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Karol Nass
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M. Marvin Seibert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Robert L. Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Garth J. Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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Abstract
Next-generation synchrotron radiation sources, such as X-ray free-electron lasers, energy recovery linacs, and ultra-low-emittance storage rings, are catalyzing novel methods of biomolecular microcrystallography and solution scattering. These methods are described and future trends are predicted. Importantly, there is a growing realization that serial microcrystallography and certain cutting-edge solution scattering experiments can be performed at existing storage ring sources by utilizing new technology. In this sense, next-generation sources are serving two distinct functions, namely, provision of new capabilities that require the newer sources and inspiration of new methods that can be performed at existing sources.
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29
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Liu H, Zatsepin NA, Spence JCH. Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells. IUCrJ 2014; 1:19-27. [PMID: 25075316 PMCID: PMC4104966 DOI: 10.1107/s2052252513025530] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/14/2013] [Indexed: 06/01/2023]
Abstract
X-ray free electron lasers are used in measuring diffraction patterns from nanocrystals in the 'diffract-before-destroy' mode by outrunning radiation damage. The finite-sized nanocrystals provide an opportunity to recover intensity between Bragg spots by removing the modulating function that depends on crystal shape, i.e. the transform of the crystal shape. This shape-transform dividing-out scheme for solving the phase problem has been tested using simulated examples with cubic crystals. It provides a phasing method which does not require atomic resolution data, chemical modification to the sample, or modelling based on the protein databases. It is common to find multiple structural units (e.g. molecules, in symmetry-related positions) within a single unit cell, therefore incomplete unit cells (e.g. one additional molecule) can be observed at surface layers of crystals. In this work, the effects of such incomplete unit cells on the 'dividing-out' phasing algorithm are investigated using 2D crystals within the projection approximation. It is found that the incomplete unit cells do not hinder the recovery of the scattering pattern from a single unit cell (after dividing out the shape transforms from data merged from many nanocrystals of different sizes), assuming that certain unit-cell types are preferred. The results also suggest that the dynamic range of the data is a critical issue to be resolved in order to apply the shape transform method practically.
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Affiliation(s)
- Haiguang Liu
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Nadia A. Zatsepin
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - John C. H. Spence
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
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30
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Abstract
Structure elucidation of large membrane protein complexes is still a considerable challenge, yet is a key factor in drug development and disease combat. Femtosecond nanocrystallography is an emerging technique with which structural information of membrane proteins is obtained without the need to grow large crystals, thus overcoming the experimental riddle faced in traditional crystallography methods. Here, we demonstrate for the first time a microfluidic device capable of sorting membrane protein crystals based on size using dielectrophoresis. We demonstrate the excellent sorting power of this new approach with numerical simulations of selected submicrometer beads in excellent agreement with experimental observations. Crystals from batch crystallization broths of the huge membrane protein complex photosystem I were sorted without further treatment, resulting in a high degree of monodispersity and crystallinity in the ~100 nm size range. Microfluidic integration, continuous sorting, and nanometer-sized crystal fractions make this method ideal for direct coupling to femtosecond nanocrystallography.
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Affiliation(s)
| | - Tzu-Chiao Chao
- Department of Biology, University of Regina, Regina, SK, S4S0A2, Canada
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31
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Shah AB, Sivapalan ST, DeVetter BM, Yang TK, Wen J, Bhargava R, Murphy CJ, Zuo JM. High-index facets in gold nanocrystals elucidated by coherent electron diffraction. Nano Lett 2013; 13:1840-6. [PMID: 23484620 PMCID: PMC3659235 DOI: 10.1021/nl400609t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Characterization of high-index facets in noble metal nanocrystals for plasmonics and catalysis has been a challenge due to their small sizes and complex shapes. Here, we present an approach to determine the high-index facets of nanocrystals using streaked Bragg reflections in coherent electron diffraction patterns, and provide a comparison of high-index facets on unusual nanostructures such as trisoctahedra. We report new high-index facets in trisoctahedra and previous unappreciated diversity in facet sharpness.
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Affiliation(s)
- Amish B Shah
- Center for Microanalysis of Materials, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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