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Ran X, Parikh P, Abendroth J, Arakaki TL, Clifton MC, Edwards TE, Lorimer DD, Mayclin S, Staker BL, Myler P, McLaughlin KJ. Structural and functional characterization of FabG4 from Mycolicibacterium smegmatis. Acta Crystallogr F Struct Biol Commun 2024; 80:82-91. [PMID: 38656226 PMCID: PMC11058512 DOI: 10.1107/s2053230x2400356x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024] Open
Abstract
The rise in antimicrobial resistance is a global health crisis and necessitates the development of novel strategies to treat infections. For example, in 2022 tuberculosis (TB) was the second leading infectious killer after COVID-19, with multi-drug-resistant strains of TB having an ∼40% fatality rate. Targeting essential biosynthetic pathways in pathogens has proven to be successful for the development of novel antimicrobial treatments. Fatty-acid synthesis (FAS) in bacteria proceeds via the type II pathway, which is substantially different from the type I pathway utilized in animals. This makes bacterial fatty-acid biosynthesis (Fab) enzymes appealing as drug targets. FabG is an essential FASII enzyme, and some bacteria, such as Mycobacterium tuberculosis, the causative agent of TB, harbor multiple homologs. FabG4 is a conserved, high-molecular-weight FabG (HMwFabG) that was first identified in M. tuberculosis and is distinct from the canonical low-molecular-weight FabG. Here, structural and functional analyses of Mycolicibacterium smegmatis FabG4, the third HMwFabG studied to date, are reported. Crystal structures of NAD+ and apo MsFabG4, along with kinetic analyses, show that MsFabG4 preferentially binds and uses NADH when reducing CoA substrates. As M. smegmatis is often used as a model organism for M. tuberculosis, these studies may aid the development of drugs to treat TB and add to the growing body of research that distinguish HMwFabGs from the archetypal low-molecular-weight FabG.
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Affiliation(s)
- Xinping Ran
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Prashit Parikh
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | | | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- UCB Pharma, Bedford, Massachusetts, USA
| | | | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Peter Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Krystle J. McLaughlin
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
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2
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Pierce PG, Hartnett BE, Laughlin TM, Blain JM, Mayclin SJ, Bolejack MJ, Myers JB, Higgins TW, Dranow DM, Sullivan A, Lorimer DD, Edwards TE, Hagen TJ, Horn JR, Myler PJ. Crystal structure and biophysical characterization of IspD from Burkholderia thailandensis and Mycobacterium paratuberculosis. Acta Crystallogr F Struct Biol Commun 2024; 80:43-51. [PMID: 38305785 PMCID: PMC10836425 DOI: 10.1107/s2053230x24000621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
The methylerythritol phosphate (MEP) pathway is a metabolic pathway that produces the isoprenoids isopentyl pyrophosphate and dimethylallyl pyrophosphate. Notably, the MEP pathway is present in bacteria and not in mammals, which makes the enzymes of the MEP pathway attractive targets for discovering new anti-infective agents due to the reduced chances of off-target interactions leading to side effects. There are seven enzymes in the MEP pathway, the third of which is IspD. Two crystal structures of Burkholderia thailandensis IspD (BtIspD) were determined: an apo structure and that of a complex with cytidine triphosphate (CTP). Comparison of the CTP-bound BtIspD structure with the apo structure revealed that CTP binding stabilizes the loop composed of residues 13-19. The apo structure of Mycobacterium paratuberculosis IspD (MpIspD) is also reported. The melting temperatures of MpIspD and BtIspD were evaluated by circular dichroism. The moderate Tm values suggest that a thermal shift assay may be feasible for future inhibitor screening. Finally, the binding affinity of CTP for BtIspD was evaluated by isothermal titration calorimetry. These structural and biophysical data will aid in the discovery of IspD inhibitors.
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Affiliation(s)
- Phillip G Pierce
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
| | - Brian E Hartnett
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 Lincoln Highway, DeKalb, IL 60115, USA
| | - Tosha M Laughlin
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 Lincoln Highway, DeKalb, IL 60115, USA
| | - Joy M Blain
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 Lincoln Highway, DeKalb, IL 60115, USA
| | | | | | - Janette B Myers
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
| | - Tate W Higgins
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
| | - David M Dranow
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Amy Sullivan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
| | - Donald D Lorimer
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E Edwards
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Timothy J Hagen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 Lincoln Highway, DeKalb, IL 60115, USA
| | - James R Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 Lincoln Highway, DeKalb, IL 60115, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
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3
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Moorefield J, Konuk Y, Norman JO, Abendroth J, Edwards TE, Lorimer DD, Mayclin SJ, Staker BL, Craig JK, Barett KF, Barrett LK, Van Voorhis WC, Myler PJ, McLaughlin KJ. Characterization of a family I inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1. Acta Crystallogr F Struct Biol Commun 2023; 79:257-266. [PMID: 37728609 PMCID: PMC10565794 DOI: 10.1107/s2053230x23008002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/13/2023] [Indexed: 09/21/2023] Open
Abstract
Inorganic pyrophosphate (PPi) is generated as an intermediate or byproduct of many fundamental metabolic pathways, including DNA/RNA synthesis. The intracellular concentration of PPi must be regulated as buildup can inhibit many critical cellular processes. Inorganic pyrophosphatases (PPases) hydrolyze PPi into two orthophosphates (Pi), preventing the toxic accumulation of the PPi byproduct in cells and making Pi available for use in biosynthetic pathways. Here, the crystal structure of a family I inorganic pyrophosphatase from Legionella pneumophila is reported at 2.0 Å resolution. L. pneumophila PPase (LpPPase) adopts a homohexameric assembly and shares the oligonucleotide/oligosaccharide-binding (OB) β-barrel core fold common to many other bacterial family I PPases. LpPPase demonstrated hydrolytic activity against a general substrate, with Mg2+ being the preferred metal cofactor for catalysis. Legionnaires' disease is a severe respiratory infection caused primarily by L. pneumophila, and thus increased characterization of the L. pneumophila proteome is of interest.
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Affiliation(s)
- Julia Moorefield
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Yagmur Konuk
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Jordan O. Norman
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Stephen J. Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Justin K. Craig
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Kayleigh F. Barett
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lynn K. Barrett
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Krystle J. McLaughlin
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
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4
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Ghafoori SM, Petersen GF, Conrady DG, Calhoun BM, Stigliano MZZ, Baydo RO, Grice R, Abendroth J, Lorimer DD, Edwards TE, Forwood JK. Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site. Sci Rep 2023; 13:6940. [PMID: 37117205 PMCID: PMC10140725 DOI: 10.1038/s41598-023-33529-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/14/2023] [Indexed: 04/30/2023] Open
Abstract
Influenza virus (IV) causes several outbreaks of the flu each year resulting in an economic burden to the healthcare system in the billions of dollars. Several influenza pandemics have occurred during the last century and estimated to have caused 100 million deaths. There are four genera of IV, A (IVA), B (IVB), C (IVC), and D (IVD), with IVA being the most virulent to the human population. Hemagglutinin (HA) is an IVA surface protein that allows the virus to attach to host cell receptors and enter the cell. Here we have characterised the high-resolution structures of seven IVA HAs, with one in complex with the anti-influenza head-binding antibody C05. Our analysis revealed conserved receptor binding residues in all structures, as seen in previously characterised IV HAs. Amino acid conservation is more prevalent on the stalk than the receptor binding domain (RBD; also called the head domain), allowing the virus to escape from antibodies targeting the RBD. The equivalent site of C05 antibody binding to A/Denver/57 HA appears hypervariable in the other H1N1 IV HAs. Modifications within this region appear to disrupt binding of the C05 antibody, as these HAs no longer bind the C05 antibody by analytical SEC. Our study brings new insights into the structural and functional recognition of IV HA proteins and can contribute to further development of anti-influenza vaccines.
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Affiliation(s)
- Seyed Mohammad Ghafoori
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Gayle F Petersen
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Deborah G Conrady
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Brandy M Calhoun
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Matthew Z Z Stigliano
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Ruth O Baydo
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Rena Grice
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Donald D Lorimer
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Thomas E Edwards
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia.
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5
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Lowe MA, Cardenas A, Valentin JP, Zhu Z, Abendroth J, Castro JL, Class R, Delaunois A, Fleurance R, Gerets H, Gryshkova V, King L, Lorimer DD, MacCoss M, Rowley JH, Rosseels ML, Royer L, Taylor RD, Wong M, Zaccheo O, Chavan VP, Ghule GA, Tapkir BK, Burrows JN, Duffey M, Rottmann M, Wittlin S, Angulo-Barturen I, Jiménez-Díaz MB, Striepen J, Fairhurst KJ, Yeo T, Fidock DA, Cowman AF, Favuzza P, Crespo-Fernandez B, Gamo FJ, Goldberg DE, Soldati-Favre D, Laleu B, de Haro T. Discovery and Characterization of Potent, Efficacious, Orally Available Antimalarial Plasmepsin X Inhibitors and Preclinical Safety Assessment of UCB7362. J Med Chem 2022; 65:14121-14143. [PMID: 36216349 DOI: 10.1021/acs.jmedchem.2c01336] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Plasmepsin X (PMX) is an essential aspartyl protease controlling malaria parasite egress and invasion of erythrocytes, development of functional liver merozoites (prophylactic activity), and blocking transmission to mosquitoes, making it a potential multistage drug target. We report the optimization of an aspartyl protease binding scaffold and the discovery of potent, orally active PMX inhibitors with in vivo antimalarial efficacy. Incorporation of safety evaluation early in the characterization of PMX inhibitors precluded compounds with a long human half-life (t1/2) to be developed. Optimization focused on improving the off-target safety profile led to the identification of UCB7362 that had an improved in vitro and in vivo safety profile but a shorter predicted human t1/2. UCB7362 is estimated to achieve 9 log 10 unit reduction in asexual blood-stage parasites with once-daily dosing of 50 mg for 7 days. This work demonstrates the potential to deliver PMX inhibitors with in vivo efficacy to treat malaria.
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Affiliation(s)
| | | | | | - Zhaoning Zhu
- UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom
| | - Jan Abendroth
- UCB, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | | | - Reiner Class
- UCB, Chem. du Foriest 1, 1420 Braine-l'Alleud, Belgium
| | | | | | - Helga Gerets
- UCB, Chem. du Foriest 1, 1420 Braine-l'Alleud, Belgium
| | | | - Lloyd King
- UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom
| | - Donald D Lorimer
- UCB, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Malcolm MacCoss
- Bohicket Pharma Consulting LLC, 2556 Seabrook Island Road, Seabrook Island, South Carolina 29455, United States
| | | | | | - Leandro Royer
- UCB, Chem. du Foriest 1, 1420 Braine-l'Alleud, Belgium
| | | | - Melanie Wong
- UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom
| | | | - Vishal P Chavan
- Sai Life Sciences Limited, Plot DS-7, IKP Knowledge Park, Genome Valley, Turkapally, Hyderabad 500078, Telangana, India
| | - Gokul A Ghule
- Sai Life Sciences Limited, Plot DS-7, IKP Knowledge Park, Genome Valley, Turkapally, Hyderabad 500078, Telangana, India
| | - Bapusaheb K Tapkir
- Sai Life Sciences Limited, Plot DS-7, IKP Knowledge Park, Genome Valley, Turkapally, Hyderabad 500078, Telangana, India
| | - Jeremy N Burrows
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Maëlle Duffey
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Matthias Rottmann
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | - Iñigo Angulo-Barturen
- The Art of Discovery, SL Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Building, no. 612, Derio 48160, Bizkaia, Basque Country, Spain
| | - María Belén Jiménez-Díaz
- The Art of Discovery, SL Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Building, no. 612, Derio 48160, Bizkaia, Basque Country, Spain
| | - Josefine Striepen
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Kate J Fairhurst
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Tomas Yeo
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States.,Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Alan F Cowman
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Paola Favuzza
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | | | | | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8051, St. Louis, Missouri 63110, United States
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU, 1 rue Michel-Servet, CH-1211 Genève 4, Switzerland
| | - Benoît Laleu
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
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6
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Kesari P, Deshmukh A, Pahelkar N, Suryawanshi AB, Rathore I, Mishra V, Dupuis JH, Xiao H, Gustchina A, Abendroth J, Labaied M, Yada RY, Wlodawer A, Edwards TE, Lorimer DD, Bhaumik P. Structures of plasmepsin X from Plasmodium falciparum reveal a novel inactivation mechanism of the zymogen and molecular basis for binding of inhibitors in mature enzyme. Protein Sci 2022; 31:882-899. [PMID: 35048450 PMCID: PMC8927862 DOI: 10.1002/pro.4279] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/05/2022] [Accepted: 01/14/2022] [Indexed: 11/06/2022]
Abstract
Plasmodium falciparum plasmepsin X (PfPMX), involved in the invasion and egress of this deadliest malarial parasite, is essential for its survival and hence considered as an important drug target. We report the first crystal structure of PfPMX zymogen containing a novel fold of its prosegment. A unique twisted loop from the prosegment and arginine 244 from the mature enzyme is involved in zymogen inactivation; such mechanism, not previously reported, might be common for apicomplexan proteases similar to PfPMX. The maturation of PfPMX zymogen occurs through cleavage of its prosegment at multiple sites. Our data provide thorough insights into the mode of binding of a substrate and a potent inhibitor 49c to PfPMX. We present molecular details of inactivation, maturation, and inhibition of PfPMX that should aid in the development of potent inhibitors against pepsin-like aspartic proteases from apicomplexan parasites.
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Affiliation(s)
- Pooja Kesari
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Anuradha Deshmukh
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Nikhil Pahelkar
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Abhishek B. Suryawanshi
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Ishan Rathore
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Vandana Mishra
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - John H. Dupuis
- Food, Nutrition, and Health Program, Faculty of Land and Food SystemsUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Huogen Xiao
- Summerland Research and Development CenterAgriculture and Agri‐Food CanadaSummerlandBritish ColumbiaCanada
| | - Alla Gustchina
- Protein Structure Section, Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
| | - Jan Abendroth
- UCB PharmaBainbridge IslandWashingtonUSA
- Seattle Structural Genomics Center for Infectious DiseaseSeattleWashingtonUSA
| | - Mehdi Labaied
- UCB PharmaBainbridge IslandWashingtonUSA
- Seattle Structural Genomics Center for Infectious DiseaseSeattleWashingtonUSA
| | - Rickey Y. Yada
- Food, Nutrition, and Health Program, Faculty of Land and Food SystemsUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Alexander Wlodawer
- Protein Structure Section, Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
| | - Thomas E. Edwards
- UCB PharmaBainbridge IslandWashingtonUSA
- Seattle Structural Genomics Center for Infectious DiseaseSeattleWashingtonUSA
| | - Donald D. Lorimer
- UCB PharmaBainbridge IslandWashingtonUSA
- Seattle Structural Genomics Center for Infectious DiseaseSeattleWashingtonUSA
| | - Prasenjit Bhaumik
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
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7
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Iwasaki J, Lorimer DD, Vivoli-Vega M, Kibble EA, Peacock CS, Abendroth J, Mayclin SJ, Dranow DM, Pierce PG, Fox D, Lewis M, Bzdyl NM, Kristensen SS, Inglis TJJ, Kahler CM, Bond CS, Hasenkopf A, Seufert F, Schmitz J, Marshall LE, Scott AE, Norville IH, Myler PJ, Holzgrabe U, Harmer NJ, Sarkar-Tyson M. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1625-1634. [PMID: 35245364 PMCID: PMC9155639 DOI: 10.1093/jac/dkac065] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/23/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jua Iwasaki
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, Western Australia, 6008, Australia
- Centre for Child Health Research, University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Mirella Vivoli-Vega
- Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
- Living Systems Institute, Stocker Road, Exeter, EX4 4QD, UK
| | - Emily A. Kibble
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
- DMTC Limited, Level 2, 24 Wakefield St, Hawthorn, VIC 3122, Australia
| | - Christopher S. Peacock
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Stephen J. Mayclin
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - David M. Dranow
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Phillip G. Pierce
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - David Fox
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Maria Lewis
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Nicole M. Bzdyl
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Sofie S. Kristensen
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Timothy J. J. Inglis
- Department of Microbiology, PathWest Laboratory Medicine, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Nedlands, WA 6009, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Charles S. Bond
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Anja Hasenkopf
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Florian Seufert
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jens Schmitz
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Laura E. Marshall
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
| | - Andrew E. Scott
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
| | | | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Nicholas J. Harmer
- Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
- Living Systems Institute, Stocker Road, Exeter, EX4 4QD, UK
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
- Corresponding author. E-mail:
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8
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Ghafoori SM, Robles AM, Arada AM, Shirmast P, Dranow DM, Mayclin SJ, Lorimer DD, Myler PJ, Edwards TE, Kuhn ML, Forwood JK. Structural characterization of a Type B chloramphenicol acetyltransferase from the emerging pathogen Elizabethkingia anophelis NUHP1. Sci Rep 2021; 11:9453. [PMID: 33947893 PMCID: PMC8096840 DOI: 10.1038/s41598-021-88672-z] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/24/2021] [Indexed: 02/02/2023] Open
Abstract
Elizabethkingia anophelis is an emerging multidrug resistant pathogen that has caused several global outbreaks. E. anophelis belongs to the large family of Flavobacteriaceae, which contains many bacteria that are plant, bird, fish, and human pathogens. Several antibiotic resistance genes are found within the E. anophelis genome, including a chloramphenicol acetyltransferase (CAT). CATs play important roles in antibiotic resistance and can be transferred in genetic mobile elements. They catalyse the acetylation of the antibiotic chloramphenicol, thereby reducing its effectiveness as a viable drug for therapy. Here, we determined the high-resolution crystal structure of a CAT protein from the E. anophelis NUHP1 strain that caused a Singaporean outbreak. Its structure does not resemble that of the classical Type A CATs but rather exhibits significant similarity to other previously characterized Type B (CatB) proteins from Pseudomonas aeruginosa, Vibrio cholerae and Vibrio vulnificus, which adopt a hexapeptide repeat fold. Moreover, the CAT protein from E. anophelis displayed high sequence similarity to other clinically validated chloramphenicol resistance genes, indicating it may also play a role in resistance to this antibiotic. Our work expands the very limited structural and functional coverage of proteins from Flavobacteriaceae pathogens which are becoming increasingly more problematic.
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Affiliation(s)
| | - Alyssa M Robles
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Angelika M Arada
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Paniz Shirmast
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia.
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9
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Rodarte JV, Abendroth J, Edwards TE, Lorimer DD, Staker BL, Zhang S, Myler PJ, McLaughlin KJ. Crystal structure of acetoacetyl-CoA reductase from Rickettsia felis. Acta Crystallogr F Struct Biol Commun 2021; 77:54-60. [PMID: 33620038 PMCID: PMC7900926 DOI: 10.1107/s2053230x21001497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/08/2021] [Indexed: 11/10/2022] Open
Abstract
Rickettsia felis, a Gram-negative bacterium that causes spotted fever, is of increasing interest as an emerging human pathogen. R. felis and several other Rickettsia strains are classed as National Institute of Allergy and Infectious Diseases priority pathogens. In recent years, R. felis has been shown to be adaptable to a wide range of hosts, and many fevers of unknown origin are now being attributed to this infectious agent. Here, the structure of acetoacetyl-CoA reductase from R. felis is reported at a resolution of 2.0 Å. While R. felis acetoacetyl-CoA reductase shares less than 50% sequence identity with its closest homologs, it adopts a fold common to other short-chain dehydrogenase/reductase (SDR) family members, such as the fatty-acid synthesis II enzyme FabG from the prominent pathogens Staphylococcus aureus and Bacillus anthracis. Continued characterization of the Rickettsia proteome may prove to be an effective means of finding new avenues of treatment through comparative structural studies.
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Affiliation(s)
- Justas V. Rodarte
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, New York, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences Inc., 7869 Day Road West, Bainbridge Island, Washington, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences Inc., 7869 Day Road West, Bainbridge Island, Washington, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences Inc., 7869 Day Road West, Bainbridge Island, Washington, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Sunny Zhang
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Krystle J. McLaughlin
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, New York, USA
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10
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Plewe MB, Sokolova NV, Gantla VR, Brown ER, Naik S, Fetsko A, Lorimer DD, Dranow DM, Smutney H, Bullen J, Sidhu R, Master A, Wang J, Kallel EA, Zhang L, Kalveram B, Freiberg AN, Henkel G, McCormack K. Discovery of Adamantane Carboxamides as Ebola Virus Cell Entry and Glycoprotein Inhibitors. ACS Med Chem Lett 2020; 11:1160-1167. [PMID: 32550996 DOI: 10.1021/acsmedchemlett.0c00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/21/2020] [Indexed: 12/24/2022] Open
Abstract
We identified and explored the structure-activity-relationship (SAR) of an adamantane carboxamide chemical series of Ebola virus (EBOV) inhibitors. Selected analogs exhibited half-maximal inhibitory concentrations (EC50 values) of ∼10-15 nM in vesicular stomatitis virus (VSV) pseudotyped EBOV (pEBOV) infectivity assays, low hundred nanomolar EC50 activity against wild type EBOV, aqueous solubility >20 mg/mL, and attractive metabolic stability in human and nonhuman liver microsomes. X-ray cocrystallographic characterizations of a lead compound with the EBOV glycoprotein (GP) established the EBOV GP as a target for direct compound inhibitory activity and further provided relevant structural models that may assist in identifying optimized therapeutic candidates.
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Affiliation(s)
- Michael B. Plewe
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Nadezda V. Sokolova
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Vidyasagar Reddy Gantla
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Eric R. Brown
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Shibani Naik
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Alexandra Fetsko
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - David M. Dranow
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Hayden Smutney
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 3 Preston Court, Bedford, Massachusetts 01730, United States
| | - Jameson Bullen
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Rana Sidhu
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 3 Preston Court, Bedford, Massachusetts 01730, United States
| | - Arshil Master
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 3 Preston Court, Bedford, Massachusetts 01730, United States
| | - Junru Wang
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 3 Preston Court, Bedford, Massachusetts 01730, United States
| | - E. Adam Kallel
- Victrix, 12631 Bendito Drive, San Diego, California 92128, United States
| | | | | | | | - Greg Henkel
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Ken McCormack
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
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11
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Barrett KF, Dranow DM, Phan IQ, Michaels SA, Shaheen S, Navaluna ED, Craig JK, Tillery LM, Choi R, Edwards TE, Conrady DG, Abendroth J, Horanyi PS, Lorimer DD, Van Voorhis WC, Zhang Z, Barrett LK, Subramanian S, Staker B, Fan E, Myler PJ, Soge OO, Hybiske K, Ojo KK. Structures of glyceraldehyde 3-phosphate dehydrogenase in Neisseria gonorrhoeae and Chlamydia trachomatis. Protein Sci 2020; 29:768-778. [PMID: 31930578 DOI: 10.1002/pro.3824] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 11/02/2019] [Revised: 01/05/2020] [Accepted: 01/08/2020] [Indexed: 12/12/2022]
Abstract
Neisseria gonorrhoeae (Ng) and Chlamydia trachomatis (Ct) are the most commonly reported sexually transmitted bacteria worldwide and usually present as co-infections. Increasing resistance of Ng to currently recommended dual therapy of azithromycin and ceftriaxone presents therapeutic challenges for syndromic management of Ng-Ct co-infections. Development of a safe, effective, and inexpensive dual therapy for Ng-Ct co-infections is an effective strategy for the global control and prevention of these two most prevalent bacterial sexually transmitted infections. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a validated drug target with two approved drugs for indications other than antibacterials. Nonetheless, any new drugs targeting GAPDH in Ng and Ct must be specific inhibitors of bacterial GAPDH that do not inhibit human GAPDH, and structural information of Ng and Ct GAPDH will aid in finding such selective inhibitors. Here, we report the X-ray crystal structures of Ng and Ct GAPDH. Analysis of the structures demonstrates significant differences in amino acid residues in the active sites of human GAPDH from those of the two bacterial enzymes suggesting design of compounds to selectively inhibit Ng and Ct is possible. We also describe an efficient in vitro assay of recombinant GAPDH enzyme activity amenable to high-throughput drug screening to aid in identifying inhibitory compounds and begin to address selectivity.
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Affiliation(s)
- Kayleigh F Barrett
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Samantha A Michaels
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Shareef Shaheen
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Edelmar D Navaluna
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Justin K Craig
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Logan M Tillery
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Ryan Choi
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Deborah G Conrady
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bedford, Massachusetts
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Peter S Horanyi
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bedford, Massachusetts
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Wesley C Van Voorhis
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Lynn K Barrett
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Bart Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington.,Department of Biomedical Informatics & Medical Education
| | - Olusegun O Soge
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Kevin Hybiske
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Kayode K Ojo
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
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12
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Tillery LM, Barrett KF, Dranow DM, Craig J, Shek R, Chun I, Barrett LK, Phan IQ, Subramanian S, Abendroth J, Lorimer DD, Edwards TE, Van Voorhis WC. Toward a structome of Acinetobacter baumannii drug targets. Protein Sci 2020; 29:789-802. [PMID: 31930600 DOI: 10.1002/pro.3826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Acinetobacter baumannii is well known for causing hospital-associated infections due in part to its intrinsic antibiotic resistance as well as its ability to remain viable on surfaces and resist cleaning agents. In a previous publication, A. baumannii strain AB5075 was studied by transposon mutagenesis and 438 essential gene candidates for growth on rich-medium were identified. The Seattle Structural Genomics Center for Infectious Disease entered 342 of these candidate essential genes into our pipeline for structure determination, in which 306 were successfully cloned into expression vectors, 192 were detectably expressed, 165 screened as soluble, 121 were purified, 52 crystalized, 30 provided diffraction data, and 29 structures were deposited in the Protein Data Bank. Here, we report these structures, compare them with human orthologs where applicable, and discuss their potential as drug targets for antibiotic development against A. baumannii.
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Affiliation(s)
- Logan M Tillery
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Kayleigh F Barrett
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Justin Craig
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Roger Shek
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Ian Chun
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Lynn K Barrett
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Wesley C Van Voorhis
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
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13
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Sullivan AH, Dranow DM, Horanyi PS, Lorimer DD, Edwards TE, Abendroth J. Crystal structures of thiamine monophosphate kinase from Acinetobacter baumannii in complex with substrates and products. Sci Rep 2019; 9:4392. [PMID: 30867460 PMCID: PMC6416309 DOI: 10.1038/s41598-019-40558-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/19/2019] [Indexed: 11/08/2022] Open
Abstract
Thiamine monophosphate kinase (ThiL) catalyzes the last step of thiamine pyrophosphate (TPP) synthesis, the ATP-dependent phosphorylation of thiamine monophosphate (TMP) to thiamine pyrophosphate. We solved the structure of ThiL from the human pathogen A. baumanii in complex with a pair of substrates TMP and a non-hydrolyzable adenosine triphosphate analog, and in complex with a pair of products TPP and adenosine diphosphate. High resolution of the data and anomalous diffraction allows for a detailed description of the binding mode of substrates and products, and their metal environment. The structures further support a previously proposed in-line attack reaction mechanism and show a distinct variability of metal content of the active site.
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Affiliation(s)
- Amy H Sullivan
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
| | - David M Dranow
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
| | - Peter S Horanyi
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
| | - Donald D Lorimer
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
| | - Thomas E Edwards
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
| | - Jan Abendroth
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA.
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA.
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14
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Abendroth J, Sankaran B, Myler PJ, Lorimer DD, Edwards TE. Ab initio structure solution of a proteolytic fragment using ARCIMBOLDO. Acta Crystallogr F Struct Biol Commun 2018; 74:530-535. [PMID: 30198884 PMCID: PMC6130419 DOI: 10.1107/s2053230x18010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/12/2018] [Indexed: 11/10/2022] Open
Abstract
Crystal structure determination requires solving the phase problem. This can be accomplished using ab initio direct methods for small molecules and macromolecules at resolutions higher than 1.2 Å, whereas macromolecular structure determination at lower resolution requires either molecular replacement using a homologous structure or experimental phases using a derivative such as covalent labeling (for example selenomethionine or mercury derivatization) or heavy-atom soaking (for example iodide ions). Here, a case is presented in which crystals were obtained from a 30.8 kDa protein sample and yielded a 1.6 Å resolution data set with a unit cell that could accommodate approximately 8 kDa of protein. Thus, it was unclear what had been crystallized. Molecular replacement with pieces of homologous proteins and attempts at iodide ion soaking failed to yield a solution. The crystals could not be reproduced. Sequence-independent molecular replacement using the structures available in the Protein Data Bank also failed to yield a solution. Ultimately, ab initio structure solution proved successful using the program ARCIMBOLDO, which identified two α-helical elements and yielded interpretable maps. The structure was the C-terminal dimerization domain of the intended target from Mycobacterium smegmatis. This structure is presented as a user-friendly test case in which an unknown protein fragment could be determined using ARCIMBOLDO.
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Affiliation(s)
- Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
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15
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Asojo OA, Subramanian S, Abendroth J, Exley I, Lorimer DD, Edwards TE, Myler PJ. Crystal structure of chorismate mutase from Burkholderia phymatum. Acta Crystallogr F Struct Biol Commun 2018; 74:187-192. [PMID: 29633965 PMCID: PMC5894103 DOI: 10.1107/s2053230x18002868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/18/2018] [Indexed: 11/10/2022] Open
Abstract
The bacterium Burkholderia phymatum is a promiscuous symbiotic nitrogen-fixating bacterium that belongs to one of the largest groups of Betaproteobacteria. Other Burkholderia species are known to cause disease in plants and animals, and some are potential agents for biological warfare. Structural genomics efforts include characterizing the structures of enzymes from pathways that can be targeted for drug development. As part of these efforts, chorismate mutase from B. phymatum was produced and crystallized, and a 1.95 Å resolution structure is reported. This enzyme shares less than 33% sequence identity with other homologs of known structure. There are two classes of chorismate mutase: AroQ and AroH. The bacterial subclass AroQγ has reported roles in virulence. Chorismate mutase from B. phymatum has the prototypical AroQγ topology and retains the characteristic chorismate mutase active site. This suggests that substrate-based chorismate mutase inhibitors will not be specific and are likely to affect beneficial bacteria such as B. phymatum.
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Affiliation(s)
- Oluwatoyin A. Asojo
- National School of Tropical Medicine, Baylor College of Medicine, 1102 Bates Avenue Suite 550, Mail Stop BCM320, Houston, TX 77030-3411, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Ilyssa Exley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
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16
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Varela-Ramirez A, Abendroth J, Mejia AA, Phan IQ, Lorimer DD, Edwards TE, Aguilera RJ. Structure of acid deoxyribonuclease. Nucleic Acids Res 2017; 45:6217-6227. [PMID: 28369538 PMCID: PMC5449587 DOI: 10.1093/nar/gkx222] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/23/2017] [Indexed: 01/06/2023] Open
Abstract
Deoxyribonuclease II (DNase II) is also known as acid deoxyribonuclease because it has optimal activity at the low pH environment of lysosomes where it is typically found in higher eukaryotes. Interestingly, DNase II has also been identified in a few genera of bacteria and is believed to have arisen via horizontal transfer. Here, we demonstrate that recombinant Burkholderia thailandensis DNase II is highly active at low pH in the absence of divalent metal ions, similar to eukaryotic DNase II. The crystal structure of B. thailandensis DNase II shows a dimeric quaternary structure which appears capable of binding double-stranded DNA. Each monomer of B. thailandensis DNase II exhibits a similar overall fold as phospholipase D (PLD), phosphatidylserine synthase (PSS) and tyrosyl-DNA phosphodiesterase (TDP), and conserved catalytic residues imply a similar mechanism. The structural and biochemical data presented here provide insights into the atomic structure and catalytic mechanism of DNase II.
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Affiliation(s)
- Armando Varela-Ramirez
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98110, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Adrian A Mejia
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98110, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Seattle, WA 98109, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98110, 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 98110, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Renato J Aguilera
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
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17
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Abendroth J, Varela-Ramirez A, Mejia AA, Phan IQ, Lorimer DD, Aguilera RJ, Edwards TE. Crystal structure of acid deoxyribonuclease. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s010876731709763x] [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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18
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Moen SO, Edwards TE, Dranow DM, Clifton MC, Sankaran B, Van Voorhis WC, Sharma A, Manoil C, Staker BL, Myler PJ, Lorimer DD. Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms. Sci Rep 2017; 7:223. [PMID: 28303005 PMCID: PMC5428304 DOI: 10.1038/s41598-017-00367-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/20/2017] [Indexed: 12/15/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) charge tRNAs with their cognate amino acid, an essential precursor step to loading of charged tRNAs onto the ribosome and addition of the amino acid to the growing polypeptide chain during protein synthesis. Because of this important biological function, aminoacyl-tRNA synthetases have been the focus of anti-infective drug development efforts and two aaRS inhibitors have been approved as drugs. Several researchers in the scientific community requested aminoacyl-tRNA synthetases to be targeted in the Seattle Structural Genomics Center for Infectious Disease (SSGCID) structure determination pipeline. Here we investigate thirty-one aminoacyl-tRNA synthetases from infectious disease organisms by co-crystallization in the presence of their cognate amino acid, ATP, and/or inhibitors. Crystal structures were determined for a CysRS from Borrelia burgdorferi bound to AMP, GluRS from Borrelia burgdorferi and Burkholderia thailandensis bound to glutamic acid, a TrpRS from the eukaryotic pathogen Encephalitozoon cuniculi bound to tryptophan, a HisRS from Burkholderia thailandensis bound to histidine, and a LysRS from Burkholderia thailandensis bound to lysine. Thus, the presence of ligands may promote aaRS crystallization and structure determination. Comparison with homologous structures shows conformational flexibility that appears to be a recurring theme with this enzyme class.
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Affiliation(s)
- Spencer O Moen
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA. .,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA.
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Berkeley, CA, 94720, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,University of Washington, Seattle, WA, 98195-6423, USA
| | - Amit Sharma
- International Center for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Colin Manoil
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195-5065, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, 98109, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, 98109, USA.,University of Washington, Department of Medical Education and Biomedical Informatics & Department of Global Health, Seattle, WA, 98195, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
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19
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Hewitt SN, Dranow DM, Horst BG, Abendroth JA, Forte B, Hallyburton I, Jansen C, Baragaña B, Choi R, Rivas KL, Hulverson MA, Dumais M, Edwards TE, Lorimer DD, Fairlamb AH, Gray DW, Read KD, Lehane AM, Kirk K, Myler PJ, Wernimont A, Walpole C, Stacy R, Barrett LK, Gilbert IH, Van Voorhis WC. Biochemical and Structural Characterization of Selective Allosteric Inhibitors of the Plasmodium falciparum Drug Target, Prolyl-tRNA-synthetase. ACS Infect Dis 2017; 3:34-44. [PMID: 27798837 PMCID: PMC5241706 DOI: 10.1021/acsinfecdis.6b00078] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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] [Indexed: 12/12/2022]
Abstract
Plasmodium falciparum (Pf) prolyl-tRNA synthetase (ProRS) is one of the few chemical-genetically validated drug targets for malaria, yet highly selective inhibitors have not been described. In this paper, approximately 40,000 compounds were screened to identify compounds that selectively inhibit PfProRS enzyme activity versus Homo sapiens (Hs) ProRS. X-ray crystallography structures were solved for apo, as well as substrate- and inhibitor-bound forms of PfProRS. We identified two new inhibitors of PfProRS that bind outside the active site. These two allosteric inhibitors showed >100 times specificity for PfProRS compared to HsProRS, demonstrating this class of compounds could overcome the toxicity related to HsProRS inhibition by halofuginone and its analogues. Initial medicinal chemistry was performed on one of the two compounds, guided by the cocrystallography of the compound with PfProRS, and the results can instruct future medicinal chemistry work to optimize these promising new leads for drug development against malaria.
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Affiliation(s)
- Stephen Nakazawa Hewitt
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - David M. Dranow
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Beryllium Discovery Corporation, 7869 N.E. Day Road West, Bainbridge Island, Washington 98110, United States
| | - Benjamin G. Horst
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Jan A. Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Beryllium Discovery Corporation, 7869 N.E. Day Road West, Bainbridge Island, Washington 98110, United States
| | - Barbara Forte
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Irene Hallyburton
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Chimed Jansen
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Beatriz Baragaña
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Ryan Choi
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Kasey L. Rivas
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Matthew A. Hulverson
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Mitchell Dumais
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Beryllium Discovery Corporation, 7869 N.E. Day Road West, Bainbridge Island, Washington 98110, United States
| | - Donald D. Lorimer
- Beryllium Discovery Corporation, 7869 N.E. Day Road West, Bainbridge Island, Washington 98110, United States
| | - Alan H. Fairlamb
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David W. Gray
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kevin D. Read
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Adele M. Lehane
- Research School of Biology, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Kiaran Kirk
- Research School of Biology, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109, United States
- Departments of Global Health and Biomedical
Informatics and Medical Education, University of Washington, Seattle, Washington 98195, United States
| | - Amy Wernimont
- Structure-guided Drug Discovery Coalition (SDDC), Structural Genomic Consortium, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada
| | - Chris Walpole
- Structure-guided Drug Discovery Coalition (SDDC), Structural Genomic Consortium, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109, United States
| | - Lynn K. Barrett
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Ian H. Gilbert
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Wesley C. Van Voorhis
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
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21
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Guaitoli G, Raimondi F, Gilsbach BK, Gómez-Llorente Y, Deyaert E, Renzi F, Li X, Schaffner A, Jagtap PKA, Boldt K, von Zweydorf F, Gotthardt K, Lorimer DD, Yue Z, Burgin A, Janjic N, Sattler M, Versées W, Ueffing M, Ubarretxena-Belandia I, Kortholt A, Gloeckner CJ. Structural model of the dimeric Parkinson's protein LRRK2 reveals a compact architecture involving distant interdomain contacts. Proc Natl Acad Sci U S A 2016; 113:E4357-66. [PMID: 27357661 PMCID: PMC4968714 DOI: 10.1073/pnas.1523708113] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [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: 11/18/2022] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a large, multidomain protein containing two catalytic domains: a Ras of complex proteins (Roc) G-domain and a kinase domain. Mutations associated with familial and sporadic Parkinson's disease (PD) have been identified in both catalytic domains, as well as in several of its multiple putative regulatory domains. Several of these mutations have been linked to increased kinase activity. Despite the role of LRRK2 in the pathogenesis of PD, little is known about its overall architecture and how PD-linked mutations alter its function and enzymatic activities. Here, we have modeled the 3D structure of dimeric, full-length LRRK2 by combining domain-based homology models with multiple experimental constraints provided by chemical cross-linking combined with mass spectrometry, negative-stain EM, and small-angle X-ray scattering. Our model reveals dimeric LRRK2 has a compact overall architecture with a tight, multidomain organization. Close contacts between the N-terminal ankyrin and C-terminal WD40 domains, and their proximity-together with the LRR domain-to the kinase domain suggest an intramolecular mechanism for LRRK2 kinase activity regulation. Overall, our studies provide, to our knowledge, the first structural framework for understanding the role of the different domains of full-length LRRK2 in the pathogenesis of PD.
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Affiliation(s)
- Giambattista Guaitoli
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Francesco Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; Cell Networks, University of Heidelberg, 69120 Heidelberg, Germany
| | - Bernd K Gilsbach
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, The Netherlands; Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Yacob Gómez-Llorente
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Egon Deyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Vlaams Instituut voor Biotechnologie, Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Fabiana Renzi
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Xianting Li
- Departments of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Adam Schaffner
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029; Departments of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Pravin Kumar Ankush Jagtap
- Center for Integrated Protein Science Munich at Department of Chemistry, Technische Universität München, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Karsten Boldt
- Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Felix von Zweydorf
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Katja Gotthardt
- Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | | | - Zhenyu Yue
- Departments of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | | | | | - Michael Sattler
- Center for Integrated Protein Science Munich at Department of Chemistry, Technische Universität München, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Vlaams Instituut voor Biotechnologie, Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Marius Ueffing
- Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Iban Ubarretxena-Belandia
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029;
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, The Netherlands;
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany;
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22
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Clifton MC, Bruhn JF, Atkins K, Webb TL, Baydo RO, Raymond A, Lorimer DD, Edwards TE, Myler PJ, Saphire EO. High-resolution Crystal Structure of Dimeric VP40 From Sudan ebolavirus. J Infect Dis 2015; 212 Suppl 2:S167-71. [PMID: 25957961 DOI: 10.1093/infdis/jiv090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ebolaviruses cause severe hemorrhagic fever. Central to the Ebola life cycle is the matrix protein VP40, which oligomerizes and drives viral budding. Here we present the crystal structure of the Sudan virus (SUDV) matrix protein. This structure is higher resolution (1.6 Å) than previously achievable. Despite differences in the protein purification, we find that it still forms a stable dimer in solution, as was noted for other Ebola VP40s. Although the N-terminal domain interface by which VP40 dimerizes is conserved between Ebola virus and SUDV, the C-terminal domain interface by which VP40 dimers may further assemble is significantly smaller in this SUDV assembly.
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Affiliation(s)
- Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease Beryllium, Bedford, Massachusetts
| | | | - Kateri Atkins
- Seattle Structural Genomics Center for Infectious Disease Beryllium, Bedford, Massachusetts
| | - Terry L Webb
- Seattle Structural Genomics Center for Infectious Disease Beryllium, Bainbridge Island, Washington
| | - Ruth O Baydo
- Seattle Structural Genomics Center for Infectious Disease Beryllium, Bainbridge Island, Washington
| | - Amy Raymond
- Seattle Structural Genomics Center for Infectious Disease Beryllium, Bainbridge Island, Washington
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease Beryllium, Bainbridge Island, Washington
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease Beryllium, Bainbridge Island, Washington
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease Seattle Biomedical Research Institute
| | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California
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Edwards TE, Gardberg AS, Phan IQH, Zhang Y, Staker BL, Myler PJ, Lorimer DD. Structure of uridine diphosphate N-acetylglucosamine pyrophosphorylase from Entamoeba histolytica. Acta Crystallogr F Struct Biol Commun 2015; 71:560-5. [PMID: 25945709 PMCID: PMC4427165 DOI: 10.1107/s2053230x1500179x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 01/27/2015] [Indexed: 11/10/2022] Open
Abstract
Uridine diphosphate N-acetylglucosamine pyrophosphorylase (UAP) catalyzes the final step in the synthesis of UDP-GlcNAc, which is involved in cell-wall biogenesis in plants and fungi and in protein glycosylation. Small-molecule inhibitors have been developed against UAP from Trypanosoma brucei that target an allosteric pocket to provide selectivity over the human enzyme. A 1.8 Å resolution crystal structure was determined of UAP from Entamoeba histolytica, an anaerobic parasitic protozoan that causes amoebic dysentery. Although E. histolytica UAP exhibits the same three-domain global architecture as other UAPs, it appears to lack three α-helices at the N-terminus and contains two amino acids in the allosteric pocket that make it appear more like the enzyme from the human host than that from the other parasite T. brucei. Thus, allosteric inhibitors of T. brucei UAP are unlikely to target Entamoeba UAPs.
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Affiliation(s)
- Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Anna S. Gardberg
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Isabelle Q. H. Phan
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Yang Zhang
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, 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
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
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24
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Lorimer DD, Choi R, Abramov A, Nakazawa Hewitt S, Gardberg AS, Van Voorhis WC, Staker BL, Myler PJ, Edwards TE. Structures of a histidine triad family protein from Entamoeba histolytica bound to sulfate, AMP and GMP. Acta Crystallogr F Struct Biol Commun 2015; 71:572-6. [PMID: 25945711 DOI: 10.1107/s2053230x1500237x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/04/2015] [Indexed: 11/10/2022]
Abstract
Three structures of the histidine triad family protein from Entamoeba histolytica, the causative agent of amoebic dysentery, were solved at high resolution within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The structures have sulfate (PDB entry 3oj7), AMP (PDB entry 3omf) or GMP (PDB entry 3oxk) bound in the active site, with sulfate occupying the same space as the α-phosphate of the two nucleotides. The C(α) backbones of the three structures are nearly superimposable, with pairwise r.m.s.d.s ranging from 0.06 to 0.13 Å.
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Affiliation(s)
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, USA
| | - Ariel Abramov
- Seattle Structural Genomics Center for Infectious Disease, USA
| | | | - Anna S Gardberg
- Seattle Structural Genomics Center for Infectious Disease, USA
| | | | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
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25
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Moen SO, Fairman JW, Barnes SR, Sullivan A, Nakazawa-Hewitt S, Van Voorhis WC, Staker BL, Lorimer DD, Myler PJ, Edwards TE. Structures of prostaglandin F synthase from the protozoa Leishmania major and Trypanosoma cruzi with NADP. Acta Crystallogr F Struct Biol Commun 2015; 71:609-14. [PMID: 25945716 DOI: 10.1107/s2053230x15006883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/06/2015] [Indexed: 11/10/2022]
Abstract
The crystal structures of prostaglandin F synthase (PGF) from both Leishmania major and Trypanosoma cruzi with and without their cofactor NADP have been determined to resolutions of 2.6 Å for T. cruzi PGF, 1.25 Å for T. cruzi PGF with NADP, 1.6 Å for L. major PGF and 1.8 Å for L. major PGF with NADP. These structures were determined by molecular replacement to a final R factor of less than 18.6% (Rfree of less than 22.9%). PGF in the infectious protozoa L. major and T. cruzi is a potential therapeutic target.
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Affiliation(s)
- Spencer O Moen
- Seattle Structural Genomics Center for Infectious Disease, USA
| | - James W Fairman
- Seattle Structural Genomics Center for Infectious Disease, USA
| | - Steve R Barnes
- Seattle Structural Genomics Center for Infectious Disease, USA
| | - Amy Sullivan
- Seattle Structural Genomics Center for Infectious Disease, USA
| | | | | | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
| | | | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
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26
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Armour BL, Barnes SR, Moen SO, Smith E, Raymond AC, Fairman JW, Stewart LJ, Staker BL, Begley DW, Edwards TE, Lorimer DD. Multi-target parallel processing approach for gene-to-structure determination of the influenza polymerase PB2 subunit. J Vis Exp 2013. [PMID: 23851357 PMCID: PMC3747311 DOI: 10.3791/4225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Pandemic outbreaks of highly virulent influenza strains can cause widespread morbidity and mortality in human populations worldwide. In the United States alone, an average of 41,400 deaths and 1.86 million hospitalizations are caused by influenza virus infection each year 1. Point mutations in the polymerase basic protein 2 subunit (PB2) have been linked to the adaptation of the viral infection in humans 2. Findings from such studies have revealed the biological significance of PB2 as a virulence factor, thus highlighting its potential as an antiviral drug target. The structural genomics program put forth by the National Institute of Allergy and Infectious Disease (NIAID) provides funding to Emerald Bio and three other Pacific Northwest institutions that together make up the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The SSGCID is dedicated to providing the scientific community with three-dimensional protein structures of NIAID category A-C pathogens. Making such structural information available to the scientific community serves to accelerate structure-based drug design. Structure-based drug design plays an important role in drug development. Pursuing multiple targets in parallel greatly increases the chance of success for new lead discovery by targeting a pathway or an entire protein family. Emerald Bio has developed a high-throughput, multi-target parallel processing pipeline (MTPP) for gene-to-structure determination to support the consortium. Here we describe the protocols used to determine the structure of the PB2 subunit from four different influenza A strains.
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27
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Begley DW, Edwards TE, Raymond AC, Smith ER, Hartley RC, Abendroth J, Sankaran B, Lorimer DD, Myler PJ, Staker BL, Stewart LJ. Inhibitor-bound complexes of dihydrofolate reductase-thymidylate synthase from Babesia bovis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1070-7. [PMID: 21904052 PMCID: PMC3169404 DOI: 10.1107/s1744309111029009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 07/18/2011] [Indexed: 02/03/2023]
Abstract
Structural characterization of the bifunctional enzyme dihydrofolate reductase-thymidylate synthase from B. bovis in the apo state and complexed with antifolate inhibitors in both enzymatic active sites is reported. Babesiosis is a tick-borne disease caused by eukaryotic Babesia parasites which are morphologically similar to Plasmodium falciparum, the causative agent of malaria in humans. Like Plasmodium, different species of Babesia are tuned to infect different mammalian hosts, including rats, dogs, horses and cattle. Most species of Plasmodium and Babesia possess an essential bifunctional enzyme for nucleotide synthesis and folate metabolism: dihydrofolate reductase-thymidylate synthase. Although thymidylate synthase is highly conserved across organisms, the bifunctional form of this enzyme is relatively uncommon in nature. The structural characterization of dihydrofolate reductase-thymidylate synthase in Babesia bovis, the causative agent of babesiosis in livestock cattle, is reported here. The apo state is compared with structures that contain dUMP, NADP and two different antifolate inhibitors: pemetrexed and raltitrexed. The complexes reveal modes of binding similar to that seen in drug-resistant malaria strains and point to the utility of applying structural studies with proven cancer chemotherapies towards infectious disease research.
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Affiliation(s)
- Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA.
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28
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Buggy JJ, Sideris ML, Mak P, Lorimer DD, McIntosh B, Clark JM. Cloning and characterization of a novel human histone deacetylase, HDAC8. Biochem J 2000; 350 Pt 1:199-205. [PMID: 10926844 PMCID: PMC1221242] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Histone deacetylases (HDACs) are a growing family of enzymes implicated in transcriptional regulation by affecting the acetylation state of core histones in the nucleus of cells. HDACs are known to have key roles in the regulation of cell proliferation [Brehm, Miska, McCance, Reid, Bannister and Kouzarides (1998) Nature (London) 391, 597-600], and aberrant recruitment of an HDAC complex has been shown to be a key step in the mechanism of cell transformation in acute promyelocytic leukaemia [Grignani, De Matteis, Nervi, Tomassoni, Gelmetti, Cioce, Fanelli, Ruthardt, Ferrara, Zamir et al. (1998) Nature (London) 391, 815-818; Lin, Nagy, Inoue, Shao, Miller and Evans (1998), Nature (London) 391, 811-814]. Here we present the complete nucleotide sequence of a cDNA clone, termed HDAC8, that encodes a protein product with similarity to the RPD3 class (I) of HDACs. The predicted 377-residue HDAC8 product contains a shorter C-terminal extension relative to other members of its class. After expression in two cell systems, immunopurified HDAC8 is shown to possess trichostatin A- and sodium butyrate-inhibitable HDAC activity on histone H4 peptide substrates as well as on core histones. Expression profiling reveals the expression of HDAC8 to various degrees in every tissue tested and also in several tumour lines. Mutation of two adjacent histidine residues within the predicted active site severely decreases activity, confirming these residues as important for HDAC8 enzyme activity. Finally, linkage analysis after radiation hybrid mapping has localized HDAC8 to chromosomal position Xq21.2-Xq21.3. These results confirm HDAC8 as a new member of the HDAC family.
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Affiliation(s)
- J J Buggy
- AXYS Pharmaceuticals, 180 Kimball Way, South San Francisco, CA 94080, USA.
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29
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Lorimer DD, Matkowskj K, Benya RV. Cloning, chromosomal location, and transcriptional regulation of the human galanin-1 receptor gene (GALN1R). Biochem Biophys Res Commun 1997; 241:558-64. [PMID: 9425310 DOI: 10.1006/bbrc.1997.7838] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Galanin is a neuroendocrine peptide that modulates many different normal physiological effects including memory, weight, and pain perception. To better understand galanin receptor function, we cloned and characterized the galanin-1 receptor (GALN1R) gene isolated from a human P1 library. We determined that this gene contains 2 introns of approximately 2.1 and 2.9 Kb, both of which are located in the 3rd intracellular loop. We identified transcriptional initiation sites 61 and 63 bp upstream of the translation initiation codon ATG. Sequencing of the GALN1R gene 5' flanking region revealed it to be GC rich and devoid of TATA or CCAAT boxes, features of housekeeping genes. To identify potential sites regulating promoter activity, variable lengths of the 5' flanking region were fused to a CAT gene and studied in Bowes human melanoma cells. Significant losses in CAT activity were observed only with the elimination of 2 NF-kappa B sites, located -269 and -809 bp upstream from the translational start site, respectively. These findings suggest the novel possibility that GALN1R gene expression may be regulated as a consequence of inflammatory conditions. Finally fluorescent in situ hybridization (FISH) assigned this gene to chromosome 15q24.
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Affiliation(s)
- D D Lorimer
- Department of Medicine, University of Illinois at Chicago 60612, USA
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30
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Gandhi S, Lorimer DD, de Lanerolle P. Expression of a mutant myosin light chain that cannot be phosphorylated increases paracellular permeability. Am J Physiol 1997; 272:F214-21. [PMID: 9124398 DOI: 10.1152/ajprenal.1997.272.2.f214] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A murine leukemia retroviral vector was engineered to contain the DNA encoding either the wild-type, rat aorta 20-kDa myosin light chain (MLC20) or a mutant form of MLC20 in which Thr18 and Ser19 were mutated into alanines. These mutations result in a MLC20 that cannot be phosphorylated by myosin light chain kinase. An 11-amino acid epitope from c-myc was added to both MLC20 sequences to facilitate identification of these proteins. Madin-Darby canine kidney cells were stably transduced, and MLC20 expression was demonstrated by Western blot analysis using a myc-specific antibody. MLC20 exchange was demonstrated by purifying myosin from the transduced cells and repeating the Western blot analysis. Actin-activated adenosinetriphosphatase assays on the purified myosins demonstrated approximately 50% decrease in the rate of ATP hydrolysis by the myosin containing the mutant MLC20. Transepithelial electrical resistance was decreased and mannitol flux was increased across monolayers of cells expressing mutant MLC20. These data demonstrate that MLC20 phosphorylation is involved in regulating paracellular permeability and epithelial barrier function.
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Affiliation(s)
- S Gandhi
- Department of Physiology and Biophysics, University of Illinois at Chicago, 60612, USA
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31
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Hecht G, Pestic L, Nikcevic G, Koutsouris A, Tripuraneni J, Lorimer DD, Nowak G, Guerriero V, Elson EL, Lanerolle PD. Expression of the catalytic domain of myosin light chain kinase increases paracellular permeability. Am J Physiol 1996; 271:C1678-84. [PMID: 8944652 DOI: 10.1152/ajpcell.1996.271.5.c1678] [Citation(s) in RCA: 110] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Contractile events resulting from phosphorylation of the 20-kDa myosin light chain (MLC20) have been implicated in the regulation of epithelial tight junction permeability. To address this question, Madin-Darby canine kidney cells were transfected with a murine leukemia retroviral vector containing DNA encoding either the catalytic domain of myosin light chain kinase (tMK) or the beta-galactosidase gene (beta-gal). Autoradiograms of sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of myosin immunoprecipitated from 32Pi-labeled transfected cells demonstrated that MLC20 phosphorylation was increased 3.1 +/- 0.9-fold in cells expressing tMK compared with cells expressing beta-gal. Phosphopeptide mapping confirmed that myosin light chain kinase was responsible for the increased MLC20 phosphorylation. Transepithelial electrical resistance, a measurement of barrier function, of tMK cell monolayers was consistently < 10% (123 +/- 20 omega.cm2) of that of monolayers comprised of wild-type cells (1,456 +/- 178 omega.cm2) or cells expressing beta-gal (1,452 +/- 174 omega.cm2). Dual 22Na+ and [3H]mannitol flux studies indicated that the decrease in resistance in tMK cells was attributable to increased paracellular flow. These data support the idea that MLC20 phosphorylation by myosin light chain kinase is involved in regulating epithelial tight junction permeability.
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Affiliation(s)
- G Hecht
- Department of Medicine, University of Illinois at Chicago 60612, USA
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32
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Lorimer DD, Benya RV. Cloning and quantification of galanin-1 receptor expression by mucosal cells lining the human gastrointestinal tract. Biochem Biophys Res Commun 1996; 222:379-85. [PMID: 8670213 DOI: 10.1006/bbrc.1996.0752] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Recent studies suggest that galanin receptors may be expressed by mucosal epithelial cells lining the GI tract and play a role in regulating ion transport. However, no information exists as to which receptor subtype is expressed by these mucosal cells, or the relative distribution of such receptors within the GI tract. In this study we cloned the human galanin-1 receptor (huGal 1-R) from small intestinal RNA, and demonstrate its expression in endoscopically obtained mucosal pinch biopsies by RT-PCR from the esophagus to the rectum. Semi-quantitative PCR (SQ-PCR) was performed and revealed the largest amount of huGal 1-R message in the duodenum and the least amount in the gastric fundus. This study for the first time directly demonstrates the presence and quantity of huGal 1-R message in human G1 tract mucosal epithelial cells, and suggests that this subtype is of primary importance in regulating galanin-induced changes in intestinal absorption.
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Affiliation(s)
- D D Lorimer
- Department of Medicine, University of Illinois at Chicago 60612, USA
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33
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Obara K, Nikcevic G, Pestic L, Nowak G, Lorimer DD, Guerriero V, Elson EL, Paul RJ, de Lanerolle P. Fibroblast contractility without an increase in basal myosin light chain phosphorylation in wild type cells and cells expressing the catalytic domain of myosin light chain kinase. J Biol Chem 1995; 270:18734-7. [PMID: 7642521 DOI: 10.1074/jbc.270.32.18734] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We investigated the role of myosin light chain (MLC20) phosphorylation (MLC-P) in non-muscle contractility by comparing MLC-P and the contractile properties of wild type 3T3 fibroblasts and 3T3 fibroblasts expressing the catalytic domain of myosin light chain kinase (tMK). MLC-P is 0.96 MOL of PO4/mol of MOL20 in cell expressing tMK compared to 0.20 mol of PO4/mol of MLC20 in control cells. Expressing tMK also results in a 2-fold increase in cortical stiffness compared to control cells. Contractile properties were quantified by growing wild type and transfected fibroblasts in collagen and attaching the ensuing fibers to an apparatus for performing mechanical measurements. Serum stimulation resulted in a dose-dependent increase in force with maximal force generated in the presence of 30% (v/v) serum. Surprisingly, MLC-P did not increase in wild type cells following stimulation with 30% serum, and tMK expression did not affect the contractile properties of fibers made from these cells. Moreover, the dose responses to serum, maximal force, force-velocity relationships, and dynamic stiffness were similar in the wild type cells and fibroblasts expressing tMK. These data demonstrate that non-muscle cells can generate force without an increase in MLC-P, and that an increase in MLC-P does not affect the contractile properties of fibroblast fibers.
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Affiliation(s)
- K Obara
- Department of Physiology and Biophysics, College of Medicine, University of Cincinnati, Ohio 45221, USA
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34
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Lorimer DD, Cao JL, Revzin A. Specific sequences downstream from -6 are not essential for proper and efficient in vitro utilization of the Escherichia coli lactose promoter. J Mol Biol 1990; 216:275-87. [PMID: 2254929 DOI: 10.1016/s0022-2836(05)80319-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A series of deletion mutants of the wild-type Escherichia coli lactose promoter, with endpoints at +25, +19, +14, +1 and -6 (relative to the start of transcription at +1), was constructed and the deleted DNA replaced with non-lac DNA. These mutants were used to show that no specific DNA sequences downstream from -6 are required for efficient promoter utilization in vitro. In all cases transcription is dependent on the presence of the catabolite activator protein (CAP) and cAMP, and begins at +1 at a level indistinguishable from that at the wild-type promoter. A set of lac DNA fragments deleted to -6 was constructed, having an A, C, G or T residue at +1 and heterologous DNA downstream. These synthetic promoters allow systematic testing of the effect of the initiating nucleotide on the transcription process. Again, transcription occurs mainly from +1, at a level similar to the normal wild-type level. No substantial differences between these promoters are observed in the rates of formation of stable complexes, in the degree of complex formation, in the rate at which polymerase "escapes" from the complex or in abortive transcription products. Equivalent results are seen with a related set of constructs based on the CAP-insensitive lac UV5 promoter. Thus, lac promoter sequences including consensus hexamers at -10 and -35, plus the spacer region between them, provide specificity and efficiency both in initiation of transcription by RNA polymerase and in CAP-polymerase interactions. A question as to whether there is a third RNA polymerase binding site at lac, in addition to the known overlapping P1 and P2 regions, was not unambiguously answered. However, if a "P3" site does exist, it must lie between P1 and P2. Alternatively, the variety of polymerase interactions at wild-type lac may reflect different structural states of the enzyme. The results presented here indicate that DNA downstream from -6 plays little part in determining the conformation of the enzyme at the lactose promoter.
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Affiliation(s)
- D D Lorimer
- Department of Biochemistry, Michigan State University, East Lansing 48824-1319
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35
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Lorimer DD, Revzin A. Solutions of RNA polymerase plus linear wild type E. coli lac DNA fragments contain a mixture of stable P1 and P2 promoter complexes. Nucleic Acids Res 1986; 14:2921-38. [PMID: 3515322 PMCID: PMC339712 DOI: 10.1093/nar/14.7.2921] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The lac promoter is known to have overlapping, mutually exclusive, binding sites for RNA polymerase. A number of techniques have been used to probe solutions of polymerase and linear lac DNA fragments, including gel electrophoresis binding assays, transcription experiments, and exonuclease III digestions. The data indicate that mixing RNA polymerase with the wild type lac promoter leads to formation of more than one kind of complex; a typical solution contains enzyme in heparin resistant, "open" complexes at the P2 site, while other DNA molecules have polymerase bound in a heparin sensitive, "closed" complex at P1. There may be other rather stable complexes as well. The presence of more than one type of complex has obvious implications for in vitro physical studies of this system. The data suggest that using truncated DNA fragments which eliminate the P2 site may allow isolation and study of P1 closed complexes. Quantitative analysis of the fractions of polymerase found at P1 and P2 implies that P2 can have only a limited effect on lac transcription in the cell.
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