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Wilamowski M, Sherrell DA, Kim Y, Lavens A, Henning RW, Lazarski K, Shigemoto A, Endres M, Maltseva N, Babnigg G, Burdette SC, Srajer V, Joachimiak A. Time-resolved β-lactam cleavage by L1 metallo-β-lactamase. Nat Commun 2022; 13:7379. [PMID: 36450742 PMCID: PMC9712583 DOI: 10.1038/s41467-022-35029-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
Serial x-ray crystallography can uncover binding events, and subsequent chemical conversions occurring during enzymatic reaction. Here, we reveal the structure, binding and cleavage of moxalactam antibiotic bound to L1 metallo-β-lactamase (MBL) from Stenotrophomonas maltophilia. Using time-resolved serial synchrotron crystallography, we show the time course of β-lactam hydrolysis and determine ten snapshots (20, 40, 60, 80, 100, 150, 300, 500, 2000 and 4000 ms) at 2.20 Å resolution. The reaction is initiated by laser pulse releasing Zn2+ ions from a UV-labile photocage. Two metal ions bind to the active site, followed by binding of moxalactam and the intact β-lactam ring is observed for 100 ms after photolysis. Cleavage of β-lactam is detected at 150 ms and the ligand is significantly displaced. The reaction product adjusts its conformation reaching steady state at 2000 ms corresponding to the relaxed state of the enzyme. Only small changes are observed in the positions of Zn2+ ions and the active site residues. Mechanistic details captured here can be generalized to other MBLs.
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Affiliation(s)
- M Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology of Jagiellonian University, 30387, Krakow, Poland
| | - D A Sherrell
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Y Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - A Lavens
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - R W Henning
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL, 60637, USA
| | - K Lazarski
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - A Shigemoto
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - M Endres
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - N Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - G Babnigg
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - S C Burdette
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - V Srajer
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL, 60637, USA
| | - A Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
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Vescovi R, Chard R, Saint ND, Blaiszik B, Pruyne J, Bicer T, Lavens A, Liu Z, Papka ME, Narayanan S, Schwarz N, Chard K, Foster IT. Linking scientific instruments and computation: Patterns, technologies, and experiences. Patterns (N Y) 2022; 3:100606. [PMID: 36277824 PMCID: PMC9583115 DOI: 10.1016/j.patter.2022.100606] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/07/2022] [Accepted: 09/14/2022] [Indexed: 11/07/2022]
Abstract
Powerful detectors at modern experimental facilities routinely collect data at multiple GB/s. Online analysis methods are needed to enable the collection of only interesting subsets of such massive data streams, such as by explicitly discarding some data elements or by directing instruments to relevant areas of experimental space. Thus, methods are required for configuring and running distributed computing pipelines—what we call flows—that link instruments, computers (e.g., for analysis, simulation, artificial intelligence [AI] model training), edge computing (e.g., for analysis), data stores, metadata catalogs, and high-speed networks. We review common patterns associated with such flows and describe methods for instantiating these patterns. We present experiences with the application of these methods to the processing of data from five different scientific instruments, each of which engages powerful computers for data inversion,model training, or other purposes. We also discuss implications of such methods for operators and users of scientific facilities. Patterns for linking instruments and computers for online analysis are reviewed Methods are presented for capturing such “flows” in reusable forms The use of Globus automation services to run flows is described Implications of these methods for scientists and facilities are discussed
The industrial revolution transformed society via large-scale automation of manufacturing. Today, AI- and robotics-driven automation of scientific research seems set to usher in a new era of accelerated discovery. But just as the industrial revolution depended on new replicable and scalable manufacturing processes and methods for delivering the copious mechanical power required by those processes, so the automated discovery revolution demands new methods for implementing research automation processes and for connecting those processes to computing and data power. We present here new methods that address these essential needs by allowing scientists to capture common automation patterns in reusable flows and to embed such flows in a global trust, data, and computing fabric that enables instant access to powerful AI, simulation, and other computational capabilities. We use examples from synchrotron light sources to show how these methods can be realized in software and applied at scale.
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Affiliation(s)
- Rafael Vescovi
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Ryan Chard
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Nickolaus D Saint
- Globus, University of Chicago, 5730 S. Ellis Ave., Chicago, IL 60615, USA
| | - Ben Blaiszik
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,Globus, University of Chicago, 5730 S. Ellis Ave., Chicago, IL 60615, USA
| | - Jim Pruyne
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,Globus, University of Chicago, 5730 S. Ellis Ave., Chicago, IL 60615, USA
| | - Tekin Bicer
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,X-ray Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Alex Lavens
- Structural Biology Center, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Zhengchun Liu
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Michael E Papka
- Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,Department of Computer Science, University of Illinois Chicago, 1200 W. Harrison St., Chicago, IL 60607, USA
| | - Suresh Narayanan
- X-ray Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Nicholas Schwarz
- X-ray Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Kyle Chard
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,Department of Computer Science, University of Chicago, 5730 S. Ellis Ave., Chicago, IL 60615, USA
| | - Ian T Foster
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,Department of Computer Science, University of Chicago, 5730 S. Ellis Ave., Chicago, IL 60615, USA
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Sherrell DA, Lavens A, Wilamowski M, Kim Y, Chard R, Lazarski K, Rosenbaum G, Vescovi R, Johnson JL, Akins C, Chang C, Michalska K, Babnigg G, Foster I, Joachimiak A. Fixed-target serial crystallography at the Structural Biology Center. J Synchrotron Radiat 2022; 29:1141-1151. [PMID: 36073872 PMCID: PMC9455217 DOI: 10.1107/s1600577522007895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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] [Received: 03/18/2022] [Accepted: 08/05/2022] [Indexed: 05/30/2023]
Abstract
Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two β-lactamases: a class D serine β-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-β-lactamase from Stenotrophomonas maltophilia K279a.
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Affiliation(s)
- Darren A. Sherrell
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Alex Lavens
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Youngchang Kim
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Ryan Chard
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Krzysztof Lazarski
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Gerold Rosenbaum
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Rafael Vescovi
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Jessica L. Johnson
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Chase Akins
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Changsoo Chang
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Karolina Michalska
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Gyorgy Babnigg
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Ian Foster
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
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Joachimiak A, Wilamowski M, Sherrell D, Kim Y, Lavens A, Henning R, Lazarski K, Endres M, Maltseva N, Babnigg G, Burdette S, Srajer V. Time-resolved β-lactam cleavage by L1 metallo-β-lactamase. Acta Crystallogr A Found Adv 2022. [DOI: 10.1107/s2053273322099132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Sherrell D, Wilamowski M, Lavens A, Henning R. Using the ALEX nylon mesh holder for time-resolved serial crystallography: successes and drawbacks. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321099141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Wilamowski M, Sherrell DA, Minasov G, Kim Y, Shuvalova L, Lavens A, Chard R, Maltseva N, Jedrzejczak R, Rosas-Lemus M, Saint N, Foster IT, Michalska K, Satchell KJF, Joachimiak A. 2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography. Proc Natl Acad Sci U S A 2021; 118:e2100170118. [PMID: 33972410 PMCID: PMC8166198 DOI: 10.1073/pnas.2100170118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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] [Indexed: 01/08/2023] Open
Abstract
The genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus has a capping modification at the 5'-untranslated region (UTR) to prevent its degradation by host nucleases. These modifications are performed by the Nsp10/14 and Nsp10/16 heterodimers using S-adenosylmethionine as the methyl donor. Nsp10/16 heterodimer is responsible for the methylation at the ribose 2'-O position of the first nucleotide. To investigate the conformational changes of the complex during 2'-O methyltransferase activity, we used a fixed-target serial synchrotron crystallography method at room temperature. We determined crystal structures of Nsp10/16 with substrates and products that revealed the states before and after methylation, occurring within the crystals during the experiments. Here we report the crystal structure of Nsp10/16 in complex with Cap-1 analog (m7GpppAm2'-O). Inhibition of Nsp16 activity may reduce viral proliferation, making this protein an attractive drug target.
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Affiliation(s)
- Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology of Jagiellonian University, Krakow 30387, Poland
| | - Darren A Sherrell
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - Ludmilla Shuvalova
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Alex Lavens
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - Ryan Chard
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - Monica Rosas-Lemus
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Nickolaus Saint
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
| | - Ian T Foster
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
| | - Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - Karla J F Satchell
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637;
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
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Dickx N, Cagnie B, Parlevliet T, Lavens A, Danneels L. The effect of unilateral muscle pain on recruitment of the lumbar multifidus during automatic contraction. An experimental pain study. ACTA ACUST UNITED AC 2010; 15:364-9. [DOI: 10.1016/j.math.2010.02.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Revised: 02/01/2010] [Accepted: 02/08/2010] [Indexed: 11/17/2022]
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