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Helgren TR, Chen C, Wangtrakuldee P, Edwards TE, Staker BL, Abendroth J, Sankaran B, Housley NA, Myler PJ, Audia JP, Horn JR, Hagen TJ. Rickettsia prowazekii methionine aminopeptidase as a promising target for the development of antibacterial agents. Bioorg Med Chem 2017; 25:813-824. [PMID: 28089350 PMCID: PMC5319851 DOI: 10.1016/j.bmc.2016.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/06/2016] [Accepted: 11/08/2016] [Indexed: 01/07/2023]
Abstract
Methionine aminopeptidase (MetAP) is a class of ubiquitous enzymes essential for the survival of numerous bacterial species. These enzymes are responsible for the cleavage of N-terminal formyl-methionine initiators from nascent proteins to initiate post-translational modifications that are often essential to proper protein function. Thus, inhibition of MetAP activity has been implicated as a novel antibacterial target. We tested this idea in the present study by targeting the MetAP enzyme in the obligate intracellular pathogen Rickettsia prowazekii. We first identified potent RpMetAP inhibitory species by employing an in vitro enzymatic activity assay. The molecular docking program AutoDock was then utilized to compare published crystal structures of inhibited MetAP species to docked poses of RpMetAP. Based on these in silico and in vitro screens, a subset of 17 compounds was tested for inhibition of R. prowazekii growth in a pulmonary vascular endothelial cell (EC) culture infection model system. All compounds were tested over concentration ranges that were determined to be non-toxic to the ECs and 8 of the 17 compounds displayed substantial inhibition of R. prowazekii growth. These data highlight the therapeutic potential for inhibiting RpMetAP as a novel antimicrobial strategy and set the stage for future studies in pre-clinical animal models of infection.
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Affiliation(s)
- Travis R Helgren
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Congling Chen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Phumvadee Wangtrakuldee
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Thomas E Edwards
- Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Bart L Staker
- Center for Infectious Disease Research, Formerly Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle, WA 98109, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Jan Abendroth
- Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicole A Housley
- Department of Microbiology and Immunology and The Center for Lung Biology, University of South Alabama College of Medicine, Laboratory of Infectious Diseases, 307 North University Blvd, Mobile, AL 36688, USA
| | - Peter J Myler
- Center for Infectious Disease Research, Formerly Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle, WA 98109, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA; Department of Global Health and Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Jonathon P Audia
- Department of Microbiology and Immunology and The Center for Lung Biology, University of South Alabama College of Medicine, Laboratory of Infectious Diseases, 307 North University Blvd, Mobile, AL 36688, USA
| | - James R Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Timothy J Hagen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA.
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Haft DH, Pierce PG, Mayclin SJ, Sullivan A, Gardberg AS, Abendroth J, Begley DW, Phan IQ, Staker BL, Myler PJ, Marathias VM, Lorimer DD, Edwards TE. Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors. Sci Rep 2017; 7:41074. [PMID: 28120876 PMCID: PMC5264612 DOI: 10.1038/srep41074] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/12/2016] [Indexed: 01/08/2023] Open
Abstract
During human infection, Mycobacterium tuberculosis (Mtb) survives the normally bacteriocidal phagosome of macrophages. Mtb and related species may be able to combat this harsh acidic environment which contains reactive oxygen species due to the mycobacterial genomes encoding a large number of dehydrogenases. Typically, dehydrogenase cofactor binding sites are open to solvent, which allows NAD/NADH exchange to support multiple turnover. Interestingly, mycobacterial short chain dehydrogenases/reductases (SDRs) within family TIGR03971 contain an insertion at the NAD binding site. Here we present crystal structures of 9 mycobacterial SDRs in which the insertion buries the NAD cofactor except for a small portion of the nicotinamide ring. Line broadening and STD-NMR experiments did not show NAD or NADH exchange on the NMR timescale. STD-NMR demonstrated binding of the potential substrate carveol, the potential product carvone, the inhibitor tricyclazol, and an external redox partner 2,6-dichloroindophenol (DCIP). Therefore, these SDRs appear to contain a non-exchangeable NAD cofactor and may rely on an external redox partner, rather than cofactor exchange, for multiple turnover. Incidentally, these genes always appear in conjunction with the mftA gene, which encodes the short peptide MftA, and with other genes proposed to convert MftA into the external redox partner mycofactocin.
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Affiliation(s)
- Daniel H Haft
- National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Phillip G Pierce
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Amy Sullivan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Anna S Gardberg
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA.,University of Washington, Department of Medical Education and Biomedical Informatics &Department of Global Health, Seattle WA 98195, USA
| | - Vasilios M Marathias
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
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53
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Cala AR, Nadeau MT, Abendroth J, Staker BL, Reers AR, Weatherhead AW, Dobson RCJ, Myler PJ, Hudson AO. The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 Å resolution. Acta Crystallogr F Struct Biol Commun 2016; 72:885-891. [PMID: 27917836 PMCID: PMC5137465 DOI: 10.1107/s2053230x16018525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 11/19/2016] [Indexed: 11/10/2022] Open
Abstract
In bacteria, the second committed step in the diaminopimelate/lysine anabolic pathways is catalyzed by the enzyme dihydrodipicolinate reductase (DapB). DapB catalyzes the reduction of dihydrodipicolinate to yield tetrahydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of DapB from the human-pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are reported. Protein crystals were grown in conditions consisting of 5%(w/v) PEG 4000, 200 mM sodium acetate, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.3 Å resolution. They belonged to space group P4322, with unit-cell parameters a = 109.38, b = 109.38, c = 176.95 Å. Rr.i.m. was 0.11, Rwork was 0.177 and Rfree was 0.208. The three-dimensional structural features of the enzymes show that DapB from B. henselae is a tetramer consisting of four identical polypeptides. In addition, the substrate NADP+ was found to be bound to one monomer, which resulted in a closed conformational change in the N-terminal domain.
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Affiliation(s)
- Ali R. Cala
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - Maria T. Nadeau
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - Jan Abendroth
- Beryllium Discovery Inc., Bainbridge Island, WA 98110, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Alexandra R. Reers
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Anthony W. Weatherhead
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA 98195, USA
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
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Attigani A, Sun L, Wang Q, Liu Y, Bai D, Li S, Huang X. The crystal structure of the endoglucanase Cel10, a family 8 glycosyl hydrolase from Klebsiella pneumoniae. Acta Crystallogr F Struct Biol Commun 2016; 72:870-876. [PMID: 27917834 PMCID: PMC5137463 DOI: 10.1107/s2053230x16017891] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/08/2016] [Indexed: 02/04/2023] Open
Abstract
Cellulases are produced by microorganisms that grow on cellulose biomass. Here, a cellulase, Cel10, was identified in a strain of Klebsiella pneumoniae isolated from Chinese bamboo rat gut. Analysis of substrate specificity showed that Cel10 is able to hydrolyze amorphous carboxymethyl cellulose (CMC) and crystalline forms of cellulose (Avicel and xylan) but is unable to hydrolyze p-nitrophenol β-D-glucopyranoside (p-NPG), proving that Cel10 is an endoglucanase. A phylogenetic tree analysis indicates that Cel10 belongs to the glycoside hydrolase 8 (GH8) subfamily. In order to further understanding of its substrate specificity, the structure of Cel10 was solved by molecular replacement and refined to 1.76 Å resolution. The overall fold is distinct from those of most other enzymes belonging to the GH8 subfamily. Although it forms the typical (α/α)6-barrel motif fold, like Acetobacterxylinum CMCax, one helix is missing. Structural comparisons with Clostridium thermocellum CelA (CtCelA), the best characterized GH8 endoglucanase, revealed that sugar-recognition subsite -3 is completely missing in Cel10. The absence of this subsite correlates to a more open substrate-binding cleft on the cellooligosaccharide reducing-end side.
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Affiliation(s)
- Ayman Attigani
- Key Laboratory for Integrated Chinese Traditional and Western Veterinary Medicine and Animal Healthcare, College of Animal Science, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Fuzhou 350002, People’s Republic of China
| | - Lifang Sun
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Qing Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Yadan Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Dingping Bai
- Key Laboratory for Integrated Chinese Traditional and Western Veterinary Medicine and Animal Healthcare, College of Animal Science, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Fuzhou 350002, People’s Republic of China
| | - Shengping Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Xiaohong Huang
- Key Laboratory for Integrated Chinese Traditional and Western Veterinary Medicine and Animal Healthcare, College of Animal Science, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Fuzhou 350002, People’s Republic of China
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55
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McGillick BE, Kumaran D, Vieni C, Swaminathan S. β-Hydroxyacyl-acyl Carrier Protein Dehydratase (FabZ) from Francisella tularensis and Yersinia pestis: Structure Determination, Enzymatic Characterization, and Cross-Inhibition Studies. Biochemistry 2016; 55:1091-9. [DOI: 10.1021/acs.biochem.5b00832] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brian E. McGillick
- Biology
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Desigan Kumaran
- Biology
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Casey Vieni
- Biology
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
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Koday MT, Nelson J, Chevalier A, Koday M, Kalinoski H, Stewart L, Carter L, Nieusma T, Lee PS, Ward AB, Wilson IA, Dagley A, Smee DF, Baker D, Fuller DH. A Computationally Designed Hemagglutinin Stem-Binding Protein Provides In Vivo Protection from Influenza Independent of a Host Immune Response. PLoS Pathog 2016; 12:e1005409. [PMID: 26845438 PMCID: PMC4742065 DOI: 10.1371/journal.ppat.1005409] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 12/31/2015] [Indexed: 12/31/2022] Open
Abstract
Broadly neutralizing antibodies targeting a highly conserved region in the hemagglutinin (HA) stem protect against influenza infection. Here, we investigate the protective efficacy of a protein (HB36.6) computationally designed to bind with high affinity to the same region in the HA stem. We show that intranasal delivery of HB36.6 affords protection in mice lethally challenged with diverse strains of influenza independent of Fc-mediated effector functions or a host antiviral immune response. This designed protein prevents infection when given as a single dose of 6.0 mg/kg up to 48 hours before viral challenge and significantly reduces disease when administered as a daily therapeutic after challenge. A single dose of 10.0 mg/kg HB36.6 administered 1-day post-challenge resulted in substantially better protection than 10 doses of oseltamivir administered twice daily for 5 days. Thus, binding of HB36.6 to the influenza HA stem region alone, independent of a host response, is sufficient to reduce viral infection and replication in vivo. These studies demonstrate the potential of computationally designed binding proteins as a new class of antivirals for influenza.
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Affiliation(s)
- Merika Treants Koday
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jorgen Nelson
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Aaron Chevalier
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Michael Koday
- Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
| | - Hannah Kalinoski
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Lance Stewart
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Lauren Carter
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Travis Nieusma
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Peter S. Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ashley Dagley
- Institute for Antiviral Research, Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Donald F. Smee
- Institute for Antiviral Research, Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - David Baker
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
| | - Deborah Heydenburg Fuller
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
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57
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Naqvi KF, Staker BL, Dobson RCJ, Serbzhinskiy D, Sankaran B, Myler PJ, Hudson AO. Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 Å resolution. Acta Crystallogr F Struct Biol Commun 2016; 72:2-9. [PMID: 26750477 PMCID: PMC4708043 DOI: 10.1107/s2053230x15023213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022] Open
Abstract
The enzyme dihydrodipicolinate synthase catalyzes the committed step in the synthesis of diaminopimelate and lysine to facilitate peptidoglycan and protein synthesis. Dihydrodipicolinate synthase catalyzes the condensation of L-aspartate 4-semialdehyde and pyruvate to synthesize L-2,3-dihydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are presented. Protein crystals were grown in conditions consisting of 20%(w/v) PEG 4000, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.10 Å resolution. They belonged to space group P212121, with unit-cell parameters a = 79.96, b = 106.33, c = 136.25 Å. The final R values were Rr.i.m. = 0.098, Rwork = 0.183, Rfree = 0.233.
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Affiliation(s)
- Kubra F. Naqvi
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Dmitry Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Ernest Orlando Lawrence Berkeley National Laboratory, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA 98195, USA
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
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Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems. mBio 2015; 6:e01867-15. [PMID: 26646013 PMCID: PMC4676284 DOI: 10.1128/mbio.01867-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prokaryotes use type IV secretion systems (T4SSs) to translocate substrates (e.g., nucleoprotein, DNA, and protein) and/or elaborate surface structures (i.e., pili or adhesins). Bacterial genomes may encode multiple T4SSs, e.g., there are three functionally divergent T4SSs in some Bartonella species (vir, vbh, and trw). In a unique case, most rickettsial species encode a T4SS (rvh) enriched with gene duplication. Within single genomes, the evolutionary and functional implications of cross-system interchangeability of analogous T4SS protein components remains poorly understood. To lend insight into cross-system interchangeability, we analyzed the VirB8 family of T4SS channel proteins. Crystal structures of three VirB8 and two TrwG Bartonella proteins revealed highly conserved C-terminal periplasmic domain folds and dimerization interfaces, despite tremendous sequence divergence. This implies remarkable structural constraints for VirB8 components in the assembly of a functional T4SS. VirB8/TrwG heterodimers, determined via bacterial two-hybrid assays and molecular modeling, indicate that differential expression of trw and vir systems is the likely barrier to VirB8-TrwG interchangeability. We also determined the crystal structure of Rickettsia typhi RvhB8-II and modeled its coexpressed divergent paralog RvhB8-I. Remarkably, while RvhB8-I dimerizes and is structurally similar to other VirB8 proteins, the RvhB8-II dimer interface deviates substantially from other VirB8 structures, potentially preventing RvhB8-I/RvhB8-II heterodimerization. For the rvh T4SS, the evolution of divergent VirB8 paralogs implies a functional diversification that is unknown in other T4SSs. Collectively, our data identify two different constraints (spatiotemporal for Bartonellatrw and vir T4SSs and structural for rvh T4SSs) that mediate the functionality of multiple divergent T4SSs within a single bacterium. Assembly of multiprotein complexes at the right time and at the right cellular location is a fundamentally important task for any organism. In this respect, bacteria that express multiple analogous type IV secretion systems (T4SSs), each composed of around 12 different components, face an overwhelming complexity. Our work here presents the first structural investigation on factors regulating the maintenance of multiple T4SSs within a single bacterium. The structural data imply that the T4SS-expressing bacteria rely on two strategies to prevent cross-system interchangeability: (i) tight temporal regulation of expression or (ii) rapid diversification of the T4SS components. T4SSs are ideal drug targets provided that no analogous counterparts are known from eukaryotes. Drugs targeting the barriers to cross-system interchangeability (i.e., regulators) could dysregulate the structural and functional independence of discrete systems, potentially creating interference that prevents their efficient coordination throughout bacterial infection.
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59
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Serbzhinskiy DA, Clifton MC, Sankaran B, Staker BL, Edwards TE, Myler PJ. Structure of an ADP-ribosylation factor, ARF1, from Entamoeba histolytica bound to Mg(2+)-GDP. Acta Crystallogr F Struct Biol Commun 2015; 71:594-9. [PMID: 25945714 PMCID: PMC4427170 DOI: 10.1107/s2053230x15004677] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/06/2015] [Indexed: 01/21/2023] Open
Abstract
Entamoeba histolytica is the etiological agent of amebiasis, a diarrheal disease which causes amoebic liver abscesses and amoebic colitis. Approximately 50 million people are infected worldwide with E. histolytica. With only 10% of infected people developing symptomatic amebiasis, there are still an estimated 100,000 deaths each year. Because of the emergence of resistant strains of the parasite, it is necessary to find a treatment which would be a proper response to this challenge. ADP-ribosylation factor (ARF) is a member of the ARF family of GTP-binding proteins. These proteins are ubiquitous in eukaryotic cells; they generally associate with cell membranes and regulate vesicular traffic and intracellular signalling. The crystal structure of ARF1 from E. histolytica has been determined bound to magnesium and GDP at 1.8 Å resolution. Comparison with other structures of eukaryotic ARF proteins shows a highly conserved structure and supports the interswitch toggle mechanism of communicating the conformational state to partner proteins.
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Affiliation(s)
- Dmitry A. Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Beryllium West Coast Operations, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Beryllium West Coast Operations, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
- Departments of Global Health and Medical Education and Biomedical Informatics, University of Washington, Seattle, WA 98195, USA
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Abendroth J, Choi R, Wall A, Clifton MC, Lukacs CM, Staker BL, Van Voorhis W, Myler P, Lorimer DD, Edwards TE. Structures of aspartate aminotransferases from Trypanosoma brucei, Leishmania major and Giardia lamblia. Acta Crystallogr F Struct Biol Commun 2015; 71:566-71. [PMID: 25945710 PMCID: PMC4427166 DOI: 10.1107/s2053230x15001831] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/27/2015] [Indexed: 11/10/2022] Open
Abstract
The structures of three aspartate aminotransferases (AATs) from eukaryotic pathogens were solved within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). Both the open and closed conformations of AAT were observed. Pyridoxal phosphate was bound to the active site via a Schiff base to a conserved lysine. An active-site mutant showed that Trypanosoma brucei AAT still binds pyridoxal phosphate even in the absence of the tethering lysine. The structures highlight the challenges for the structure-based design of inhibitors targeting the active site, while showing options for inhibitor design targeting the N-terminal arm.
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Affiliation(s)
- Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195, USA
| | - Abigail Wall
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Christine M. Lukacs
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Seattle BioMed, 307 Westlake Avenure North, Seattle, WA 98109, USA
| | - Wesley Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195, USA
| | - Peter Myler
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Seattle BioMed, 307 Westlake Avenure North, Seattle, WA 98109, USA
| | - Don D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
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Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ. Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) 2014; 95:142-8. [PMID: 25613812 DOI: 10.1016/j.tube.2014.12.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/10/2014] [Indexed: 01/31/2023]
Abstract
High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.
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Affiliation(s)
- Loren Baugh
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Brianna Armour
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Brandy M Taylor
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Marvin M Muruthi
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - James W Fairman
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - David Fox
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Shellie H Dieterich
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Anna S Gardberg
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA 01821, United States
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Stephen N Hewitt
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Alberto J Napuli
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Janette Myers
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Lynn K Barrett
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Yang Zhang
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Micah Ferrell
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Elizabeth Mundt
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Katie Thompkins
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Ngoc Tran
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Sally Lyons-Abbott
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Ariel Abramov
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Aarthi Sekar
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Dmitri Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Don Lorimer
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, United States; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Lance J Stewart
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; Institute for Protein Design, University of Washington, Box 357350, Seattle, WA 98195, United States
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Microbiology, University of Washington, Box 357735, Seattle, WA 98195, United States
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Box 358047, Seattle, WA 98195, United States.
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Wang Y, Rauf S, Grewal Y, Spadafora LJ, Shiddiky MJA, Cangelosi GA, Schlücker S, Trau M. Duplex microfluidic SERS detection of pathogen antigens with nanoyeast single-chain variable fragments. Anal Chem 2014; 86:9930-8. [PMID: 25192256 PMCID: PMC4188274 DOI: 10.1021/ac5027012] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/05/2014] [Indexed: 11/30/2022]
Abstract
Quantitative and accurate detection of multiple biomarkers would allow for the rapid diagnosis and treatment of diseases induced by pathogens. Monoclonal antibodies are standard affinity reagents applied for biomarkers detection; however, their production is expensive and labor-intensive. Herein, we report on newly developed nanoyeast single-chain variable fragments (NYscFv) as an attractive alternative to monoclonal antibodies, which offers the unique advantage of a cost-effective production, stability in solution, and target-specificity. By combination of surface-enhanced Raman scattering (SERS) microspectroscopy using glass-coated, highly purified SERS nanoparticle clusters as labels, with a microfluidic device comprising multiple channels, a robust platform for the sensitive duplex detection of pathogen antigens has been developed. Highly sensitive detection for individual Entamoeba histolytica antigen EHI_115350 (limit of detection = 1 pg/mL, corresponding to 58.8 fM) and EHI_182030 (10 pg/mL, corresponding 453 fM) with high specificity has been achieved, employing the newly developed corresponding NYscFv as probe in combination with SERS microspectroscopy at a single laser excitation wavelength. Our first report on SERS-based immunoassays using the novel NYscFv affinity reagent demonstrates the flexibility of NYscFv fragments as viable alternatives to monoclonal antibodies in a range of bioassay platforms and paves the way for further applications.
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Affiliation(s)
- Yuling Wang
- Centre for Biomarker
Research and Development, Australian Institute
for Bioengineering and Nanotechnology (AIBN) and School of Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- Faculty
of Chemistry, University of Duisburg-Essen, Essen, D-45141, Germany
| | - Sakandar Rauf
- Centre for Biomarker
Research and Development, Australian Institute
for Bioengineering and Nanotechnology (AIBN) and School of Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yadveer
S. Grewal
- Centre for Biomarker
Research and Development, Australian Institute
for Bioengineering and Nanotechnology (AIBN) and School of Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lauren J. Spadafora
- School
for Public Health, University of Washington, Seattle, Washington 98195, United States
| | - Muhammad J. A. Shiddiky
- Centre for Biomarker
Research and Development, Australian Institute
for Bioengineering and Nanotechnology (AIBN) and School of Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gerard A. Cangelosi
- School
for Public Health, University of Washington, Seattle, Washington 98195, United States
| | | | - Matt Trau
- Centre for Biomarker
Research and Development, Australian Institute
for Bioengineering and Nanotechnology (AIBN) and School of Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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Grewal YS, Shiddiky MJ, Spadafora LJ, Cangelosi GA, Trau M. Nano-yeast–scFv probes on screen-printed gold electrodes for detection of Entamoeba histolytica antigens in a biological matrix. Biosens Bioelectron 2014; 55:417-22. [DOI: 10.1016/j.bios.2013.12.043] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/04/2013] [Accepted: 12/18/2013] [Indexed: 11/16/2022]
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Linford AS, Jiang NM, Edwards TE, Sherman NE, Van Voorhis WC, Stewart LJ, Myler PJ, Staker BL, Petri WA. Crystal structure and putative substrate identification for the Entamoeba histolytica low molecular weight tyrosine phosphatase. Mol Biochem Parasitol 2014; 193:33-44. [PMID: 24548880 DOI: 10.1016/j.molbiopara.2014.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 01/12/2014] [Accepted: 01/22/2014] [Indexed: 11/28/2022]
Abstract
Entamoeba histolytica is a eukaryotic intestinal parasite of humans, and is endemic in developing countries. We have characterized the E. histolytica putative low molecular weight protein tyrosine phosphatase (LMW-PTP). The structure for this amebic tyrosine phosphatase was solved, showing the ligand-induced conformational changes necessary for binding of substrate. In amebae, it was expressed at low but detectable levels as detected by immunoprecipitation followed by immunoblotting. A mutant LMW-PTP protein in which the catalytic cysteine in the active site was replaced with a serine lacked phosphatase activity, and was used to identify a number of trapped putative substrate proteins via mass spectrometry analysis. Seven of these putative substrate protein genes were cloned with an epitope tag and overexpressed in amebae. Five of these seven putative substrate proteins were demonstrated to interact specifically with the mutant LMW-PTP. This is the first biochemical study of a small tyrosine phosphatase in Entamoeba, and sets the stage for understanding its role in amebic biology and pathogenesis.
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Affiliation(s)
- Alicia S Linford
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA.
| | - Nona M Jiang
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - Nicholas E Sherman
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Lance J Stewart
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Seattle Biomedical Research Institute, Seattle, WA 98109, USA; Departments of Global Health and Medical Education & Biomedical Informatics, University of Washington, Seattle, WA 98195, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA; Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA.
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Raran-Kurussi S, Tözsér J, Cherry S, Tropea JE, Waugh DS. Differential temperature dependence of tobacco etch virus and rhinovirus 3C proteases. Anal Biochem 2013; 436:142-4. [PMID: 23395976 PMCID: PMC4196241 DOI: 10.1016/j.ab.2013.01.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 01/17/2013] [Accepted: 01/30/2013] [Indexed: 11/28/2022]
Abstract
Because of their stringent sequence specificity, the 3C-like proteases from tobacco etch virus (TEV) and human rhinovirus are often used for the removal of affinity tags. The latter enzyme is rumored to have greater catalytic activity at 4 °C, the temperature at which fusion protein substrates are usually digested. Here we report that experiments with fusion protein and peptide substrates confirm this conjecture. Whereas the catalytic efficiency of rhinovirus 3C protease is approximately the same at its optimum temperature (30 °C) and at 4 °C, TEV protease is 10-fold less active at the latter temperature due primarily to a reduction in k(cat).
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Affiliation(s)
- Sreejith Raran-Kurussi
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - József Tözsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Scott Cherry
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Joseph E. Tropea
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - David S. Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC. Combining functional and structural genomics to sample the essential Burkholderia structome. PLoS One 2013; 8:e53851. [PMID: 23382856 PMCID: PMC3561365 DOI: 10.1371/journal.pone.0053851] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 12/05/2012] [Indexed: 11/19/2022] Open
Abstract
Background The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. Methodology/Principal Findings We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an “ortholog rescue” strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. Conclusions/Significance This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.
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Affiliation(s)
- Loren Baugh
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Larry A. Gallagher
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Rapatbhorn Patrapuvich
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Anna S. Gardberg
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Brianna Armour
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Darren W. Begley
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | | | - David M. Dranow
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - James W. Fairman
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - David Fox
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Angela Gillespie
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Steve Nakazawa-Hewitt
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Mary Trang Nguyen
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Alberto Napuli
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Lynn Barrett
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, Washington
| | - Lance J. Stewart
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Colin Manoil
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Leibly DJ, Nguyen TN, Kao LT, Hewitt SN, Barrett LK, Van Voorhis WC. Stabilizing additives added during cell lysis aid in the solubilization of recombinant proteins. PLoS One 2012; 7:e52482. [PMID: 23285060 PMCID: PMC3527557 DOI: 10.1371/journal.pone.0052482] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 11/19/2012] [Indexed: 11/23/2022] Open
Abstract
Insoluble recombinant proteins are a major issue for both structural genomics and enzymology research. Greater than 30% of recombinant proteins expressed in Escherichia coli (E. coli) appear to be insoluble. The prevailing view is that insolubly expressed proteins cannot be easily solubilized, and are usually sequestered into inclusion bodies. However, we hypothesize that small molecules added during the cell lysis stage can yield soluble protein from insoluble protein previously screened without additives or ligands. We present a novel screening method that utilized 144 additive conditions to increase the solubility of recombinant proteins expressed in E. coli. These selected additives are natural ligands, detergents, salts, buffers, and chemicals that have been shown to increase the stability of proteins in vivo. We present the methods used for this additive solubility screen and detailed results for 41 potential drug target recombinant proteins from infectious organisms. Increased solubility was observed for 80% of the recombinant proteins during the primary and secondary screening of lysis with the additives; that is 33 of 41 target proteins had increased solubility compared with no additive controls. Eleven additives (trehalose, glycine betaine, mannitol, L-Arginine, potassium citrate, CuCl2, proline, xylitol, NDSB 201, CTAB and K2PO4) solubilized more than one of the 41 proteins; these additives can be easily screened to increase protein solubility. Large-scale purifications were attempted for 15 of the proteins using the additives identified and eight (40%) were prepared for crystallization trials during the first purification attempt. Thus, this protocol allowed us to recover about a third of seemingly insoluble proteins for crystallography and structure determination. If recombinant proteins are required in smaller quantities or less purity, the final success rate may be even higher.
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Affiliation(s)
- David J. Leibly
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
| | - Trang Nhu Nguyen
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
| | - Louis T. Kao
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
| | - Stephen N. Hewitt
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
| | - Lynn K. Barrett
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
| | - Wesley C. Van Voorhis
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
- * E-mail:
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68
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Edwards TE, Liao R, Phan I, Myler PJ, Grundner C. Mycobacterium thermoresistibile as a source of thermostable orthologs of Mycobacterium tuberculosis proteins. Protein Sci 2012; 21:1093-6. [PMID: 22544630 DOI: 10.1002/pro.2084] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 04/17/2012] [Accepted: 04/23/2012] [Indexed: 11/12/2022]
Abstract
The genus Mycobacterium comprises major human pathogens such as the causative agent of tuberculosis, Mycobacterium tuberculosis (Mtb), and many environmental species. Tuberculosis claims ~1.5 million lives every year, and drug resistant strains of Mtb are rapidly emerging. To aid the development of new tuberculosis drugs, major efforts are currently under way to determine crystal structures of Mtb drug targets and proteins involved in pathogenicity. However, a major obstacle to obtaining crystal structures is the generation of well-diffracting crystals. Proteins from thermophiles can have better crystallization and diffraction properties than proteins from mesophiles, but their sequences and structures are often divergent. Here, we establish a thermophilic mycobacterial model organism, Mycobacterium thermoresistibile (Mth), for the study of Mtb proteins. Mth tolerates higher temperatures than Mtb or other environmental mycobacteria such as M. smegmatis. Mth proteins are on average more soluble than Mtb proteins, and comparison of the crystal structures of two pairs of orthologous proteins reveals nearly identical folds, indicating that Mth structures provide good surrogates for Mtb structures. This study introduces a thermophile as a source of protein for the study of a closely related human pathogen and marks a new approach to solving challenging mycobacterial protein structures.
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Leibly DJ, Newling PA, Abendroth J, Guo W, Kelley A, Stewart LJ, Van Voorhis W. Structure of a cyclin-dependent kinase from Giardia lamblia. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1084-9. [PMID: 21904054 PMCID: PMC3169406 DOI: 10.1107/s1744309111018070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 05/12/2011] [Indexed: 11/10/2022]
Abstract
Giardia lamblia is the etiologic agent of giardiasis, a water-borne infection that is prevalent throughout the world. The need for new therapeutics for the treatment of giardiasis is of paramount importance. Owing to the ubiquitous nature of kinases and their vital importance in organisms, they are potential drug targets. In this paper, the first structure of a cyclin-dependent kinase (CDK) from G. lamblia (GlCDK; UniProt A8BZ95) is presented. CDKs are cell-cycle-associated kinases that are actively being pursued as targets for anticancer drugs as well as for antiparasitic chemotherapy. Generally, a CDK forms a complex with its associated cyclin. This CDK-cyclin complex is active and acts as a serine/threonine protein kinase. Typically, CDKs are responsible for the transition to the next phase of the cell cycle. Although the structure of GlCDK with its associated cyclin was not solved, the 1.85 Å resolution structure of apo GlCDK and a 2.0 Å resolution structure of GlCDK in complex with adenosine monophosphate are presented and the structural differences from the orthologous human CDK2 and CDK3 are discussed.
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Affiliation(s)
- David J. Leibly
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - Paul A. Newling
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Emerald BioStructures Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Wenjin Guo
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomed, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Angela Kelley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - Lance J. Stewart
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Emerald BioStructures Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Wesley Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
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70
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Nguyen TN, Abendroth J, Leibly DJ, Le KP, Guo W, Kelley A, Stewart L, Myler PJ, Van Voorhis WC. Structure of triosephosphate isomerase from Cryptosporidium parvum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1095-9. [PMID: 21904056 PMCID: PMC3169408 DOI: 10.1107/s1744309111019178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 05/19/2011] [Indexed: 11/10/2022]
Abstract
Cryptosporidium parvum is one of several Cryptosporidium spp. that cause the parasitic infection cryptosporidiosis. Cryptosporidiosis is a diarrheal infection that is spread via the fecal-oral route and is commonly caused by contaminated drinking water. Triosephosphate isomerase is an enzyme that is ubiquitous to all organisms that perform glycolysis. Triosephosphate isomerase catalyzes the formation of glyceraldehyde 3-phosphate from dihydroxyacetone phosphate, which is a critical step to ensure the maximum ATP production per glucose molecule. In this paper, the 1.55 Å resolution crystal structure of the open-loop form of triosephosphate isomerase from C. parvum Iowa II is presented. An unidentified electron density was found in the active site.
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Affiliation(s)
- Trang N. Nguyen
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Emerald BioStructures Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - David J. Leibly
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - Kristen P. Le
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - Wenjin Guo
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomed, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Angela Kelley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - Lance Stewart
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Emerald BioStructures Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomed, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
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71
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Leibly DJ, Abendroth J, Bryan CM, Sankaran B, Kelley A, Barrett LK, Stewart L, Van Voorhis WC. Structure of thymidylate kinase from Ehrlichia chaffeensis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1090-4. [PMID: 21904055 PMCID: PMC3169407 DOI: 10.1107/s174430911101493x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 04/20/2011] [Indexed: 12/04/2022]
Abstract
The enzyme thymidylate kinase phosphorylates the substrate thymidine 5'-phosphate (dTMP) to form thymidine 5'-diphosphate (dTDP), which is further phosphorylated to dTTP for incorporation into DNA. Ehrlichia chaffeensis is the etiologic agent of human monocytotropic erlichiosis (HME), a potentially life-threatening tick-borne infection. HME is endemic in the United States from the southern states up to the eastern seaboard. HME is transmitted to humans via the lone star tick Amblyomma americanum. Here, the 2.15 Å resolution crystal structure of thymidylate kinase from E. chaffeensis in the apo form is presented.
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Affiliation(s)
- David J. Leibly
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Emerald BioStructures Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Cassie M. Bryan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley Laboratory, 1 Cyclotron Road, BLDG 6R2100, Berkeley, CA 94720, USA
| | - Angela Kelley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195, USA
| | - Lynn K. Barrett
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195, USA
| | - Lance Stewart
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Emerald BioStructures Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195, USA
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Stacy R, Begley DW, Phan I, Staker BL, Van Voorhis WC, Varani G, Buchko GW, Stewart LJ, Myler PJ. Structural genomics of infectious disease drug targets: the SSGCID. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:979-84. [PMID: 21904037 PMCID: PMC3169389 DOI: 10.1107/s1744309111029204] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 07/19/2011] [Indexed: 11/29/2022]
Abstract
The Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium of researchers at Seattle BioMed, Emerald BioStructures, the University of Washington and Pacific Northwest National Laboratory that was established to apply structural genomics approaches to drug targets from infectious disease organisms. The SSGCID is currently funded over a five-year period by the National Institute of Allergy and Infectious Diseases (NIAID) to determine the three-dimensional structures of 400 proteins from a variety of Category A, B and C pathogens. Target selection engages the infectious disease research and drug-therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. The protein-expression systems, purified proteins, ligand screens and three-dimensional structures produced by SSGCID constitute a valuable resource for drug-discovery research, all of which is made freely available to the greater scientific community. This issue of Acta Crystallographica Section F, entirely devoted to the work of the SSGCID, covers the details of the high-throughput pipeline and presents a series of structures from a broad array of pathogenic organisms. Here, a background is provided on the structural genomics of infectious disease, the essential components of the SSGCID pipeline are discussed and a survey of progress to date is presented.
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Affiliation(s)
- Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109-5219, USA
| | - Darren W. Begley
- Seattle Structural Genomics Center for Infectious Disease, USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109-5219, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Box 357185, Seattle, WA 98195, USA
| | - Gabriele Varani
- Seattle Structural Genomics Center for Infectious Disease, USA
- Departments of Chemistry and Biochemistry, University of Washington, Box 351700, Seattle, WA 98185, USA
| | - Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Lance J. Stewart
- Seattle Structural Genomics Center for Infectious Disease, USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109-5219, USA
- Departments of Global Health and Medical Education and Biomedical Informatics, University of Washington, Box 357238, Seattle, WA 98195, USA
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Choi R, Kelley A, Leibly D, Nakazawa Hewitt S, Napuli A, Van Voorhis W. Immobilized metal-affinity chromatography protein-recovery screening is predictive of crystallographic structure success. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:998-1005. [PMID: 21904040 PMCID: PMC3169392 DOI: 10.1107/s1744309111017374] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 05/08/2011] [Indexed: 11/10/2022]
Abstract
The recombinant expression of soluble proteins in Escherichia coli continues to be a major bottleneck in structural genomics. The establishment of reliable protocols for the performance of small-scale expression and solubility testing is an essential component of structural genomic pipelines. The SSGCID Protein Production Group at the University of Washington (UW-PPG) has developed a high-throughput screening (HTS) protocol for the measurement of protein recovery from immobilized metal-affinity chromatography (IMAC) which predicts successful purification of hexahistidine-tagged proteins. The protocol is based on manual transfer of samples using multichannel pipettors and 96-well plates and does not depend on the use of robotic platforms. This protocol has been applied to evaluate the expression and solubility of more than 4000 proteins expressed in E. coli. The UW-PPG also screens large-scale preparations for recovery from IMAC prior to purification. Analysis of these results show that our low-cost non-automated approach is a reliable method for the HTS demands typical of large structural genomic projects. This paper provides a detailed description of these protocols and statistical analysis of the SSGCID screening results. The results demonstrate that screening for proteins that yield high recovery after IMAC, both after small-scale and large-scale expression, improves the selection of proteins that can be successfully purified and will yield a crystal structure.
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Affiliation(s)
- Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - Angela Kelley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - David Leibly
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - Stephen Nakazawa Hewitt
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - Alberto Napuli
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
| | - Wesley Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195-6423, USA
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Buchko GW, Hewitt SN, Napuli AJ, Van Voorhis WC, Myler PJ. Solution structure of an arsenate reductase-related protein, YffB, from Brucella melitensis, the etiological agent responsible for brucellosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1129-36. [PMID: 21904062 PMCID: PMC3169414 DOI: 10.1107/s1744309111006336] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 02/19/2011] [Indexed: 11/28/2022]
Abstract
Brucella melitensis is the etiological agent responsible for brucellosis. Present in the B. melitensis genome is a 116-residue protein related to arsenate reductases (Bm-YffB; BR0369). Arsenate reductases (ArsC) convert arsenate ion (H(2)AsO(4)(-)), a compound that is toxic to bacteria, to arsenite ion (AsO(2)(-)), a product that may be efficiently exported out of the cell. Consequently, Bm-YffB is a potential drug target because if arsenate reduction is the protein's major biological function then disabling the cell's ability to reduce arsenate would make these cells more sensitive to the deleterious effects of arsenate. Size-exclusion chromatography and NMR spectroscopy indicate that Bm-YffB is a monomer in solution. The solution structure of Bm-YffB (PDB entry 2kok) shows that the protein consists of two domains: a four-stranded mixed β-sheet flanked by two α-helices on one side and an α-helical bundle. The α/β domain is characteristic of the fold of thioredoxin-like proteins and the overall structure is generally similar to those of known arsenate reductases despite the marginal sequence similarity. Chemical shift perturbation studies with (15)N-labeled Bm-YffB show that the protein binds reduced glutathione at a site adjacent to a region similar to the HX(3)CX(3)R catalytic sequence motif that is important for arsenic detoxification activity in the classical arsenate-reductase family of proteins. The latter observation supports the hypothesis that the ArsC-YffB family of proteins may function as glutathione-dependent thiol reductases. However, comparison of the structure of Bm-YffB with the structures of proteins from the classical ArsC family suggest that the mechanism and possibly the function of Bm-YffB and other related proteins (ArsC-YffB) may differ from those of the ArsC family of proteins.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA.
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