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Thibert S, Reid DJ, Wilson JW, Varikoti R, Maltseva N, Schultz KJ, Kruel A, Babnigg G, Joachimiak A, Kumar N, Zhou M. Native Mass Spectrometry Dissects the Structural Dynamics of an Allosteric Heterodimer of SARS-CoV-2 Nonstructural Proteins. J Am Soc Mass Spectrom 2024; 35:912-921. [PMID: 38535992 PMCID: PMC11066969 DOI: 10.1021/jasms.3c00453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 05/02/2024]
Abstract
Structure-based drug design, which relies on precise understanding of the target protein and its interaction with the drug candidate, is dramatically expedited by advances in computational methods for candidate prediction. Yet, the accuracy needs to be improved with more structural data from high throughput experiments, which are challenging to generate, especially for dynamic and weak associations. Herein, we applied native mass spectrometry (native MS) to rapidly characterize ligand binding of an allosteric heterodimeric complex of SARS-CoV-2 nonstructural proteins (nsp) nsp10 and nsp16 (nsp10/16), a complex essential for virus survival in the host and thus a desirable drug target. Native MS showed that the dimer is in equilibrium with monomeric states in solution. Consistent with the literature, well characterized small cosubstrate, RNA substrate, and product bind with high specificity and affinity to the dimer but not the free monomers. Unsuccessfully designed ligands bind indiscriminately to all forms. Using neutral gas collision, the nsp16 monomer with bound cosubstrate can be released from the holo dimer complex, confirming the binding to nsp16 as revealed by the crystal structure. However, we observed an unusual migration of the endogenous zinc ions bound to nsp10 to nsp16 after collisional dissociation. The metal migration can be suppressed by using surface collision with reduced precursor charge states, which presumably resulted in minimal gas-phase structural rearrangement and highlighted the importance of complementary techniques. With minimal sample input (∼μg), native MS can rapidly detect ligand binding affinities and locations in dynamic multisubunit protein complexes, demonstrating the potential of an "all-in-one" native MS assay for rapid structural profiling of protein-to-AI-based compound systems to expedite drug discovery.
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Affiliation(s)
- Stephanie
M. Thibert
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Deseree J. Reid
- Chemical
and Biological Signature Sciences, Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jesse W. Wilson
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Rohith Varikoti
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Natalia Maltseva
- Center
for Structural Biology of Infectious Diseases, Consortium for Advanced
Science and Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Structural
Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Katherine J. Schultz
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Agustin Kruel
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Gyorgy Babnigg
- Center
for Structural Biology of Infectious Diseases, Consortium for Advanced
Science and Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Biosciences
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Andrzej Joachimiak
- Center
for Structural Biology of Infectious Diseases, Consortium for Advanced
Science and Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Structural
Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Neeraj Kumar
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Mowei Zhou
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
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2
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Kim Y, Maltseva N, Tesar C, Jedrzejczak R, Endres M, Ma H, Dugan HL, Stamper CT, Chang C, Li L, Changrob S, Zheng NY, Huang M, Ramanathan A, Wilson P, Michalska K, Joachimiak A. Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies. iScience 2024; 27:108976. [PMID: 38327783 PMCID: PMC10847736 DOI: 10.1016/j.isci.2024.108976] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/02/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Coronavirus nucleocapsid protein (NP) of SARS-CoV-2 plays a central role in many functions important for virus proliferation including packaging and protecting genomic RNA. The protein shares sequence, structure, and architecture with nucleocapsid proteins from betacoronaviruses. The N-terminal domain (NPRBD) binds RNA and the C-terminal domain is responsible for dimerization. After infection, NP is highly expressed and triggers robust host immune response. The anti-NP antibodies are not protective and not neutralizing but can effectively detect viral proliferation soon after infection. Two structures of SARS-CoV-2 NPRBD were determined providing a continuous model from residue 48 to 173, including RNA binding region and key epitopes. Five structures of NPRBD complexes with human mAbs were isolated using an antigen-bait sorting. Complexes revealed a distinct complement-determining regions and unique sets of epitope recognition. This may assist in the early detection of pathogens and designing peptide-based vaccines. Mutations that significantly increase viral load were mapped on developed, full length NP model, likely impacting interactions with host proteins and viral RNA.
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Affiliation(s)
- Youngchang Kim
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Natalia Maltseva
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Christine Tesar
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Robert Jedrzejczak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Endres
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Heng Ma
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Haley L. Dugan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Christopher T. Stamper
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Changsoo Chang
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Lei Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Siriruk Changrob
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Nai-Ying Zheng
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Min Huang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Arvind Ramanathan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Patrick Wilson
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine, New York, NY 10021, USA
| | - Karolina Michalska
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
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3
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Rosas-Lemus M, Dey S, Minasov G, Tan K, Anderson SM, Brunzelle J, Nocadello S, Shabalin I, Filippova E, Halavaty A, Kim Y, Maltseva N, Osipiuk J, Minor W, Joachimiak A, Savchenko A, Anderson WF, Satchell KJF. A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile. Microbiol Resour Announc 2023; 12:e0050723. [PMID: 37747257 PMCID: PMC10586155 DOI: 10.1128/mra.00507-23] [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: 06/23/2023] [Accepted: 08/15/2023] [Indexed: 09/26/2023] Open
Abstract
Clostridioides difficile causes life-threatening gastrointestinal infections. It is a high-risk pathogen due to a lack of effective treatments, antimicrobial resistance, and a poorly conserved genomic core. Herein, we report 30 X-ray structures from a structure genomics pipeline spanning 13 years, representing 10.2% of the X-ray structures for this important pathogen.
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Affiliation(s)
- Monica Rosas-Lemus
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Supratim Dey
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Kemin Tan
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Spencer M. Anderson
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Joseph Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Salvatore Nocadello
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Ivan Shabalin
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ekaterina Filippova
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Andrei Halavaty
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Youngchang Kim
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Natalia Maltseva
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Jerzy Osipiuk
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Wladek Minor
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Andrzej Joachimiak
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Alexei Savchenko
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Wayne F. Anderson
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Center for Structural Biology of Infectious Diseases team members
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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4
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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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5
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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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6
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Modi G, Marqus GM, Vippila MR, Gollapalli DR, Kim Y, Manna AC, Chacko S, Maltseva N, Wang X, Cullinane RT, Zhang Y, Kotler JLM, Kuzmic P, Zhang M, Lawson AP, Joachimiak A, Cheung A, Snider BB, Rothstein DM, Cuny GD, Hedstrom L. The Enzymatic Activity of Inosine 5'-Monophosphate Dehydrogenase May Not Be a Vulnerable Target for Staphylococcus aureus Infections. ACS Infect Dis 2021; 7:3062-3076. [PMID: 34590817 DOI: 10.1021/acsinfecdis.1c00342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many bacterial pathogens, including Staphylococcus aureus, require inosine 5'-monophosphate dehydrogenase (IMPDH) for infection, making this enzyme a promising new target for antibiotics. Although potent selective inhibitors of bacterial IMPDHs have been reported, relatively few have displayed antibacterial activity. Here we use structure-informed design to obtain inhibitors of S. aureus IMPDH (SaIMPDH) that have potent antibacterial activity (minimal inhibitory concentrations less than 2 μM) and low cytotoxicity in mammalian cells. The physicochemical properties of the most active compounds were within typical Lipinski/Veber space, suggesting that polarity is not a general requirement for achieving antibacterial activity. Five compounds failed to display activity in mouse models of septicemia and abscess infection. Inhibitor-resistant S. aureus strains readily emerged in vitro. Resistance resulted from substitutions in the cofactor/inhibitor binding site of SaIMPDH, confirming on-target antibacterial activity. These mutations decreased the binding of all inhibitors tested, but also decreased catalytic activity. Nonetheless, the resistant strains had comparable virulence to wild-type bacteria. Surprisingly, strains expressing catalytically inactive SaIMPDH displayed only a mild virulence defect. Collectively these observations question the vulnerability of the enzymatic activity of SaIMPDH as a target for the treatment of S. aureus infections, suggesting other functions of this protein may be responsible for its role in infection.
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Affiliation(s)
- Gyan Modi
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Gary M. Marqus
- Graduate Program in Chemistry, Brandeis University, Waltham Massachusetts 02453, United States
| | - Mohana Rao Vippila
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Health Building 2, 4849 Calhoun Rd., Houston, Texas 77204, United States
| | | | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Adhar C. Manna
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Shibin Chacko
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Xingyou Wang
- Graduate Program in Chemistry, Brandeis University, Waltham Massachusetts 02453, United States
| | - Ryan T. Cullinane
- Department of Biochemistry, Brandeis University, Massachusetts 02453, United States
| | - Yubo Zhang
- Department of Biochemistry, Brandeis University, Massachusetts 02453, United States
| | - Judy L. M. Kotler
- Graduate Program in Biochemistry and Biophysics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Petr Kuzmic
- BioKin Ltd., Watertown, Massachusetts 02472, United States
| | - Minjia Zhang
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Ann P. Lawson
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60367, United States
| | - Ambrose Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Barry B. Snider
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - David M. Rothstein
- David Rothstein Consulting, LLC, Lexington, Massachusetts 02421, United States
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Health Building 2, 4849 Calhoun Rd., Houston, Texas 77204, United States
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
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7
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Kim Y, Maltseva N, Chang C, Wilamowski M, Jedrzejczak R, Wower J, Randall G, Michalska K, Joachimiak A. Structural characterization of endoribonuclease Nsp15 from SARS CoV-2. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321089078] [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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8
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Michalska K, Wellington S, Maltseva N, Jedrzejczak R, Selem-Mojica N, Rosas-Becerra LR, Barona-Gómez F, Hung DT, Joachimiak A. Catalytically impaired TrpA subunit of tryptophan synthase from Chlamydia trachomatis is an allosteric regulator of TrpB. Protein Sci 2021; 30:1904-1918. [PMID: 34107106 PMCID: PMC8376405 DOI: 10.1002/pro.4143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 02/23/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/10/2022]
Abstract
Intracellular growth and pathogenesis of Chlamydia species is controlled by the availability of tryptophan, yet the complete biosynthetic pathway for l‐Trp is absent among members of the genus. Some representatives, however, preserve genes encoding tryptophan synthase, TrpAB – a bifunctional enzyme catalyzing the last two steps in l‐Trp synthesis. TrpA (subunit α) converts indole‐3‐glycerol phosphate into indole and glyceraldehyde‐3‐phosphate (α reaction). The former compound is subsequently used by TrpB (subunit β) to produce l‐Trp in the presence of l‐Ser and a pyridoxal 5′‐phosphate cofactor (β reaction). Previous studies have indicated that in Chlamydia, TrpA has lost its catalytic activity yet remains associated with TrpB to support the β reaction. Here, we provide detailed analysis of the TrpAB from C. trachomatis D/UW‐3/CX, confirming that accumulation of mutations in the active site of TrpA renders it enzymatically inactive, despite the conservation of the catalytic residues. We also show that TrpA remains a functional component of the TrpAB complex, increasing the activity of TrpB by four‐fold. The side chain of non‐conserved βArg267 functions as cation effector, potentially rendering the enzyme less susceptible to the solvent ion composition. The observed structural and functional changes detected herein were placed in a broader evolutionary and genomic context, allowing identification of these mutations in relation to their trp gene contexts in which they occur. Moreover, in agreement with the in vitro data, partial relaxation of purifying selection for TrpA, but not for TrpB, was detected, reinforcing a partial loss of TrpA functions during the course of evolution. PDB Code(s): 6V82;
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Affiliation(s)
- Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, Illinois, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Samantha Wellington
- Department of Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, Illinois, USA
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, Illinois, USA
| | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Mexico
| | - L Rodrigo Rosas-Becerra
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Mexico
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Mexico
| | - Deborah T Hung
- Department of Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, Illinois, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
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9
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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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10
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Kim Y, Wower J, Maltseva N, Chang C, Jedrzejczak R, Wilamowski M, Kang S, Nicolaescu V, Randall G, Michalska K, Joachimiak A. Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2. Commun Biol 2021; 4:193. [PMID: 33564093 PMCID: PMC7873276 DOI: 10.1038/s42003-021-01735-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 Nsp15 is a uridine-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family that is highly conserved in coronaviruses. As endoribonuclease activity seems to be responsible for the interference with the innate immune response, Nsp15 emerges as an attractive target for therapeutic intervention. Here we report the first structures with bound nucleotides and show how the enzyme specifically recognizes uridine moiety. In addition to a uridine site we present evidence for a second base binding site that can accommodate any base. The structure with a transition state analog, uridine vanadate, confirms interactions key to catalytic mechanisms. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. This acquired knowledge was instrumental in identifying Tipiracil, an FDA approved drug that is used in the treatment of colorectal cancer, as a potential anti-COVID-19 drug. Using crystallography, biochemical, and whole-cell assays, we demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme’s active site. Our findings provide new insights for the development of uracil scaffold-based drugs. Youngchang Kim, Jacek Wower, and colleagues explore the sequence specificity, metal ion dependence and catalytic mechanism of the Nsp15 endoribonuclease NendoU from SARS-CoV-2. The authors also solve five new crystal structures of the enzyme in complex with 5’UMP, 3’UMP, 5’cGpU, uridine 2′,3′-vanadate (transition state analog) and Tipiracil (uracil mimic), and demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme’s active site.
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Affiliation(s)
- Youngchang 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
| | - Jacek Wower
- Department of Animal Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Natalia Maltseva
- 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
| | - Changsoo Chang
- 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
| | - Robert Jedrzejczak
- 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
| | - Mateusz Wilamowski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA
| | - Soowon Kang
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, 60367, USA
| | - Vlad Nicolaescu
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, 60367, USA
| | - Glenn Randall
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, 60367, USA
| | - Karolina Michalska
- 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
| | - Andrzej Joachimiak
- 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. .,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA.
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11
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Joachimiak A, Chang C, Endres M, Jedrzejczak R, Kim Y, Maltseva N, Michalska K, Osipiuk J, Stols L, Tan K, Tesar C, Wilamowski M. Crystallography of SARS-CoV-2 non-structural proteins. Acta Crystallogr A Found Adv 2020. [DOI: 10.1107/s0108767320097858] [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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12
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Kim Y, Maltseva N, Wilamowski M, Tesar C, Endres M, Joachimiak A. Structural and biochemical analysis of the metallo-β-lactamase L1 from emerging pathogen Stenotrophomonas maltophilia revealed the subtle but distinct di-metal scaffold for catalytic activity. Protein Sci 2019; 29:723-743. [PMID: 31846104 PMCID: PMC7020990 DOI: 10.1002/pro.3804] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 10/08/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 01/05/2023]
Abstract
Emergence of Enterobacteriaceae harboring metallo‐β‐lactamases (MBL) has raised global threats due to their broad antibiotic resistance profiles and the lack of effective inhibitors against them. We have been studied one of the emerging environmental MBL, the L1 from Stenotrophomonas maltophilia K279a. We determined several crystal structures of L1 complexes with three different classes of β‐lactam antibiotics (penicillin G, moxalactam, meropenem, and imipenem), with the inhibitor captopril and different metal ions (Zn+2, Cd+2, and Cu+2). All hydrolyzed antibiotics and the inhibitor were found binding to two Zn+2 ions mainly through the opened lactam ring and some hydrophobic interactions with the binding pocket atoms. Without a metal ion, the active site is very similarly maintained as that of the native form with two Zn+2 ions, however, the protein does not bind the substrate moxalactam. When two Zn+2 ions were replaced with other metal ions, the same di‐metal scaffold was maintained and the added moxalactam was found hydrolyzed in the active site. Differential scanning fluorimetry and isothermal titration calorimetry were used to study thermodynamic properties of L1 MBL compared with New Deli Metallo‐β‐lactamase‐1 (NDM‐1). Both enzymes are significantly stabilized by Zn+2 and other divalent metals but showed different dependency. These studies also suggest that moxalactam and its hydrolyzed form may bind and dissociate with different kinetic modes with or without Zn+2 for each of L1 and NDM‐1. Our analysis implicates metal ions, in forming a distinct di‐metal scaffold, which is central to the enzyme stability, promiscuous substrate binding and versatile catalytic activity. Statement The L1 metallo‐β‐lactamase from an environmental multidrug‐resistant opportunistic pathogen Stenotrophomonas maltophilia K279a has been studied by determining 3D structures of L1 enzyme in the complexes with several β‐lactam antibiotics and different divalent metals and characterizing its biochemical and ligand binding properties. We found that the two‐metal center in the active site is critical in the enzymatic process including antibiotics recognition and binding, which explains the enzyme's activity toward diverse antibiotic substrates. This study provides the critical information for understanding the ligand recognition and for advanced drug development.
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Affiliation(s)
- Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois
| | - Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois
| | - Christine Tesar
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Michael Endres
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
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13
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Alcala A, Ramirez G, Solis A, Kim Y, Tan K, Luna O, Nguyen K, Vazquez D, Ward M, Zhou M, Mulligan R, Maltseva N, Kuhn ML. Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species. Protein Sci 2019; 29:695-710. [PMID: 31762145 DOI: 10.1002/pro.3793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022]
Abstract
Chloramphenicol acetyltransferases (CATs) were among the first antibiotic resistance enzymes identified and have long been studied as model enzymes for examining plasmid-mediated antibiotic resistance. These enzymes acetylate the antibiotic chloramphenicol, which renders it incapable of inhibiting bacterial protein synthesis. CATs can be classified into different types: Type A CATs are known to be important for antibiotic resistance to chloramphenicol and fusidic acid. Type B CATs are often called xenobiotic acetyltransferases and adopt a similar structural fold to streptogramin acetyltransferases, which are known to be critical for streptogramin antibiotic resistance. Type C CATs have recently been identified and can also acetylate chloramphenicol, but their roles in antibiotic resistance are largely unknown. Here, we structurally and kinetically characterized three Vibrio CAT proteins from a nonpathogenic species (Aliivibrio fisheri) and two important human pathogens (Vibrio cholerae and Vibrio vulnificus). We found all three proteins, including one in a superintegron (V. cholerae), acetylated chloramphenicol, but did not acetylate aminoglycosides or dalfopristin. We also determined the 3D crystal structures of these CATs alone and in complex with crystal violet and taurocholate. These compounds are known inhibitors of Type A CATs, but have not been explored in Type B and Type C CATs. Based on sequence, structure, and kinetic analysis, we concluded that the V. cholerae and V. vulnificus CATs belong to the Type B class and the A. fisheri CAT belongs to the Type C class. Ultimately, our results provide a framework for studying the evolution of antibiotic resistance gene acquisition and chloramphenicol acetylation in Vibrio and other species.
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Affiliation(s)
- Ashley Alcala
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Guadalupe Ramirez
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Allan Solis
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois.,Structural Biology Center X-ray Science Division Argonne National Laboratory, Argonne, Illinois
| | - Kemin Tan
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois.,Structural Biology Center X-ray Science Division Argonne National Laboratory, Argonne, Illinois
| | - Oscar Luna
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Karen Nguyen
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Daniel Vazquez
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Michael Ward
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Min Zhou
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois.,Structural Biology Center X-ray Science Division Argonne National Laboratory, Argonne, Illinois
| | - Rory Mulligan
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois.,Structural Biology Center X-ray Science Division Argonne National Laboratory, Argonne, Illinois
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois.,Structural Biology Center X-ray Science Division Argonne National Laboratory, Argonne, Illinois
| | - Misty L Kuhn
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
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14
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Yu R, Kim Y, Maltseva N, Braunstein P, Joachimiak A, Hedstrom L. Oxanosine Monophosphate Is a Covalent Inhibitor of Inosine 5'-Monophosphate Dehydrogenase. Chem Res Toxicol 2019; 32:456-466. [PMID: 30746940 DOI: 10.1021/acs.chemrestox.8b00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reactive nitrogen species (RNS) are produced during infection and inflammation, and the effects of these agents on proteins, DNA, and lipids are well recognized. In contrast, the effects of RNS damaged metabolites are less appreciated. 5-Amino-3-β-(d-ribofuranosyl)-3 H-imidazo-[4,5- d][1,3]oxazine-7-one (oxanosine) and its nucleotides are products of guanosine nitrosation. Here we demonstrate that oxanosine monophosphate (OxMP) is a potent reversible competitive inhibitor of IMPDH. The value of Ki varies from 50 to 340 nM among IMPDHs from five different organisms. UV spectroscopy and X-ray crystallography indicate that OxMP forms a ring-opened covalent adduct with the active site Cys (E-OxMP*). Unlike the covalent intermediate of the normal catalytic reaction, E-OxMP* does not hydrolyze, but instead recyclizes to OxMP. IMPDH inhibitors block proliferation and can induce apoptosis, so the inhibition of IMPDH by OxMP presents another potential mechanism for RNS toxicity.
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Affiliation(s)
- Runhan Yu
- Department of Chemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Youngchang Kim
- Structural Biology Center, Biosciences , Argonne National Laboratory , Argonne , Illinois 60439 , United States.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering , University of Chicago , Chicago , Illinois 60637 , United States
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering , University of Chicago , Chicago , Illinois 60637 , United States
| | - Philip Braunstein
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences , Argonne National Laboratory , Argonne , Illinois 60439 , United States.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering , University of Chicago , Chicago , Illinois 60637 , United States.,Department of Biochemistry and Molecular Biology , University of Chicago , Chicago , Illinois 60557 , United States
| | - Lizbeth Hedstrom
- Department of Chemistry , Brandeis University , Waltham , Massachusetts 02454 , United States.,Department of Biology , Brandeis University , Waltham , Massachusetts 02454 , United States
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15
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16
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Makowska-Grzyska M, Kim Y, Gorla SK, Wei Y, Mandapati K, Zhang M, Maltseva N, Modi G, Boshoff HI, Gu M, Aldrich C, Cuny GD, Hedstrom L, Joachimiak A. Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds. PLoS One 2015; 10:e0138976. [PMID: 26440283 PMCID: PMC4594927 DOI: 10.1371/journal.pone.0138976] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/07/2015] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis (TB) remains a worldwide problem and the need for new drugs is increasingly more urgent with the emergence of multidrug- and extensively-drug resistant TB. Inosine 5’-monophosphate dehydrogenase 2 (IMPDH2) from Mycobacterium tuberculosis (Mtb) is an attractive drug target. The enzyme catalyzes the conversion of inosine 5’-monophosphate into xanthosine 5’-monophosphate with the concomitant reduction of NAD+ to NADH. This reaction controls flux into the guanine nucleotide pool. We report seventeen selective IMPDH inhibitors with antitubercular activity. The crystal structures of a deletion mutant of MtbIMPDH2 in the apo form and in complex with the product XMP and substrate NAD+ are determined. We also report the structures of complexes with IMP and three structurally distinct inhibitors, including two with antitubercular activity. These structures will greatly facilitate the development of MtbIMPDH2-targeted antibiotics.
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Affiliation(s)
- Magdalena Makowska-Grzyska
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S Cass Ave. Argonne, IL, United States of America
| | - Suresh Kumar Gorla
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Yang Wei
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Kavitha Mandapati
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Minjia Zhang
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
| | - Gyan Modi
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Helena I. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States of America
| | - Minyi Gu
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
| | - Courtney Aldrich
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN, United States of America
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 549A Science and Research Building 2, Houston, TX, United States of America
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, United States of America
- * E-mail: (LH); (AJ)
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S Cass Ave. Argonne, IL, United States of America
- * E-mail: (LH); (AJ)
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17
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Makowska-Grzyska M, Kim Y, Maltseva N, Osipiuk J, Gu M, Zhang M, Mandapati K, Gollapalli DR, Gorla SK, Hedstrom L, Joachimiak A. A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity. J Biol Chem 2015; 290:5893-911. [PMID: 25572472 PMCID: PMC4342496 DOI: 10.1074/jbc.m114.619767] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD(+), which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD(+) and XMP/NAD(+). In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD(+) adenosine moiety. More importantly, this new NAD(+)-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD(+)-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. These findings offer a potential strategy for further ligand optimization.
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Affiliation(s)
- Magdalena Makowska-Grzyska
- From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Youngchang Kim
- From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Natalia Maltseva
- From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Jerzy Osipiuk
- From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Minyi Gu
- From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637
| | | | | | | | | | - Lizbeth Hedstrom
- the Departments of Biology and Chemistry, Brandeis University, Waltham, Massachusetts 024549110
| | - Andrzej Joachimiak
- From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637,
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18
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Tan K, Kim Y, Hatzos-Skintges C, Chang C, Cuff M, Chhor G, Osipiuk J, Michalska K, Nocek B, An H, Babnigg G, Bigelow L, Joachimiak G, Li H, Mack J, Makowska-Grzyska M, Maltseva N, Mulligan R, Tesar C, Zhou M, Joachimiak A. Salvage of failed protein targets by reductive alkylation. Methods Mol Biol 2014; 1140:189-200. [PMID: 24590719 PMCID: PMC4078742 DOI: 10.1007/978-1-4939-0354-2_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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] [Indexed: 01/21/2023]
Abstract
The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins.
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Affiliation(s)
- Kemin Tan
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL, 60439, USA
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Makowska-Grzyska M, Kim Y, Wu R, Wilton R, Gollapalli DR, Wang XK, Zhang R, Jedrzejczak R, Mack JC, Maltseva N, Mulligan R, Binkowski TA, Gornicki P, Kuhn ML, Anderson WF, Hedstrom L, Joachimiak A. Bacillus anthracis inosine 5'-monophosphate dehydrogenase in action: the first bacterial series of structures of phosphate ion-, substrate-, and product-bound complexes. Biochemistry 2012; 51:6148-63. [PMID: 22788966 DOI: 10.1021/bi300511w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the first unique step of the GMP branch of the purine nucleotide biosynthetic pathway. This enzyme is found in organisms of all three kingdoms. IMPDH inhibitors have broad clinical applications in cancer treatment, as antiviral drugs and as immunosuppressants, and have also displayed antibiotic activity. We have determined three crystal structures of Bacillus anthracis IMPDH, in a phosphate ion-bound (termed "apo") form and in complex with its substrate, inosine 5'-monophosphate (IMP), and product, xanthosine 5'-monophosphate (XMP). This is the first example of a bacterial IMPDH in more than one state from the same organism. Furthermore, for the first time for a prokaryotic enzyme, the entire active site flap, containing the conserved Arg-Tyr dyad, is clearly visible in the structure of the apoenzyme. Kinetic parameters for the enzymatic reaction were also determined, and the inhibitory effect of XMP and mycophenolic acid (MPA) has been studied. In addition, the inhibitory potential of two known Cryptosporidium parvum IMPDH inhibitors was examined for the B. anthracis enzyme and compared with those of three bacterial IMPDHs from Campylobacter jejuni, Clostridium perfringens, and Vibrio cholerae. The structures contribute to the characterization of the active site and design of inhibitors that specifically target B. anthracis and other microbial IMPDH enzymes.
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Affiliation(s)
- Magdalena Makowska-Grzyska
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
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20
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Nusca TD, Kim Y, Maltseva N, Lee JY, Eschenfeldt W, Stols L, Schofield MM, Scaglione JB, Dixon SD, Oves-Costales D, Challis GL, Hanna PC, Pfleger BF, Joachimiak A, Sherman DH. Functional and structural analysis of the siderophore synthetase AsbB through reconstitution of the petrobactin biosynthetic pathway from Bacillus anthracis. J Biol Chem 2012; 287:16058-72. [PMID: 22408253 PMCID: PMC3346087 DOI: 10.1074/jbc.m112.359349] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [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: 03/06/2012] [Indexed: 01/03/2023] Open
Abstract
Petrobactin, a mixed catechol-carboxylate siderophore, is required for full virulence of Bacillus anthracis, the causative agent of anthrax. The asbABCDEF operon encodes the biosynthetic machinery for this secondary metabolite. Here, we show that the function of five gene products encoded by the asb operon is necessary and sufficient for conversion of endogenous precursors to petrobactin using an in vitro system. In this pathway, the siderophore synthetase AsbB catalyzes formation of amide bonds crucial for petrobactin assembly through use of biosynthetic intermediates, as opposed to primary metabolites, as carboxylate donors. In solving the crystal structure of the B. anthracis siderophore biosynthesis protein B (AsbB), we disclose a three-dimensional model of a nonribosomal peptide synthetase-independent siderophore (NIS) synthetase. Structural characteristics provide new insight into how this bifunctional condensing enzyme can bind and adenylate multiple citrate-containing substrates followed by incorporation of both natural and unnatural polyamine nucleophiles. This activity enables formation of multiple end-stage products leading to final assembly of petrobactin. Subsequent enzymatic assays with the nonribosomal peptide synthetase-like AsbC, AsbD, and AsbE polypeptides show that the alternative products of AsbB are further converted to petrobactin, verifying previously proposed convergent routes to formation of this siderophore. These studies identify potential therapeutic targets to halt deadly infections caused by B. anthracis and other pathogenic bacteria and suggest new avenues for the chemoenzymatic synthesis of novel compounds.
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Affiliation(s)
- Tyler D. Nusca
- From the Life Sciences Institute and
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Youngchang Kim
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Natalia Maltseva
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | | | - William Eschenfeldt
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Lucy Stols
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | | | | | - Shandee D. Dixon
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Daniel Oves-Costales
- the Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gregory L. Challis
- the Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Philip C. Hanna
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Brian F. Pfleger
- From the Life Sciences Institute and
- the Department of Chemical and Biological Engineering, University of Wisconsin, Madison, Wisconsin 53706-1691
| | - Andrzej Joachimiak
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
- the Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, and
| | - David H. Sherman
- From the Life Sciences Institute and
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
- the Departments of Medicinal Chemistry and Chemistry, University of Michigan, Arbor, Michigan 48109
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Kim Y, Babnigg G, Jedrzejczak R, Eschenfeldt WH, Li H, Maltseva N, Hatzos-Skintges C, Gu M, Makowska-Grzyska M, Wu R, An H, Chhor G, Joachimiak A. High-throughput protein purification and quality assessment for crystallization. Methods 2011; 55:12-28. [PMID: 21907284 DOI: 10.1016/j.ymeth.2011.07.010] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 07/14/2011] [Accepted: 07/14/2011] [Indexed: 12/31/2022] Open
Abstract
The ultimate goal of structural biology is to understand the structural basis of proteins in cellular processes. In structural biology, the most critical issue is the availability of high-quality samples. "Structural biology-grade" proteins must be generated in the quantity and quality suitable for structure determination using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The purification procedures must reproducibly yield homogeneous proteins or their derivatives containing marker atom(s) in milligram quantities. The choice of protein purification and handling procedures plays a critical role in obtaining high-quality protein samples. With structural genomics emphasizing a genome-based approach in understanding protein structure and function, a number of unique structures covering most of the protein folding space have been determined and new technologies with high efficiency have been developed. At the Midwest Center for Structural Genomics (MCSG), we have developed semi-automated protocols for high-throughput parallel protein expression and purification. A protein, expressed as a fusion with a cleavable affinity tag, is purified in two consecutive immobilized metal affinity chromatography (IMAC) steps: (i) the first step is an IMAC coupled with buffer-exchange, or size exclusion chromatography (IMAC-I), followed by the cleavage of the affinity tag using the highly specific Tobacco Etch Virus (TEV) protease; the second step is IMAC and buffer exchange (IMAC-II) to remove the cleaved tag and tagged TEV protease. These protocols have been implemented on multidimensional chromatography workstations and, as we have shown, many proteins can be successfully produced in large-scale. All methods and protocols used for purification, some developed by MCSG, others adopted and integrated into the MCSG purification pipeline and more recently the Center for Structural Genomics of Infectious Diseases (CSGID) purification pipeline, are discussed in this chapter.
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Affiliation(s)
- Youngchang Kim
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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Eschenfeldt WH, Maltseva N, Stols L, Donnelly MI, Gu M, Nocek B, Tan K, Kim Y, Joachimiak A. Cleavable C-terminal His-tag vectors for structure determination. J Struct Funct Genomics 2010; 11:31-9. [PMID: 20213425 PMCID: PMC2885959 DOI: 10.1007/s10969-010-9082-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [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: 10/07/2009] [Accepted: 02/11/2010] [Indexed: 10/19/2022]
Abstract
High-throughput structural genomics projects seek to delineate protein structure space by determining the structure of representatives of all major protein families. Generally this is accomplished by processing numerous proteins through standardized protocols, for the most part involving purification of N-terminally His-tagged proteins. Often proteins that fail this approach are abandoned, but in many cases further effort is warranted because of a protein's intrinsic value. In addition, failure often occurs relatively far into the path to structure determination, and many failed proteins passed the first critical step, expression as a soluble protein. Salvage pathways seek to recoup the investment in this subset of failed proteins through alternative cloning, nested truncations, chemical modification, mutagenesis, screening buffers, ligands and modifying processing steps. To this end we have developed a series of ligation-independent cloning expression vectors that append various cleavable C-terminal tags instead of the conventional N-terminal tags. In an initial set of 16 proteins that failed with an N-terminal appendage, structures were obtained for C-terminally tagged derivatives of five proteins, including an example for which several alternative salvaging steps had failed. The new vectors allow appending C-terminal His(6)-tag and His(6)- and MBP-tags, and are cleavable with TEV or with both TEV and TVMV proteases.
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Affiliation(s)
- William H. Eschenfeldt
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, IL 60667, USA
| | - Lucy Stols
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Mark I. Donnelly
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Minyi Gu
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, IL 60667, USA
| | - Boguslaw Nocek
- Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, IL 60667, USA
| | - Kemin Tan
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Youngchang Kim
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, IL 60667, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, IL 60667, USA
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Kim Y, Quartey P, Li H, Volkart L, Hatzos C, Chang C, Nocek B, Cuff M, Osipiuk J, Tan K, Fan Y, Bigelow L, Maltseva N, Wu R, Borovilos M, Duggan E, Zhou M, Binkowski TA, Zhang RG, Joachimiak A. Large-scale evaluation of protein reductive methylation for improving protein crystallization. Nat Methods 2008; 5:853-4. [PMID: 18825126 DOI: 10.1038/nmeth1008-853] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kim Y, Quartey P, Volkart L, Hatzos C, Chang C, Nocek B, Cuff M, Osipiuk J, Tan K, Fan Y, Bigelow L, Maltseva N, Wu R, Borovilos M, Duggan E, Li H. Improving protein crystallization: a large-scale evaluation of protein reductive methylation. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308092271] [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: 11/11/2022] Open
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Osipiuk J, Maltseva N, Dementieva I, Clancy S, Collart F, Joachimiak A. Structure of YidB protein from Shigella flexneri shows a new fold with homeodomain motif. Proteins 2006; 65:509-13. [PMID: 16927377 PMCID: PMC2885951 DOI: 10.1002/prot.21054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | | | | | | | | | - Andrzej Joachimiak
- Correspondence to: Dr. Andrzej Joachimiak, Biosciences Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, 9700 S Cass Ave. Argonne, IL 60439.
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Kim Y, Maltseva N, Dementieva I, Collart F, Holzle D, Joachimiak A. Crystal structure of hypothetical protein YfiH from Shigella flexneri at 2 A resolution. Proteins 2006; 63:1097-101. [PMID: 16498617 PMCID: PMC2792012 DOI: 10.1002/prot.20589] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | | | | | | | - Andrzej Joachimiak
- Correspondence to: Andrzej Joachimiak, Biosciences Division, Midwest Center for Structural Genomics and Structural Biology, Center, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439.
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27
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Kim Y, Quartey P, Lezondra L, Hatzos C, Zhou M, Maltseva N, Li H, Wu R, Joachimiak A. Use of reductive methylation of proteins to increase crystallization efficiency at the Midwest Center for Structural Genomics. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305081651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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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28
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Maltseva N, Manovich Z, Seletskaya T, Kaptsova T, Nikulina V. Rapid diagnosis of viral neuroinfections by immunofluorescent and immunoperoxidase technics. J Neurol 1979; 220:125-30. [PMID: 87496 DOI: 10.1007/bf00313953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The results of immunofluorescent (IF) and immunoperoxidase (IP) technics applied for the detection of antigen in cerebrospinal fluid (CSF) cells in patients with mumps, herpes zoster and herpes simplex meningitis and meningoencephalitis are presented. Thirty patients were under study. The detection of mumps and herpes zoster viral antigen in CSF cells was possible in 100% of cases investigated. Herpes simplex virus antigen was detected in four of seven cases with symptoms of severe meningoencephalitis. Complement fixation (CF) antibodies to herpes simplex virus (type I) and positive seroconversion were detected in the four latter patients. The diagnostic value of the methods used for the detection of mumps, herpes simplex and herpes zoster viral antigens in CSF cells of patients is discussed.
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