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Lykins J, Moschitto MJ, Zhou Y, Filippova EV, Le HV, Tomita T, Fox BA, Bzik DJ, Su C, Rajagopala SV, Flores K, Spano F, Woods S, Roberts CW, Hua C, El Bissati K, Wheeler KM, Dovgin S, Muench SP, McPhillie M, Fishwick CW, Anderson WF, Lee PJ, Hickman M, Weiss LM, Dubey JP, Lorenzi HA, Silverman RB, McLeod RL. From TgO/GABA-AT, GABA, and T-263 Mutant to Conception of Toxoplasma. iScience 2024; 27:108477. [PMID: 38205261 PMCID: PMC10776954 DOI: 10.1016/j.isci.2023.108477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 04/28/2023] [Accepted: 11/13/2023] [Indexed: 01/12/2024] Open
Abstract
Toxoplasma gondii causes morbidity, mortality, and disseminates widely via cat sexual stages. Here, we find T. gondii ornithine aminotransferase (OAT) is conserved across phyla. We solve TgO/GABA-AT structures with bound inactivators at 1.55 Å and identify an inactivator selective for TgO/GABA-AT over human OAT and GABA-AT. However, abrogating TgO/GABA-AT genetically does not diminish replication, virulence, cyst-formation, or eliminate cat's oocyst shedding. Increased sporozoite/merozoite TgO/GABA-AT expression led to our study of a mutagenized clone with oocyst formation blocked, arresting after forming male and female gametes, with "Rosetta stone"-like mutations in genes expressed in merozoites. Mutations are similar to those in organisms from plants to mammals, causing defects in conception and zygote formation, affecting merozoite capacitation, pH/ionicity/sodium-GABA concentrations, drawing attention to cyclic AMP/PKA, and genes enhancing energy or substrate formation in TgO/GABA-AT-related-pathways. These candidates potentially influence merozoite's capacity to make gametes that fuse to become zygotes, thereby contaminating environments and causing disease.
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Affiliation(s)
- Joseph Lykins
- Pritzker School of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Matthew J. Moschitto
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
| | - Ying Zhou
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Ekaterina V. Filippova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hoang V. Le
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
| | - Tadakimi Tomita
- Division of Parasitology, Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Barbara A. Fox
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - David J. Bzik
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Chunlei Su
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Seesandra V. Rajagopala
- Department of Infectious Diseases, The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Kristin Flores
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Furio Spano
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stuart Woods
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow Scotland, UK
| | - Craig W. Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow Scotland, UK
| | - Cong Hua
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Kamal El Bissati
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Kelsey M. Wheeler
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Sarah Dovgin
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Stephen P. Muench
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, The University of Leeds, Leeds, West York LS2 9JT, UK
| | - Martin McPhillie
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Colin W.G. Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Patricia J. Lee
- Division of Experimental Therapeutics, Military Malaria Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Mark Hickman
- Division of Experimental Therapeutics, Military Malaria Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Louis M. Weiss
- Division of Parasitology, Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jitender P. Dubey
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Hernan A. Lorenzi
- Department of Infectious Diseases, The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Richard B. Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Rima L. McLeod
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
- Department of Pediatrics (Infectious Diseases), Institute of Genomics, Genetics, and Systems Biology, Global Health Center, Toxoplasmosis Center, CHeSS, The College, University of Chicago, Chicago, IL 60637, USA
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Rosas-Lemus M, Dey S, Minasov G, Tan K, Anderson SM, Brunzelle J, Nocadello S, Shabalin I, Filippova E, Halavaty A, Kim Y, Maltseva N, Osipiuk J, Minor W, Joachimiak A, Savchenko A, Anderson WF, Satchell KJF. A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile. Microbiol Resour Announc 2023; 12:e0050723. [PMID: 37747257 PMCID: PMC10586155 DOI: 10.1128/mra.00507-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/15/2023] [Indexed: 09/26/2023] Open
Abstract
Clostridioides difficile causes life-threatening gastrointestinal infections. It is a high-risk pathogen due to a lack of effective treatments, antimicrobial resistance, and a poorly conserved genomic core. Herein, we report 30 X-ray structures from a structure genomics pipeline spanning 13 years, representing 10.2% of the X-ray structures for this important pathogen.
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Affiliation(s)
- Monica Rosas-Lemus
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Supratim Dey
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Kemin Tan
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Spencer M. Anderson
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Joseph Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Salvatore Nocadello
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Ivan Shabalin
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ekaterina Filippova
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Andrei Halavaty
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Youngchang Kim
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Natalia Maltseva
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Jerzy Osipiuk
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Wladek Minor
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Andrzej Joachimiak
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Alexei Savchenko
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Wayne F. Anderson
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Center for Structural Biology of Infectious Diseases team members
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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Minasov G, Inniss NL, Shuvalova L, Anderson WF, Satchell KJF. Structure of the Monkeypox virus profilin-like protein A42R reveals potential functional differences from cellular profilins. Acta Crystallogr F Struct Biol Commun 2022; 78:371-377. [PMID: 36189721 PMCID: PMC9527652 DOI: 10.1107/s2053230x22009128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
The structure of the Monkeypox virus protein A42R has been determined at a resolution of 1.52 Å. This protein has a backbone structure similar to that of cellular profilin, but structural variation in loop regions and a surface basic patch support biochemical data showing that this protein has distinct binding interactions with actin and phosphatidylinositol lipids and is not likely to bind proline-rich domain proteins or microtubules. The infectious disease human monkeypox is spreading rapidly in 2022, causing a global health crisis. The genomics of Monkeypox virus (MPXV) have been extensively analyzed and reported, although little is known about the virus-encoded proteome. In particular, there are no reported experimental MPXV protein structures other than computational models. Here, a 1.52 Å resolution X-ray structure of the MPXV protein A42R, the first MPXV-encoded protein with a known structure, is reported. A42R shows structural similarity to profilins, which are cellular proteins that are known to function in the regulation of actin cytoskeletal assembly. However, structural comparison of A42R with known members of the profilin family reveals critical differences that support prior biochemical findings that A42R only weakly binds actin and does not bind poly(l-proline). In addition, the analysis suggests that A42R may make distinct interactions with phosphatidylinositol lipids. Overall, the data suggest that the role of A42R in the replication of orthopoxviruses may not be readily determined by comparison to cellular profilins. Furthermore, these findings support the need for increased efforts to determine high-resolution structures of other MPXV proteins to inform physiological studies of the poxvirus infection cycle and to reveal potential new strategies to combat human monkeypox should this emerging infectious disease with pandemic potential become more common in the future.
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Anderson WF. To bind, or not to bind, that is the question…. IUCrJ 2022; 9:536-537. [PMID: 36071803 PMCID: PMC9438501 DOI: 10.1107/s2052252522008685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The unexpected findings that are described by Czub et al. [IUCrJ (2022), 9, 551-561] provide a very interesting study demonstrating how small differences in structure can result in significant changes in the relative affinities of the seemingly promiscuous binding sites that are seen with serum albumins.
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Affiliation(s)
- Wayne F. Anderson
- Northwestern University Medical School, 303 E. Chicago Ave, Chicago, IL 60611, USA
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Cahoon LA, Alejandro‐Navarreto X, Gururaja AN, Light SH, Alonzo F, Anderson WF, Freitag NE. Listeria monocytogenes two component system PieRS regulates secretion chaperones PrsA1 and PrsA2 and enhances bacterial translocation across the intestine. Mol Microbiol 2022; 118:278-293. [PMID: 35943959 PMCID: PMC9545042 DOI: 10.1111/mmi.14967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Abstract
Listeria monocytogenes (Lm) is a widespread environmental Gram-positive bacterium that can transition into a pathogen following ingestion by a susceptible host. To cross host barriers and establish infection, Lm is dependent upon the regulated secretion and activity of many proteins including PrsA2, a peptidyl-prolyl cis-trans isomerase with foldase activity. PrsA2 contributes to the stability and activity of a number of secreted virulence factors that are required for Lm invasion, replication, and cell-to-cell spread within the infected host. In contrast, a second related secretion chaperone, PrsA1, has thus far no identified contributions to Lm pathogenesis. Here we describe the characterization of a two-component signal transduction system PieRS that regulates the expression of a regulon that includes the secretion chaperones PrsA1 and PrsA2. PieRS regulated gene products are required for bacterial resistance to ethanol exposure and are important for bacterial survival during transit through the gastrointestinal tract. PrsA1 was also found to make a unique contribution to Lm survival in the GI tract, revealing for the first time a non-overlapping requirement for both secretion chaperones PrsA1 and PrsA2 during the process of intra-gastric infection.
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Affiliation(s)
- Laty A. Cahoon
- Department of Microbiology and ImmunologyUniversity of Illinois at ChicagoChicagoIllinoisUSA
| | | | - Avinash N. Gururaja
- Department of Microbiology and ImmunologyUniversity of Illinois at ChicagoChicagoIllinoisUSA
| | - Sam H. Light
- Department of MicrobiologyUniversity of ChicagoChicagoIllinoisUSA
| | - Francis Alonzo
- Department of Microbiology and ImmunologyLoyola UniversityChicagoIllinoisUSA
| | - Wayne F. Anderson
- Center for Genomics and Infectious Diseases, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Nancy E. Freitag
- Department of Microbiology and ImmunologyUniversity of Illinois at ChicagoChicagoIllinoisUSA
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Roy SM, Minasov G, Arancio O, Chico LW, Van Eldik LJ, Anderson WF, Pelletier JC, Watterson DM. Correction to "A Selective and Brain Penetrant p38αMAPK Inhibitor Candidate for Neurologic and Neuropsychiatric Disorders That Attenuates Neuroinflammation and Cognitive Dysfunction". J Med Chem 2020; 63:8649. [PMID: 32672466 PMCID: PMC8154559 DOI: 10.1021/acs.jmedchem.0c01060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Filippova EV, Kuhn ML, Osipiuk J, Kiryukhina O, Joachimiak A, Ballicora MA, Anderson WF. Corrigendum to "A Novel Polyamine Allosteric Site of SpeG from Vibrio Cholerae is Revealed by its Dodecameric Structure" [J. Mol. Biol. 427 (6 Part B) (2015) 1316-1334]. J Mol Biol 2019; 431:4527. [PMID: 31653437 DOI: 10.1016/j.jmb.2019.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Ekaterina V Filippova
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Misty L Kuhn
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Jerzy Osipiuk
- Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Olga Kiryukhina
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Andrzej Joachimiak
- Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60626, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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8
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Filippova EV, Weigand S, Kiryukhina O, Wolfe AJ, Anderson WF. Analysis of crystalline and solution states of ligand-free spermidine N-acetyltransferase (SpeG) from Escherichia coli. Acta Crystallogr D Struct Biol 2019; 75:545-553. [PMID: 31205017 DOI: 10.1107/s2059798319006545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/08/2019] [Indexed: 11/10/2022]
Abstract
Spermidine N-acetyltransferase (SpeG) transfers an acetyl group from acetyl-coenzyme A to an N-terminal amino group of intracellular spermidine. This acetylation inactivates spermidine, reducing the polyamine toxicity that tends to occur under certain chemical and physical stresses. The structure of the SpeG protein from Vibrio cholerae has been characterized: while the monomer possesses a structural fold similar to those of other Gcn5-related N-acetyltransferase superfamily members, its dodecameric structure remains exceptional. In this paper, structural analyses of SpeG isolated from Escherichia coli are described. Like V. cholerae SpeG, E. coli SpeG forms dodecamers, as revealed by two crystal structures of the ligand-free E. coli SpeG dodecamer determined at 1.75 and 2.9 Å resolution. Although both V. cholerae SpeG and E. coli SpeG can adopt an asymmetric open dodecameric state, solution analysis showed that the oligomeric composition of ligand-free E. coli SpeG differs from that of ligand-free V. cholerae SpeG. Based on these data, it is proposed that the equilibrium balance of SpeG oligomers in the absence of ligands differs from one species to another and thus might be important for SpeG function.
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Affiliation(s)
- Ekaterina V Filippova
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Steven Weigand
- DND-CAT Synchrotron Research Center, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Olga Kiryukhina
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, IL 60153, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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9
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Roy SM, Minasov G, Arancio O, Chico LW, Van Eldik LJ, Anderson WF, Pelletier JC, Watterson DM. A Selective and Brain Penetrant p38αMAPK Inhibitor Candidate for Neurologic and Neuropsychiatric Disorders That Attenuates Neuroinflammation and Cognitive Dysfunction. J Med Chem 2019; 62:5298-5311. [PMID: 30978288 PMCID: PMC6580366 DOI: 10.1021/acs.jmedchem.9b00058] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 12/14/2022]
Abstract
![]()
The p38αMAPK
is a serine/threonine protein kinase and a key
node in the intracellular signaling networks that transduce and amplify
stress signals into physiological changes. A preponderance of preclinical
data and clinical observations established p38αMAPK as a brain
drug discovery target involved in neuroinflammatory responses and
synaptic dysfunction in multiple degenerative and neuropsychiatric
brain disorders. We summarize the discovery of highly selective, brain-penetrant,
small molecule p38αMAPK inhibitors that are efficacious in diverse
animal models of neurologic disorders. A crystallography and pharmacoinformatic
approach to fragment expansion enabled the discovery of an efficacious
hit. The addition of secondary pharmacology screens to refinement
delivered lead compounds with improved selectivity, appropriate pharmacodynamics,
and efficacy. Safety considerations and additional secondary pharmacology
screens drove optimization that delivered the drug candidate MW01-18-150SRM
(MW150), currently in early stage clinical trials.
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Affiliation(s)
- Saktimayee M Roy
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - George Minasov
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - Ottavio Arancio
- Columbia University , New York , New York 10032 , United States
| | - Laura W Chico
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | | | - Wayne F Anderson
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - Jeffrey C Pelletier
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - D Martin Watterson
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
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Hu LI, Filippova EV, Dang J, Pshenychnyi S, Ruan J, Kiryukhina O, Anderson WF, Kuhn ML, Wolfe AJ. The spermidine acetyltransferase SpeG regulates transcription of the small RNA rprA. PLoS One 2018; 13:e0207563. [PMID: 30562360 PMCID: PMC6298664 DOI: 10.1371/journal.pone.0207563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 10/30/2018] [Accepted: 11/23/2018] [Indexed: 01/02/2023] Open
Abstract
Spermidine N-acetyltransferase (SpeG) acetylates and thus neutralizes toxic polyamines. Studies indicate that SpeG plays an important role in virulence and pathogenicity of many bacteria, which have evolved SpeG-dependent strategies to control polyamine concentrations and survive in their hosts. In Escherichia coli, the two-component response regulator RcsB is reported to be subject to Nε-acetylation on several lysine residues, resulting in reduced DNA binding affinity and reduced transcription of the small RNA rprA; however, the physiological acetylation mechanism responsible for this behavior has not been fully determined. Here, we performed an acetyltransferase screen and found that SpeG inhibits rprA promoter activity in an acetylation-independent manner. Surface plasmon resonance analysis revealed that SpeG can physically interact with the DNA-binding carboxyl domain of RcsB. We hypothesize that SpeG interacts with the DNA-binding domain of RcsB and that this interaction might be responsible for SpeG-dependent inhibition of RcsB-dependent rprA transcription. This work provides a model for SpeG as a modulator of E. coli transcription through its ability to interact with the transcription factor RcsB. This is the first study to provide evidence that an enzyme involved in polyamine metabolism can influence the function of the global regulator RcsB, which integrates information concerning envelope stresses and central metabolic status to regulate diverse behaviors.
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Affiliation(s)
- Linda I. Hu
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, IL, United States of America
| | - Ekaterina V. Filippova
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, IL, United States of America
| | - Joseph Dang
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States of America
| | - Sergii Pshenychnyi
- Recombinant Protein Production Core at Chemistry of Life Processes Institute, Northwestern University, Chicago, IL, United States of America
| | - Jiapeng Ruan
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, IL, United States of America
| | - Olga Kiryukhina
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, IL, United States of America
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, IL, United States of America
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States of America
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, IL, United States of America
- * E-mail:
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11
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Lykins JD, Filippova EV, Halavaty AS, Minasov G, Zhou Y, Dubrovska I, Flores KJ, Shuvalova LA, Ruan J, El Bissati K, Dovgin S, Roberts CW, Woods S, Moulton JD, Moulton H, McPhillie MJ, Muench SP, Fishwick CWG, Sabini E, Shanmugam D, Roos DS, McLeod R, Anderson WF, Ngô HM. CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii. Front Cell Infect Microbiol 2018; 8:352. [PMID: 30345257 PMCID: PMC6182094 DOI: 10.3389/fcimb.2018.00352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/14/2018] [Indexed: 12/23/2022] Open
Abstract
Toxoplasma gondii, an Apicomplexan parasite, causes significant morbidity and mortality, including severe disease in immunocompromised hosts and devastating congenital disease, with no effective treatment for the bradyzoite stage. To address this, we used the Tropical Disease Research database, crystallography, molecular modeling, and antisense to identify and characterize a range of potential therapeutic targets for toxoplasmosis. Phosphoglycerate mutase II (PGMII), nucleoside diphosphate kinase (NDK), ribulose phosphate 3-epimerase (RPE), ribose-5-phosphate isomerase (RPI), and ornithine aminotransferase (OAT) were structurally characterized. Crystallography revealed insights into the overall structure, protein oligomeric states and molecular details of active sites important for ligand recognition. Literature and molecular modeling suggested potential inhibitors and druggability. The targets were further studied with vivoPMO to interrupt enzyme synthesis, identifying the targets as potentially important to parasitic replication and, therefore, of therapeutic interest. Targeted vivoPMO resulted in statistically significant perturbation of parasite replication without concomitant host cell toxicity, consistent with a previous CRISPR/Cas9 screen showing PGM, RPE, and RPI contribute to parasite fitness. PGM, RPE, and RPI have the greatest promise for affecting replication in tachyzoites. These targets are shared between other medically important parasites and may have wider therapeutic potential.
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Affiliation(s)
- Joseph D. Lykins
- Pritzker School of Medicine, University of Chicago, Chicago, IL, United States
| | - Ekaterina V. Filippova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Andrei S. Halavaty
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ying Zhou
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
| | - Ievgeniia Dubrovska
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kristin J. Flores
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ludmilla A. Shuvalova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jiapeng Ruan
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kamal El Bissati
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
| | - Sarah Dovgin
- Illinois Math and Science Academy, Aurora, IL, United States
| | - Craig W. Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Stuart Woods
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | | | - Hong Moulton
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Martin J. McPhillie
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Colin W. G. Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Elisabetta Sabini
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | | | - David S. Roos
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Rima McLeod
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
- Department of Pediatrics (Infectious Diseases), Institute of Genomics, Genetics, and Systems Biology, Global Health Center, Toxoplasmosis Center, CHeSS, The College, University of Chicago, Chicago, IL, United States
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Huân M. Ngô
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- BrainMicro LLC, New Haven, CT, United States
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12
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Biancucci M, Minasov G, Banerjee A, Herrera A, Woida PJ, Kieffer MB, Bindu L, Abreu-Blanco M, Anderson WF, Gaponenko V, Stephen AG, Holderfield M, Satchell KJF. The bacterial Ras/Rap1 site-specific endopeptidase RRSP cleaves Ras through an atypical mechanism to disrupt Ras-ERK signaling. Sci Signal 2018; 11:11/550/eaat8335. [PMID: 30279169 DOI: 10.1126/scisignal.aat8335] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Ras-extracellular signal-regulated kinase pathway is critical for controlling cell proliferation, and its aberrant activation drives the growth of various cancers. Because many pathogens produce toxins that inhibit Ras activity, efforts to develop effective Ras inhibitors to treat cancer could be informed by studies of Ras inhibition by pathogens. Vibrio vulnificus causes fatal infections in a manner that depends on multifunctional autoprocessing repeats-in-toxin, a toxin that releases bacterial effector domains into host cells. One such domain is the Ras/Rap1-specific endopeptidase (RRSP), which site-specifically cleaves the Switch I domain of the small GTPases Ras and Rap1. We solved the crystal structure of RRSP and found that its backbone shares a structural fold with the EreA/ChaN-like superfamily of enzymes. Unlike other proteases in this family, RRSP is not a metalloprotease. Through nuclear magnetic resonance analysis and nucleotide exchange assays, we determined that the processing of KRAS by RRSP did not release any fragments or cause KRAS to dissociate from its bound nucleotide but instead only locally affected its structure. However, this structural alteration of KRAS was sufficient to disable guanine nucleotide exchange factor-mediated nucleotide exchange and prevent KRAS from binding to RAF. Thus, RRSP is a bacterial effector that represents a previously unrecognized class of protease that disconnects Ras from its signaling network while inducing limited structural disturbance in its target.
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Affiliation(s)
- Marco Biancucci
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.,Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Avik Banerjee
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alfa Herrera
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Patrick J Woida
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Matthew B Kieffer
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lakshman Bindu
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Maria Abreu-Blanco
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Andrew G Stephen
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Matthew Holderfield
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. .,Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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13
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Gokey T, Halavaty AS, Minasov G, Anderson WF, Kuhn ML. Structure of the Bacillus anthracis dTDP-l-rhamnose biosynthetic pathway enzyme: dTDP-α-d-glucose 4,6-dehydratase, RfbB. J Struct Biol 2018; 202:175-181. [PMID: 29331609 DOI: 10.1016/j.jsb.2018.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/08/2018] [Accepted: 01/09/2018] [Indexed: 11/27/2022]
Abstract
Many bacteria require l-rhamnose as a key cell wall component. This sugar is transferred to the cell wall using an activated donor dTDP-l-rhamnose, which is produced by the dTDP-l-rhamnose biosynthetic pathway. We determined the crystal structure of the second enzyme of this pathway dTDP-α-d-glucose 4,6-dehydratase (RfbB) from Bacillus anthracis. Interestingly, RfbB only crystallized in the presence of the third enzyme of the pathway RfbC; however, RfbC was not present in the crystal. Our work represents the first complete structural characterization of the four proteins of this pathway in a single Gram-positive bacterium.
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Affiliation(s)
- Trevor Gokey
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Andrei S Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA; Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA; Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA; Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, USA.
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14
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Davis R, Écija-Conesa A, Gallego-Jara J, de Diego T, Filippova EV, Kuffel G, Anderson WF, Gibson BW, Schilling B, Canovas M, Wolfe AJ. An acetylatable lysine controls CRP function in E. coli. Mol Microbiol 2017; 107:116-131. [PMID: 29105190 DOI: 10.1111/mmi.13874] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 01/02/2023]
Abstract
Transcriptional regulation is the key to ensuring that proteins are expressed at the proper time and the proper amount. In Escherichia coli, the transcription factor cAMP receptor protein (CRP) is responsible for much of this regulation. Questions remain, however, regarding the regulation of CRP activity itself. Here, we demonstrate that a lysine (K100) on the surface of CRP has a dual function: to promote CRP activity at Class II promoters, and to ensure proper CRP steady state levels. Both functions require the lysine's positive charge; intriguingly, the positive charge of K100 can be neutralized by acetylation using the central metabolite acetyl phosphate as the acetyl donor. We propose that CRP K100 acetylation could be a mechanism by which the cell downwardly tunes CRP-dependent Class II promoter activity, whilst elevating CRP steady state levels, thus indirectly increasing Class I promoter activity. This mechanism would operate under conditions that favor acetate fermentation, such as during growth on glucose as the sole carbon source or when carbon flux exceeds the capacity of the central metabolic pathways.
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Affiliation(s)
- Robert Davis
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Ana Écija-Conesa
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', Murcia, E-30100, Spain
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', Murcia, E-30100, Spain
| | - Teresa de Diego
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', Murcia, E-30100, Spain
| | - Ekaterina V Filippova
- Department of Biochemistry and Molecular Genetics, Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Gina Kuffel
- Loyola Genomics Facility, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | | | | | - Manuel Canovas
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', Murcia, E-30100, Spain
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
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15
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Shornikov A, Tran H, Macias J, Halavaty AS, Minasov G, Anderson WF, Kuhn ML. Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC). Acta Crystallogr F Struct Biol Commun 2017; 73:664-671. [PMID: 29199987 DOI: 10.1107/s2053230x17015849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/31/2017] [Indexed: 11/10/2022]
Abstract
The exosporium layer of Bacillus anthracis spores is rich in L-rhamnose, a common bacterial cell-wall component, which often contributes to the virulence of pathogens by increasing their adherence and immune evasion. The biosynthetic pathway used to form the activated L-rhamnose donor dTDP-L-rhamnose consists of four enzymes (RfbA, RfbB, RfbC and RfbD) and is an attractive drug target because there are no homologs in mammals. It was found that co-purifying and screening RfbC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) from B. anthracis in the presence of the other three B. anthracis enzymes of the biosynthetic pathway yielded crystals that were suitable for data collection. RfbC crystallized as a dimer and its structure was determined at 1.63 Å resolution. Two different ligands were bound in the protein structure: pyrophosphate in the active site of one monomer and dTDP in the other monomer. A structural comparison with RfbC homologs showed that the key active-site residues are conserved across kingdoms.
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Affiliation(s)
| | - Ha Tran
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Jennifer Macias
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Andrei S Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, USA
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16
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Law A, Stergioulis A, Halavaty AS, Minasov G, Anderson WF, Kuhn ML. Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose reductase (RfbD). Acta Crystallogr F Struct Biol Commun 2017; 73:644-650. [PMID: 29199984 DOI: 10.1107/s2053230x17015746] [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] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/30/2017] [Indexed: 01/27/2023]
Abstract
Bacillus anthracis is the causative agent of the deadly disease Anthrax. Its use in bioterrorism and its ability to re-emerge have brought renewed interest in this organism. B. anthracis is a Gram-positive bacterium that adds L-rhamnose to its cell-wall polysaccharides using the activated donor dTDP-β-L-rhamnose. The enzymes involved in the biosynthesis of the activated donor are absent in humans, which make them ideal targets for therapeutic development to combat pathogens. Here, the 2.65 Å resolution crystal structure of the fourth enzyme in the dTDP-β-L-rhamnose-biosynthetic pathway from B. anthracis, dTDP-4-dehydro-β-L-rhamnose reductase (RfbD), is presented in complex with NADP+. This enzyme catalyzes the reduction of dTDP-4-dehydro-β-L-rhamnose to dTDP-β-L-rhamnose. Although the protein was co-crystallized in the presence of Mg2+, the protein lacks the conserved residues that coordinate Mg2+.
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Affiliation(s)
- Ashley Law
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | | | - Andrei S Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, USA
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17
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Baumgartner J, Lee J, Halavaty AS, Minasov G, Anderson WF, Kuhn ML. Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme glucose-1-phosphate thymidylyltransferase (RfbA). Acta Crystallogr F Struct Biol Commun 2017; 73:621-628. [PMID: 29095156 DOI: 10.1107/s2053230x17015357] [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] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/22/2017] [Indexed: 11/10/2022]
Abstract
L-Rhamnose is a ubiquitous bacterial cell-wall component. The biosynthetic pathway for its precursor dTDP-L-rhamnose is not present in humans, which makes the enzymes of the pathway potential drug targets. In this study, the three-dimensional structure of the first protein of this pathway, glucose-1-phosphate thymidylyltransferase (RfbA), from Bacillus anthracis was determined. In other organisms this enzyme is referred to as RmlA. RfbA was co-crystallized with the products of the enzymatic reaction, dTDP-α-D-glucose and pyrophosphate, and its structure was determined at 2.3 Å resolution. This is the first reported thymidylyltransferase structure from a Gram-positive bacterium. RfbA shares overall structural characteristics with known RmlA homologs. However, RfbA exhibits a shorter sequence at its C-terminus, which results in the absence of three α-helices involved in allosteric site formation. Consequently, RfbA was observed to exhibit a quaternary structure that is unique among currently reported glucose-1-phosphate thymidylyltransferase bacterial homologs. These structural analyses suggest that RfbA may not be allosterically regulated in some organisms and is structurally distinct from other RmlA homologs.
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Affiliation(s)
- Jackson Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Jesi Lee
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Andrei S Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, USA
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18
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Biancucci M, Dolores JS, Wong J, Grimshaw S, Anderson WF, Satchell KJF, Kwon K. New ligation independent cloning vectors for expression of recombinant proteins with a self-cleaving CPD/6xHis-tag. BMC Biotechnol 2017; 17:1. [PMID: 28056928 PMCID: PMC5216533 DOI: 10.1186/s12896-016-0323-4] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/09/2016] [Indexed: 12/30/2022] Open
Abstract
Background Recombinant protein purification is a crucial step for biochemistry and structural biology fields. Rapid robust purification methods utilize various peptide or protein tags fused to the target protein for affinity purification using corresponding matrices and to enhance solubility. However, affinity/solubility-tags often need to be removed in order to conduct functional and structural studies, adding complexities to purification protocols. Results In this work, the Vibrio cholerae MARTX toxin Cysteine Protease Domain (CPD) was inserted in a ligation-independent cloning (LIC) vector to create a C-terminal 6xHis-tagged inducible autoprocessing enzyme tag, called “the CPD-tag”. The pCPD and alternative pCPD/ccdB cloning vectors allow for easy insertion of DNA and expression of the target protein fused to the CPD-tag, which is removed at the end of the purification step by addition of the inexpensive small molecule inositol hexakisphosphate to induce CPD autoprocessing. This process is demonstrated using a small bacterial membrane localization domain and for high yield purification of the eukaryotic small GTPase KRas. Subsequently, pCPD was tested with 40 proteins or sub-domains selected from a high throughput crystallization pipeline. Conclusion pCPD vectors are easily used LIC compatible vectors for expression of recombinant proteins with a C-terminal CPD/6xHis-tag. Although intended only as a strategy for rapid tag removal, this pilot study revealed the CPD-tag may also increase expression and solubility of some recombinant proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0323-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Biancucci
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Avenue, Ward 6-205, Chicago, IL, 60611, USA
| | - Jazel S Dolores
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Avenue, Ward 6-205, Chicago, IL, 60611, USA.,Present address: Northwestern Memorial Hospital, Chicago, IL, USA
| | - Jennifer Wong
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Avenue, Ward 6-205, Chicago, IL, 60611, USA.,Present address: Indiana University, Bloomington, IN, USA
| | - Sarah Grimshaw
- Infectious Diseases Group, J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA.,Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Avenue, Ward 6-205, Chicago, IL, 60611, USA. .,Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Keehwan Kwon
- Infectious Diseases Group, J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA. .,Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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19
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Majorek KA, Osinski T, Tran DT, Revilla A, Anderson WF, Minor W, Kuhn ML. Insight into the 3D structure and substrate specificity of previously uncharacterized GNAT superfamily acetyltransferases from pathogenic bacteria. Biochim Biophys Acta Proteins Proteom 2017; 1865:55-64. [PMID: 27783928 PMCID: PMC5127773 DOI: 10.1016/j.bbapap.2016.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 09/26/2016] [Accepted: 10/20/2016] [Indexed: 01/07/2023]
Abstract
Members of the Gcn5-related N-acetyltransferase (GNAT) superfamily catalyze the acetylation of a wide range of small molecule and protein substrates. Due to their abundance in all kingdoms of life and diversity of their functions, they are implicated in many aspects of eukaryotic and prokaryotic physiology. Although numerous GNATs have been identified thus far, many remain structurally and functionally uncharacterized. The elucidation of their structures and functions is critical for broadening our knowledge of this diverse and important superfamily. In this work, we present the structural and kinetic analyses of two previously uncharacterized bacterial acetyltransferases - SACOL1063 from Staphylococcus aureus strain COL and CD1211 from Clostridium difficile strain 630. Our structures of SACOL1063 show substantial flexibility of a loop that is likely responsible for substrate recognition and binding compared to structures of other homologs. In the CoA complex structure, we found two CoA molecules bound in both the canonical AcCoA/CoA-binding site and the acceptor-substrate-binding site. Our work also provides initial clues regarding the substrate specificity of these two enzymes; however, their native function(s) remain unknown. We found both proteins act as N- rather than O-acetyltransferases and preferentially acetylate l-threonine. The combination of structural and kinetic analyses of these two previously uncharacterized GNATs provides fundamental knowledge and a framework on which future studies can be built to elucidate their native functions.
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Affiliation(s)
- Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA, Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Tomasz Osinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA, Center for Structural Genomics of Infectious Diseases (CSGID)
| | - David T. Tran
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Alina Revilla
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Wayne F. Anderson
- Northwestern University Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Chicago, IL 60611, USA, Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA, Center for Structural Genomics of Infectious Diseases (CSGID), To whom correspondence may be addressed: Dept. of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132. Tel.: 415-405-2112; or Dept. of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Ave., Charlottesville, VA 22908. Tel.: 434-243-6865; Fax: 434-982-1616;
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA, To whom correspondence may be addressed: Dept. of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132. Tel.: 415-405-2112; or Dept. of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Ave., Charlottesville, VA 22908. Tel.: 434-243-6865; Fax: 434-982-1616;
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Lee H, Ren J, Nocadello S, Rice AJ, Ojeda I, Light S, Minasov G, Vargas J, Nagarathnam D, Anderson WF, Johnson ME. Identification of novel small molecule inhibitors against NS2B/NS3 serine protease from Zika virus. Antiviral Res 2016; 139:49-58. [PMID: 28034741 DOI: 10.1016/j.antiviral.2016.12.016] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [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: 11/07/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 01/11/2023]
Abstract
Zika flavivirus infection during pregnancy appears to produce higher risk of microcephaly, and also causes multiple neurological problems such as Guillain-Barré syndrome. The Zika virus is now widespread in Central and South America, and is anticipated to become an increasing risk in the southern United States. With continuing global travel and the spread of the mosquito vector, the exposure is expected to accelerate, but there are no currently approved treatments against the Zika virus. The Zika NS2B/NS3 protease is an attractive drug target due to its essential role in viral replication. Our studies have identified several compounds with inhibitory activity (IC50) and binding affinity (KD) of ∼5-10 μM against the Zika NS2B-NS3 protease from testing 71 HCV NS3/NS4A inhibitors that were initially discovered by high-throughput screening of 40,967 compounds. Competition surface plasmon resonance studies and mechanism of inhibition analyses by enzyme kinetics subsequently determined the best compound to be a competitive inhibitor with a Ki value of 9.5 μM. We also determined the X-ray structure of the Zika NS2B-NS3 protease in a "pre-open conformation", a conformation never observed before for any flavivirus proteases. This provides the foundation for new structure-based inhibitor design.
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Affiliation(s)
- Hyun Lee
- Novalex Therapeutics, Inc., 2242 W Harrison Suite 201, Chicago, IL 60612, USA
| | - Jinhong Ren
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA
| | - Salvatore Nocadello
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Amy J Rice
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | - Isabel Ojeda
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | - Samuel Light
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Jason Vargas
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | | | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Michael E Johnson
- Novalex Therapeutics, Inc., 2242 W Harrison Suite 201, Chicago, IL 60612, USA.
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21
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Filippova EV, Wawrzak Z, Ruan J, Pshenychnyi S, Schultz RM, Wolfe AJ, Anderson WF. Crystal structure of nonphosphorylated receiver domain of the stress response regulator RcsB from Escherichia coli. Protein Sci 2016; 25:2216-2224. [PMID: 27670836 DOI: 10.1002/pro.3050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 07/13/2016] [Revised: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 11/12/2022]
Abstract
RcsB, the transcription-associated response regulator of the Rcs phosphorelay two-component signal transduction system, activates cell stress responses associated with desiccation, cell wall biosynthesis, cell division, virulence, biofilm formation, and antibiotic resistance in enteric bacterial pathogens. RcsB belongs to the FixJ/NarL family of transcriptional regulators, which are characterized by a highly conserved C-terminal DNA-binding domain. The N-terminal domain of RcsB belongs to the family of two-component receiver domains. This receiver domain contains the phosphoacceptor site and participates in RcsB dimer formation; it also contributes to dimer formation with other transcription factor partners. Here, we describe the crystal structure of the Escherichia coli RcsB receiver domain in its nonphosphorylated state. The structure reveals important molecular details of phosphorylation-independent dimerization of RcsB and has implication for the formation of heterodimers.
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Affiliation(s)
- Ekaterina V Filippova
- Department of Biochemistry and Molecular Genetics, Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611
| | - Zdzislaw Wawrzak
- Life Science Collaborative Access Team, Synchrotron Research Center, Northwestern University, Argonne, Illinois, 60439
| | - Jiapeng Ruan
- Yale University School of Medicine, Department of Digestive Diseases, New Haven, CT 06510
| | - Sergii Pshenychnyi
- Recombinant Protein Production Core, Northwestern University, Chemistry of Life Processes Institute, Evanston, Illinois 60208
| | - Richard M Schultz
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, 60153
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, 60153
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611
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22
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Kuhn ML, Alexander E, Minasov G, Page HJ, Warwrzak Z, Shuvalova L, Flores KJ, Wilson DJ, Shi C, Aldrich CC, Anderson WF. Structure of the Essential Mtb FadD32 Enzyme: A Promising Drug Target for Treating Tuberculosis. ACS Infect Dis 2016; 2:579-591. [PMID: 27547819 DOI: 10.1021/acsinfecdis.6b00082] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 12/22/2022]
Abstract
Mycolic acids are indispensible lipids of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), and contribute to the distinctive architecture and impermeability of the mycobacterial cell envelope. FadD32 plays a pivotal role in mycolic acid biosynthesis by functionally linking fatty acid synthase (FAS) and polyketide synthase (PKS) biosynthetic pathways. FadD32, a fatty acyl-AMP ligase (FAAL), represents one of the best genetically and chemically validated new TB drug targets. We have determined the three-dimensional crystal structure of Mtb FadD32 in complex with a ligand specifically designed to stabilize the catalytically active adenylate-conformation, which provides a foundation for structure-based drug design efforts against this essential protein. The structure also captures the unique interactions of a FAAL-specific insertion sequence and provides insight into the specificity and mechanism of fatty acid transfer.
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Affiliation(s)
- Misty L. Kuhn
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | | | - George Minasov
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Holland J. Page
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Zdzislaw Warwrzak
- LS-CAT,
Synchrotron Research Center, Northwestern University, Argonne, Illinois 60439, United States
| | - Ludmilla Shuvalova
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Kristin J. Flores
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | | | | | | | - Wayne F. Anderson
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
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23
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Nocadello S, Minasov G, Shuvalova LS, Dubrovska I, Sabini E, Anderson WF. Crystal Structures of the SpoIID Lytic Transglycosylases Essential for Bacterial Sporulation. J Biol Chem 2016; 291:14915-26. [PMID: 27226615 PMCID: PMC4946911 DOI: 10.1074/jbc.m116.729749] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 03/28/2016] [Revised: 05/11/2016] [Indexed: 01/07/2023] Open
Abstract
Bacterial spores are the most resistant form of life known on Earth and represent a serious problem for (i) bioterrorism attack, (ii) horizontal transmission of microbial pathogens in the community, and (iii) persistence in patients and in a nosocomial environment. Stage II sporulation protein D (SpoIID) is a lytic transglycosylase (LT) essential for sporulation. The LT superfamily is a potential drug target because it is active in essential bacterial processes involving the peptidoglycan, which is unique to bacteria. However, the absence of structural information for the sporulation-specific LT enzymes has hindered mechanistic understanding of SpoIID. Here, we report the first crystal structures with and without ligands of the SpoIID family from two community relevant spore-forming pathogens, Bacillus anthracis and Clostridium difficile. The structures allow us to visualize the overall architecture, characterize the substrate recognition model, identify critical residues, and provide the structural basis for catalysis by this new family of enzymes.
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Affiliation(s)
- Salvatore Nocadello
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - George Minasov
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Ludmilla S Shuvalova
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Ievgeniia Dubrovska
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Elisabetta Sabini
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Wayne F Anderson
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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24
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Filippova EV, Kieser KJ, Luan CH, Wawrzak Z, Kiryukhina O, Rubin EJ, Anderson WF. Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin-binding protein PonA1 reveal potential mechanisms of antibiotic resistance. FEBS J 2016; 283:2206-18. [PMID: 27101811 PMCID: PMC5245116 DOI: 10.1111/febs.13738] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/30/2016] [Accepted: 04/15/2016] [Indexed: 01/21/2023]
Abstract
UNLABELLED Mycobacterium tuberculosis is a human respiratory pathogen that causes the deadly disease tuberculosis. The rapid global spread of antibiotic-resistant M. tuberculosis makes tuberculosis infections difficult to treat. To overcome this problem new effective antimicrobial strategies are urgently needed. One promising target for new therapeutic approaches is PonA1, a class A penicillin-binding protein, which is required for maintaining physiological cell wall synthesis and cell shape during growth in mycobacteria. Here, crystal structures of the transpeptidase domain, the enzymatic domain responsible for penicillin binding, of PonA1 from M. tuberculosis in the inhibitor-free form and in complex with penicillin V are reported. We used site-directed mutagenesis, antibiotic profiling experiments, and fluorescence thermal shift assays to measure PonA1's sensitivity to different classes of β-lactams. Structural comparison of the PonA1 apo-form and the antibiotic-bound form shows that binding of penicillin V induces conformational changes in the position of the loop β4'-α3 surrounding the penicillin-binding site. We have also found that binding of different antibiotics including penicillin V positively impacts protein stability, while other tested β-lactams such as clavulanate or meropenem resulted in destabilization of PonA1. Our antibiotic profiling experiments indicate that the transpeptidase activity of PonA1 in both M. tuberculosis and M. smegmatis mediates tolerance to specific cell wall-targeting antibiotics, particularly to penicillin V and meropenem. Because M. tuberculosis is an important human pathogen, these structural data provide a template to design novel transpeptidase inhibitors to treat tuberculosis infections. DATABASE Structural data are available in the PDB database under the accession numbers 5CRF and 5CXW.
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Affiliation(s)
- Ekaterina V Filippova
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karen J Kieser
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Chi-Hao Luan
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- High Throughput Analysis Laboratory and Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Zdzislaw Wawrzak
- Life Science Collaborative Access Team, Synchrotron Research Center, Northwestern University, Evanston, IL, USA
| | - Olga Kiryukhina
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Anderson WF, Pfeiffer RM, Wohlfahrt J, Ejlertsen B, Jensen MB, Kroman NT. Abstract P1-07-03: Reproductive factors and subtype specific breast cancer risk. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p1-07-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Reproductive history and breast cancer risk reportedly differ by the estrogen receptor (ER±) and by the joint expression of ER and the human epidermal growth factor-2 receptor (ER±/HER2±). However, large sample sizes are needed to identify risk factor associations for the relatively less common ER- subtypes.
Material and Methods: We, therefore, linked two large-scale and population-based Danish registries to assess the associations for parity, number of live births, and age at first live birth (AFLB) with receptor-specific breast cancer risk. Relative risks (RRs) and 95% confidence intervals (CIs) for associations were estimated with Poisson regression models.
Results: With nearly 31 million women-years of follow-up, there were 45786 Danish women between the ages 20-84 years who developed an invasive breast cancer during the study period 1992-2011. Parity significantly reduced risk for ER+ and ER+/HER2- subtypes (RR for ER+/HER2- = 0.92; 0.87, 0.98) and suggestively increased risk for ER- and ER-/HER2- subtypes (RR for ER-/HER2- = 1.16; 0.99, 1.36). RRs increased with advancing AFLB for ER+ cancers, especially among premenopausal women; and were elevated for ER- cancers among age groups 12-19 years and 30-34 years compared to the reference age group 20-24 years.
Conclusion: Associations of breast cancer risk and reproductive history varied among Danish women by ER± and by ER±/HER2±, consistent with receptor-specific etiological heterogeneity. Risk estimates for ER+ and ER+/HER2- cancers were similar to the well-established associations for breast cancer overall, whereas relative risks for ER- and ER/HER2- cancers tended to be null or the inverse of ER+ associations.
Citation Format: Anderson WF, Pfeiffer RM, Wohlfahrt J, Ejlertsen B, Jensen M-B, Kroman NT. Reproductive factors and subtype specific breast cancer risk. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-07-03.
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Affiliation(s)
- WF Anderson
- National Cancer Institute, Bethesda, MD; Statens Serum Institut, Copenhagen; Danish Breast Cancer Group, Copenhagen; Righopitalet, Copenhagen, Denmark
| | - RM Pfeiffer
- National Cancer Institute, Bethesda, MD; Statens Serum Institut, Copenhagen; Danish Breast Cancer Group, Copenhagen; Righopitalet, Copenhagen, Denmark
| | - J Wohlfahrt
- National Cancer Institute, Bethesda, MD; Statens Serum Institut, Copenhagen; Danish Breast Cancer Group, Copenhagen; Righopitalet, Copenhagen, Denmark
| | - B Ejlertsen
- National Cancer Institute, Bethesda, MD; Statens Serum Institut, Copenhagen; Danish Breast Cancer Group, Copenhagen; Righopitalet, Copenhagen, Denmark
| | - M-B Jensen
- National Cancer Institute, Bethesda, MD; Statens Serum Institut, Copenhagen; Danish Breast Cancer Group, Copenhagen; Righopitalet, Copenhagen, Denmark
| | - NT Kroman
- National Cancer Institute, Bethesda, MD; Statens Serum Institut, Copenhagen; Danish Breast Cancer Group, Copenhagen; Righopitalet, Copenhagen, Denmark
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Allott EH, Tse CK, Carey L, Anderson WF, Olshan AF, Troester MA. Abstract P1-07-04: Etiologic heterogeneity in breast cancer across quantitative levels of estrogen receptor expression. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p1-07-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: The clinical classification of breast cancer into at least four intrinsic subtypes has advanced targeted therapy and improved prognosis. However, for etiological classification, it has been proposed that breast cancer is comprised of just two main subtypes: basal-like and non-basal-like. Evidence for these two etiologic subtypes emerges strongly from bimodal age frequency distributions at diagnosis. In the absence of RNA-based intrinsic subtyping, estrogen receptor (ER) expression is a useful surrogate for these two distinct etiologic classes. Using data from the population-based Carolina Breast Cancer Study (CBCS), we examined evidence for a two-component (ER-positive vs. ER-negative) mixture model for breast cancer biologic/etiologic heterogeneity.
Methods: Automated digital scoring of ER expression was performed on immunohistochemistry-stained tissue microarrays comprising 1,920 invasive breast cancer cases from CBCS. Clinical classification of ER status has changed over time as new data have emerged regarding optimal treatment-relevant thresholds, but optimal etiologic thresholds have not been established. Therefore, we considered ER status as a quantitative, categorical variable with cut points of <1% (ER-negative) vs. ≥1% (ER-positive), with ER-positive cases further categorized as highly positive (≥80-100%), intermediate (≥40-<80%), low (≥10-<40%) or borderline (≥1-<10%). Smoothed age frequency distributions at diagnosis (i.e., density plots) were constructed and logistic regression adjusted for age and race was conducted to assess associations between patient and tumor characteristics and level of ER positivity.
Results: As expected for etiologically-distinct entities, ER-negative and highly ER-positive tumors showed predominantly unimodal early-onset and late-onset age distributions at diagnosis with peak frequencies near ages 50 and 70 years, respectively. However, tumors with low and intermediate positivity showed bimodal patterns, consistent with a mixture of two main subtypes. Consistent with these age distribution patterns, young age (<40 years) at diagnosis was associated with an elevated odds ratio (OR) for low positive (OR 1.8; 95% CI 1.1-2.9), borderline (OR 1.9; 95% CI 1.1-3.3) and ER-negative disease (OR 2.2; 95% CI 1.5-3.2). Relative to highly ER-positive tumors, low ER-positive tumors were more likely to be node-positive (OR 1.4; 95% CI 1.0-1.9), higher grade (combined grade III; OR 1.9; 95% CI 1.3-2.9), and were more likely to harbor a p53 mutation (OR 2.0; 95% CI 1.2-3.5).
Conclusions: While etiologic differences between dichotomized ER-negative and ER-positive breast cancer categories have been well described in many epidemiologic studies, differences in breast cancer etiology across quantitative levels of ER expression have not been so well-characterized. In this study, we report that ER-positive tumors with low positivity share etiologic features of ER-negative tumors, including young age at diagnosis and aggressive tumor characteristics. These data provide additional support for a two-component breast cancer mixture model, with quantitative level of ER positivity reflecting the relative distributions of ER-positive and ER-negative tumor populations.
Citation Format: Allott EH, Tse C-K, Carey L, Anderson WF, Olshan AF, Troester MA. Etiologic heterogeneity in breast cancer across quantitative levels of estrogen receptor expression. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-07-04.
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Affiliation(s)
- EH Allott
- University of North Carolina at Chapel Hill, Chapel Hill, NC; National Cancer Institute, Rockville, MD
| | - C-K Tse
- University of North Carolina at Chapel Hill, Chapel Hill, NC; National Cancer Institute, Rockville, MD
| | - L Carey
- University of North Carolina at Chapel Hill, Chapel Hill, NC; National Cancer Institute, Rockville, MD
| | - WF Anderson
- University of North Carolina at Chapel Hill, Chapel Hill, NC; National Cancer Institute, Rockville, MD
| | - AF Olshan
- University of North Carolina at Chapel Hill, Chapel Hill, NC; National Cancer Institute, Rockville, MD
| | - MA Troester
- University of North Carolina at Chapel Hill, Chapel Hill, NC; National Cancer Institute, Rockville, MD
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Light SH, Krishna SN, Minasov G, Anderson WF. An Unusual Cation-Binding Site and Distinct Domain-Domain Interactions Distinguish Class II Enolpyruvylshikimate-3-phosphate Synthases. Biochemistry 2016; 55:1239-45. [PMID: 26813771 DOI: 10.1021/acs.biochem.5b00553] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes a critical step in the biosynthesis of a number of aromatic metabolites. An essential prokaryotic enzyme and the molecular target of the herbicide glyphosate, EPSPSs are the subject of both pharmaceutical and commercial interest. Two EPSPS classes that exhibit low sequence homology, differing substrate/glyphosate affinities, and distinct cation activation properties have previously been described. Here, we report structural studies of the monovalent cation-binding class II Coxiella burnetii EPSPS (cbEPSPS). Three cbEPSPS crystal structures reveal that the enzyme undergoes substantial conformational changes that alter the electrostatic potential of the active site. A complex with shikimate-3-phosphate, inorganic phosphate (Pi), and K(+) reveals that ligand induced domain closure produces an unusual cation-binding site bordered on three sides by the N-terminal domain, C-terminal domain, and the product Pi. A crystal structure of the class I Vibrio cholerae EPSPS (vcEPSPS) clarifies the basis of differential class I and class II cation responsiveness, showing that in class I EPSPSs a lysine side chain occupies the would-be cation-binding site. Finally, we identify distinct patterns of sequence conservation at the domain-domain interface and propose that the two EPSPS classes have evolved to differently optimize domain opening-closing dynamics.
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Affiliation(s)
- Samuel H Light
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - Sankar N Krishna
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
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Weigand S, Filippova EV, Kiryukhina O, Anderson WF. Small angle X-ray scattering data and structure factor fitting for the study of the quaternary structure of the spermidine N-acetyltransferase SpeG. Data Brief 2015; 6:47-52. [PMID: 26793756 PMCID: PMC4688414 DOI: 10.1016/j.dib.2015.11.044] [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] [Received: 10/15/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 11/26/2022] Open
Abstract
Here we describe the treatment of the small-angle X-ray Scattering (SAXS) data used during SpeG quaternary structure study as part of the research article "Substrate induced allosteric change in the quaternary structure of the spermidine N-acetyltransferase SpeG" published in Journal of Molecular Biology [1]. These data were collected on two separate area detectors as separate dilution series of the SpeG and the SpeG with spermine samples along with data from their companion buffers. The data were radially integrated, corrected for incident beam variation, and scaled to absolute units. After subtraction of volume-fraction scaled buffer scattering and division by the SpeG concentration, multiple scattering curves free of an inter-molecular structure factor were derived from the dilution series. Rather than extrapolating to infinite dilution, the structure factor contribution was estimated by fitting to the full set of data provided by dividing the scattering curves of a dilution series by the curve from the most dilute sample in that series.
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Affiliation(s)
- Steven Weigand
- DND-CAT Synchrotron Research Center, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Ekaterina V Filippova
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, IL 60611, USA
| | - Olga Kiryukhina
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, IL 60611, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, IL 60611, USA
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Filippova EV, Weigand S, Osipiuk J, Kiryukhina O, Joachimiak A, Anderson WF. Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG. J Mol Biol 2015; 427:3538-3553. [PMID: 26410587 DOI: 10.1016/j.jmb.2015.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/10/2015] [Accepted: 09/17/2015] [Indexed: 01/12/2023]
Abstract
The spermidine N-acetyltransferase SpeG is a dodecameric enzyme that catalyzes the transfer of an acetyl group from acetyl coenzyme A to polyamines such as spermidine and spermine. SpeG has an allosteric polyamine-binding site and acetylating polyamines regulate their intracellular concentrations. The structures of SpeG from Vibrio cholerae in complexes with polyamines and cofactor have been characterized earlier. Here, we present the dodecameric structure of SpeG from V. cholerae in a ligand-free form in three different conformational states: open, intermediate and closed. All structures were crystallized in C2 space group symmetry and contain six monomers in the asymmetric unit cell. Two hexamers related by crystallographic 2-fold symmetry form the SpeG dodecamer. The open and intermediate states have a unique open dodecameric ring. This SpeG dodecamer is asymmetric except for the one 2-fold axis and is unlike any known dodecameric structure. Using a fluorescence thermal shift assay, size-exclusion chromatography with multi-angle light scattering, small-angle X-ray scattering analysis, negative-stain electron microscopy and structural analysis, we demonstrate that this unique open dodecameric state exists in solution. Our combined results indicate that polyamines trigger conformational changes and induce the symmetric closed dodecameric state of the protein when they bind to their allosteric sites.
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Affiliation(s)
- Ekaterina V Filippova
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Northwestern University , Chicago, IL 60611, USA
| | - Steven Weigand
- DuPont-Northwestern-Dow Collaborative Access Team, Northwestern University Synchrotron Research Center, Argonne, IL 60439, USA
| | - Jerzy Osipiuk
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Olga Kiryukhina
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Northwestern University , Chicago, IL 60611, USA
| | - Andrzej Joachimiak
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Northwestern University , Chicago, IL 60611, USA.
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Light SH, Minasov G, Shuvalova L, Duban ME, Caffrey M, Anderson WF, Lavie A. Insights into the mechanism of type I dehydroquinate dehydratases from structures of reaction intermediates. J Biol Chem 2015; 290:19008. [PMID: 26232400 PMCID: PMC4521023 DOI: 10.1074/jbc.a110.192831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023] Open
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31
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Halavaty AS, Rich RL, Chen C, Joo JC, Minasov G, Dubrovska I, Winsor JR, Myszka DG, Duban M, Shuvalova L, Yakunin AF, Anderson WF. Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus. Acta Crystallogr D Biol Crystallogr 2015; 71:1159-75. [PMID: 25945581 PMCID: PMC4427200 DOI: 10.1107/s1399004715004228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/01/2015] [Indexed: 02/02/2023]
Abstract
When exposed to high osmolarity, methicillin-resistant Staphylococcus aureus (MRSA) restores its growth and establishes a new steady state by accumulating the osmoprotectant metabolite betaine. Effective osmoregulation has also been implicated in the acquirement of a profound antibiotic resistance by MRSA. Betaine can be obtained from the bacterial habitat or produced intracellularly from choline via the toxic betaine aldehyde (BA) employing the choline dehydrogenase and betaine aldehyde dehydrogenase (BADH) enzymes. Here, it is shown that the putative betaine aldehyde dehydrogenase SACOL2628 from the early MRSA isolate COL (SaBADH) utilizes betaine aldehyde as the primary substrate and nicotinamide adenine dinucleotide (NAD(+)) as the cofactor. Surface plasmon resonance experiments revealed that the affinity of NAD(+), NADH and BA for SaBADH is affected by temperature, pH and buffer composition. Five crystal structures of the wild type and three structures of the Gly234Ser mutant of SaBADH in the apo and holo forms provide details of the molecular mechanisms of activity and substrate specificity/inhibition of this enzyme.
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Affiliation(s)
- Andrei S. Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | | | - Chao Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Jeong Chan Joo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Ievgeniia Dubrovska
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - James R. Winsor
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | | | - Mark Duban
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Ludmilla Shuvalova
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Wayne F. Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
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Roy SM, Grum-Tokars VL, Schavocky JP, Saeed F, Staniszewski A, Teich AF, Arancio O, Bachstetter AD, Webster SJ, Van Eldik LJ, Minasov G, Anderson WF, Pelletier JC, Watterson DM. Targeting human central nervous system protein kinases: An isoform selective p38αMAPK inhibitor that attenuates disease progression in Alzheimer's disease mouse models. ACS Chem Neurosci 2015; 6:666-80. [PMID: 25676389 PMCID: PMC4404319 DOI: 10.1021/acschemneuro.5b00002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
![]()
The
first kinase inhibitor drug approval in 2001 initiated a remarkable
decade of tyrosine kinase inhibitor drugs for oncology indications,
but a void exists for serine/threonine protein kinase inhibitor drugs
and central nervous system indications. Stress kinases are of special
interest in neurological and neuropsychiatric disorders due to their
involvement in synaptic dysfunction and complex disease susceptibility.
Clinical and preclinical evidence implicates the stress related kinase
p38αMAPK as a potential neurotherapeutic target, but isoform
selective p38αMAPK inhibitor candidates are lacking and the
mixed kinase inhibitor drugs that are promising in peripheral tissue
disease indications have limitations for neurologic indications. Therefore,
pursuit of the neurotherapeutic hypothesis requires kinase isoform
selective inhibitors with appropriate neuropharmacology features.
Synaptic dysfunction disorders offer a potential for enhanced pharmacological
efficacy due to stress-induced activation of p38αMAPK in both
neurons and glia, the interacting cellular components of the synaptic
pathophysiological axis, to be modulated. We report a novel isoform
selective p38αMAPK inhibitor, MW01-18-150SRM (=MW150), that
is efficacious in suppression of hippocampal-dependent associative
and spatial memory deficits in two distinct synaptic dysfunction mouse
models. A synthetic scheme for biocompatible product and positive
outcomes from pharmacological screens are presented. The high-resolution
crystallographic structure of the p38αMAPK/MW150 complex documents
active site binding, reveals a potential low energy conformation of
the bound inhibitor, and suggests a structural explanation for MW150’s
exquisite target selectivity. As far as we are aware, MW150 is without
precedent as an isoform selective p38MAPK inhibitor or as a kinase
inhibitor capable of modulating in vivo stress related behavior.
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Affiliation(s)
| | | | | | - Faisal Saeed
- Columbia University, New York, New York 10032, United States
| | | | - Andrew F. Teich
- Columbia University, New York, New York 10032, United States
| | - Ottavio Arancio
- Columbia University, New York, New York 10032, United States
| | | | - Scott J. Webster
- University of Kentucky, Lexington, Kentucky 40536, United States
| | | | - George Minasov
- Northwestern University, Chicago, Illinois 60611, United States
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Affiliation(s)
- Robin Stacy
- Seattle Biomedical
Research Institute, 307 Westlake Avenue
North, Suite 500, Seattle, Washington 98109, United States
- Seattle Structural
Genomics Center for Infectious Disease, 307 Westlake Ave North, Suite 500, Seattle, Washington 98109, United States
| | - Wayne F. Anderson
- Department
of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Morton 7-601, 303 East Chicago Avenue, Chicago, Illinois 60611, United States
- Center for Structural
Genomics of Infectious Diseases, 303
East Chicago Avenue, Chicago, Illinois 60611, United States
| | - Peter J. Myler
- Seattle Biomedical
Research Institute, 307 Westlake Avenue
North, Suite 500, Seattle, Washington 98109, United States
- Seattle Structural
Genomics Center for Infectious Disease, 307 Westlake Ave North, Suite 500, Seattle, Washington 98109, United States
- Department
of Global Health and Department of Biomedical Informatics and Medical
Education, University of Washington, Seattle, Washington 98195, United States
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Ruan J, Mouveaux T, Light SH, Minasov G, Anderson WF, Tomavo S, Ngô HM. The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions. Acta Crystallogr D Biol Crystallogr 2015; 71:417-26. [PMID: 25760592 PMCID: PMC4356359 DOI: 10.1107/s1399004714026479] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 12/01/2014] [Indexed: 12/15/2022]
Abstract
In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein in Toxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated in vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.
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Affiliation(s)
- Jiapeng Ruan
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - Thomas Mouveaux
- Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM U1019, Institut Pasteur de Lille, Université Lille Nord de France, France
| | - Samuel H. Light
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - Stanislas Tomavo
- Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM U1019, Institut Pasteur de Lille, Université Lille Nord de France, France
| | - Huân M. Ngô
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
- BrainMicro LLC, 21 Pendleton Street, New Haven, CT 06511, USA
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35
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Filippova EV, Kuhn ML, Osipiuk J, Kiryukhina O, Joachimiak A, Ballicora MA, Anderson WF. A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by its dodecameric structure. J Mol Biol 2015; 427:1316-1334. [PMID: 25623305 DOI: 10.1016/j.jmb.2015.01.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 11/04/2014] [Revised: 01/08/2015] [Accepted: 01/12/2015] [Indexed: 01/20/2023]
Abstract
Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence of a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key toward understanding the regulation of polyamine levels in bacteria during pathogenesis.
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Affiliation(s)
- Ekaterina V Filippova
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Misty L Kuhn
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jerzy Osipiuk
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Olga Kiryukhina
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrzej Joachimiak
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60626, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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36
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Tyson GH, Halavaty AS, Kim H, Geissler B, Agard M, Satchell KJ, Cho W, Anderson WF, Hauser AR. A novel phosphatidylinositol 4,5-bisphosphate binding domain mediates plasma membrane localization of ExoU and other patatin-like phospholipases. J Biol Chem 2014; 290:2919-37. [PMID: 25505182 DOI: 10.1074/jbc.m114.611251] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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: 12/16/2022] Open
Abstract
Bacterial toxins require localization to specific intracellular compartments following injection into host cells. In this study, we examined the membrane targeting of a broad family of bacterial proteins, the patatin-like phospholipases. The best characterized member of this family is ExoU, an effector of the Pseudomonas aeruginosa type III secretion system. Upon injection into host cells, ExoU localizes to the plasma membrane, where it uses its phospholipase A2 activity to lyse infected cells. The targeting mechanism of ExoU is poorly characterized, but it was recently found to bind to the phospholipid phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), a marker for the plasma membrane of eukaryotic cells. We confirmed that the membrane localization domain (MLD) of ExoU had a direct affinity for PI(4,5)P2, and we determined that this binding was required for ExoU localization. Previously uncharacterized ExoU homologs from Pseudomonas fluorescens and Photorhabdus asymbiotica also localized to the plasma membrane and required PI(4,5)P2 for this localization. A conserved arginine within the MLD was critical for interaction of each protein with PI(4,5)P2 and for localization. Furthermore, we determined the crystal structure of the full-length P. fluorescens ExoU and found that it was similar to that of P. aeruginosa ExoU. Each MLD contains a four-helical bundle, with the conserved arginine exposed at its cap to allow for interaction with the negatively charged PI(4,5)P2. Overall, these findings provide a structural explanation for the targeting of patatin-like phospholipases to the plasma membrane and define the MLD of ExoU as a member of a new class of PI(4,5)P2 binding domains.
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Affiliation(s)
| | - Andrei S Halavaty
- Biochemistry and Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois 60611 and
| | - Hyunjin Kim
- the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | | | | | | | - Wonhwa Cho
- the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Wayne F Anderson
- Biochemistry and Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois 60611 and
| | - Alan R Hauser
- From the Departments of Microbiology-Immunology, Medicine, and
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AbouElfetouh A, Kuhn ML, Hu LI, Scholle MD, Sorensen DJ, Sahu AK, Becher D, Antelmann H, Mrksich M, Anderson WF, Gibson BW, Schilling B, Wolfe AJ. The E. coli sirtuin CobB shows no preference for enzymatic and nonenzymatic lysine acetylation substrate sites. Microbiologyopen 2014; 4:66-83. [PMID: 25417765 PMCID: PMC4335977 DOI: 10.1002/mbo3.223] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/21/2014] [Accepted: 10/24/2014] [Indexed: 01/22/2023] Open
Abstract
Nε-lysine acetylation is an abundant posttranslational modification of thousands of proteins involved in diverse cellular processes. In the model bacterium Escherichia coli, the ε-amino group of a lysine residue can be acetylated either catalytically by acetyl-coenzyme A (acCoA) and lysine acetyltransferases, or nonenzymatically by acetyl phosphate (acP). It is well known that catalytic acCoA-dependent Nε-lysine acetylation can be reversed by deacetylases. Here, we provide genetic, mass spectrometric, structural and immunological evidence that CobB, a deacetylase of the sirtuin family of NAD+-dependent deacetylases, can reverse acetylation regardless of acetyl donor or acetylation mechanism. We analyzed 69 lysines on 51 proteins that we had previously detected as robustly, reproducibly, and significantly more acetylated in a cobB mutant than in its wild-type parent. Functional and pathway enrichment analyses supported the hypothesis that CobB regulates protein function in diverse and often essential cellular processes, most notably translation. Combined mass spectrometry, bioinformatics, and protein structural data provided evidence that the accessibility and three-dimensional microenvironment of the target acetyllysine help determine CobB specificity. Finally, we provide evidence that CobB is the predominate deacetylase in E. coli.
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Affiliation(s)
- Alaa AbouElfetouh
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, 60153; Department of Microbiology, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
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Abstract
In Structural Genomics projects, virtual high-throughput ligand screening can be utilized to provide important functional details for newly determined protein structures. Using a variety of publicly available software tools, it is possible to computationally model, predict, and evaluate how different ligands interact with a given protein. At the Center for Structural Genomics of Infectious Diseases (CSGID) a series of protein analysis, docking and molecular dynamics software is scripted into a single hierarchical pipeline allowing for an exhaustive investigation of protein-ligand interactions. The ability to conduct accurate computational predictions of protein-ligand binding is a vital component in improving both the efficiency and economics of drug discovery. Computational simulations can minimize experimental efforts, the slowest and most cost prohibitive aspect of identifying new therapeutics.
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Affiliation(s)
- T Andrew Binkowski
- Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, Chicago, IL, USA,
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Krishna SN, Luan CH, Clutter MR, Mishra RK, Scheidt KA, Anderson WF, Bergan RC. Abstract 5394: A high-throughput screening platform for the identification of small molecule inhibitors of MAP2K4. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-5394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Prostate cancer (PCa) is the second highest cause of cancer death in United States males. If the metastatic movement of PCa cells could be inhibited, then mortality from PCa could be greatly reduced. Mitogen-activated protein kinase kinase 4 (MAP2K4) has previously been shown to activate pro-invasion signaling pathways in human PCa. Recognizing that MAP2K4 represents a novel and validated therapeutic target, we sought to develop and characterize an efficient process for the identification of small molecules that target MAP2K4. Using a fluorescence-based thermal shift assay (FTS) assay, we first evaluated an 80 compound library of known kinase inhibitors, thereby identifying 8 hits that thermally stabilized MAP2K4 in a concentration dependent manner. We then developed two in vitro MAP2K4 kinase assays to evaluate kinase inhibitory function, one a western-blot based assay employing the biologically relevant downstream substrates, JNK1 and p38 MAPK, and the other an Alphascreen based activity assay. In this manner, we validated the performance of our initial FTS screen. Finally, by coupling our structure-activity relationship data to MAP2K4's crystal structure, we constructed a model for inhibitor binding. It predicted binding of our identified inhibitors to MAP2K4's ATP pocket. We next applied this approach in a high-throughput fashion to over 2200 chemically diverse compounds and identified new inhibitors of MAP2K4. Herein we report the creation of a robust inhibitor-screening platform with the ability to inform the discovery and design of new and potent MAP2K4 inhibitors.
Citation Format: Sankar Narayan Krishna, Chi-Hao Luan, Matthew R. Clutter, Rama K. Mishra, Karl A. Scheidt, Wayne F. Anderson, Raymond C. Bergan. A high-throughput screening platform for the identification of small molecule inhibitors of MAP2K4. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5394. doi:10.1158/1538-7445.AM2014-5394
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Majorek KA, Kuhn ML, Chruszcz M, Anderson WF, Minor W. Double trouble-Buffer selection and His-tag presence may be responsible for nonreproducibility of biomedical experiments. Protein Sci 2014; 23:1359-68. [PMID: 25044180 PMCID: PMC4286991 DOI: 10.1002/pro.2520] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [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: 05/29/2014] [Revised: 07/06/2014] [Accepted: 07/11/2014] [Indexed: 01/07/2023]
Abstract
The availability of purified and active protein is the starting point for the majority of in vitro biomedical, biochemical, and drug discovery experiments. The use of polyhistidine affinity tags has resulted in great increases of the efficiency of the protein purification process, but can negatively affect structure and/or activity measurements. Similarly, buffer molecules may perturb the conformational stability of a protein or its activity. During the determination of the structure of a Gcn5-related N-acetyltransferase (GNAT) from Pseudomonas aeruginosa (PA4794), we found that both HEPES and the polyhistidine affinity tag bind (separately) in the substrate-binding site. In the case of HEPES, the molecule induces conformational changes in the active site, but does not significantly affect enzyme activity. In contrast, the uncleaved His-tag does not induce major conformational changes but acts as a weak competitive inhibitor of peptide substrate. In two other GNAT enzymes, we observed that the presence of the His-tag had a strong influence on the activity of these proteins. The influence of protein preparation on functional studies may affect the reproducibility of experiments in other laboratories, even when changes between protocols seem at first glance to be insignificant. Moreover, the results presented here show how critical it is to adjust the experimental conditions for each protein or family of proteins, and investigate the influence of these factors on protein activity and structure, as they may significantly alter the effectiveness of functional characterization and screening methods. Thus, we show that a polyhistidine tag and the buffer molecule HEPES bind in the substrate-binding site and influence the conformation of the active site and the activity of GNAT acetyltransferases. We believe that such discrepancies can influence the reproducibility of some experiments and therefore could have a significant "ripple effect" on subsequent studies.
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Affiliation(s)
- Karolina A Majorek
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia, 22908,Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61–614, Poznan, Poland,Midwest Center for Structural GenomicsUSA,Center for Structural Genomics of Infectious Diseases (CSGID)USA
| | - Misty L Kuhn
- Center for Structural Genomics of Infectious Diseases (CSGID)USA,Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of MedicineChicago, Illinois, 60611
| | - Maksymilian Chruszcz
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia, 22908,Midwest Center for Structural GenomicsUSA,Center for Structural Genomics of Infectious Diseases (CSGID)USA,Department of Chemistry and Biochemistry, University of South CarolinaColumbia, South Carolina, 29208
| | - Wayne F Anderson
- Midwest Center for Structural GenomicsUSA,Center for Structural Genomics of Infectious Diseases (CSGID)USA,Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of MedicineChicago, Illinois, 60611
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia, 22908,Midwest Center for Structural GenomicsUSA,Center for Structural Genomics of Infectious Diseases (CSGID)USA,*Correspondence to: Wladek Minor, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Ave., Charlottesville, VA 22908. E-mail:
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Hoyland CN, Aldridge C, Cleverley RM, Duchêne MC, Minasov G, Onopriyenko O, Sidiq K, Stogios PJ, Anderson WF, Daniel RA, Savchenko A, Vollmer W, Lewis RJ. Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition. Structure 2014; 22:949-60. [PMID: 24909784 PMCID: PMC4087270 DOI: 10.1016/j.str.2014.04.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/24/2014] [Accepted: 04/29/2014] [Indexed: 01/30/2023]
Abstract
Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like β-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.
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Affiliation(s)
- Christopher N Hoyland
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Christine Aldridge
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Robert M Cleverley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marie-Clémence Duchêne
- Institut des Sciences de la Vie, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - George Minasov
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Olena Onopriyenko
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Karzan Sidiq
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Peter J Stogios
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Wayne F Anderson
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Richard A Daniel
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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42
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Kuhn ML, Zemaitaitis B, Hu LI, Sahu A, Sorensen D, Minasov G, Lima BP, Scholle M, Mrksich M, Anderson WF, Gibson BW, Schilling B, Wolfe AJ. Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation. PLoS One 2014; 9:e94816. [PMID: 24756028 PMCID: PMC3995681 DOI: 10.1371/journal.pone.0094816] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 03/19/2014] [Indexed: 01/27/2023] Open
Abstract
The emerging view of Nε-lysine acetylation in eukaryotes is of a relatively abundant post-translational modification (PTM) that has a major impact on the function, structure, stability and/or location of thousands of proteins involved in diverse cellular processes. This PTM is typically considered to arise by the donation of the acetyl group from acetyl-coenzyme A (acCoA) to the ε-amino group of a lysine residue that is reversibly catalyzed by lysine acetyltransferases and deacetylases. Here, we provide genetic, mass spectrometric, biochemical and structural evidence that Nε-lysine acetylation is an equally abundant and important PTM in bacteria. Applying a recently developed, label-free and global mass spectrometric approach to an isogenic set of mutants, we detected acetylation of thousands of lysine residues on hundreds of Escherichia coli proteins that participate in diverse and often essential cellular processes, including translation, transcription and central metabolism. Many of these acetylations were regulated in an acetyl phosphate (acP)-dependent manner, providing compelling evidence for a recently reported mechanism of bacterial Nε-lysine acetylation. These mass spectrometric data, coupled with observations made by crystallography, biochemistry, and additional mass spectrometry showed that this acP-dependent acetylation is both non-enzymatic and specific, with specificity determined by the accessibility, reactivity and three-dimensional microenvironment of the target lysine. Crystallographic evidence shows acP can bind to proteins in active sites and cofactor binding sites, but also potentially anywhere molecules with a phosphate moiety could bind. Finally, we provide evidence that acP-dependent acetylation can impact the function of critical enzymes, including glyceraldehyde-3-phosphate dehydrogenase, triosephosphate isomerase, and RNA polymerase.
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Affiliation(s)
- Misty L. Kuhn
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bozena Zemaitaitis
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Linda I. Hu
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Alexandria Sahu
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Dylan Sorensen
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bruno P. Lima
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Michael Scholle
- Departments of Biomedical Engineering, Chemistry, and Cell & Molecular Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Milan Mrksich
- Departments of Biomedical Engineering, Chemistry, and Cell & Molecular Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bradford W. Gibson
- Buck Institute for Research on Aging, Novato, California, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
- * E-mail:
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43
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Halavaty AS, Anderson SM, Wawrzak Z, Kudritska M, Skarina T, Anderson WF, Savchenko A. Type III effector NleH2 from Escherichia coli O157:H7 str. Sakai features an atypical protein kinase domain. Biochemistry 2014; 53:2433-5. [PMID: 24712300 DOI: 10.1021/bi500016j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The crystal structure of a C-terminal domain of enterohemorrhagic Escherichia coli type III effector NleH2 has been determined to 2.6 Å resolution. The structure resembles those of protein kinases featuring the catalytic, activation, and glycine-rich loop motifs and ATP-binding site. The position of helix αC and the lack of a conserved arginine within an equivalent HRD motif suggested that the NleH2 kinase domain's active conformation might not require phosphorylation. The activation segment markedly contributed to the dimerization interface of NleH2, which can also accommodate the NleH1-NleH2 heterodimer. The C-terminal PDZ-binding motif of NleH2 provided bases for interaction with host proteins.
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Affiliation(s)
- Andrei S Halavaty
- Center for Structural Genomics of Infectious Diseases (CSGID), Molecular Pharmacology and Biological Chemistry, Northwestern University , Chicago, Illinois 60611, United States
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44
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Ratia K, Light SH, Antanasijevic A, Anderson WF, Caffrey M, Lavie A. Discovery of selective inhibitors of the Clostridium difficile dehydroquinate dehydratase. PLoS One 2014; 9:e89356. [PMID: 24586713 PMCID: PMC3931744 DOI: 10.1371/journal.pone.0089356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [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: 11/22/2013] [Accepted: 01/18/2014] [Indexed: 12/18/2022] Open
Abstract
A vibrant and healthy gut flora is essential for preventing the proliferation of Clostridium difficile, a pathogenic bacterium that causes severe gastrointestinal symptoms. In fact, most C. difficile infections (CDIs) occur after broad-spectrum antibiotic treatment, which, by eradicating the commensal gut bacteria, allows its spores to proliferate. Hence, a C. difficile specific antibiotic that spares the gut flora would be highly beneficial in treating CDI. Towards this goal, we set out to discover small molecule inhibitors of the C. difficile enzyme dehydroquinate dehydratase (DHQD). DHQD is the 3(rd) of seven enzymes that compose the shikimate pathway, a metabolic pathway absent in humans, and is present in bacteria as two phylogenetically and mechanistically distinct types. Using a high-throughput screen we identified three compounds that inhibited the type I C. difficile DHQD but not the type II DHQD from Bacteroides thetaiotaomicron, a highly represented commensal gut bacterial species. Kinetic analysis revealed that the compounds inhibit the C. difficile enzyme with Ki values ranging from 10 to 20 µM. Unexpectedly, kinetic and biophysical studies demonstrate that inhibitors also exhibit selectivity between type I DHQDs, inhibiting the C. difficile but not the highly homologous Salmonella enterica DHQD. Therefore, the three identified compounds seem to be promising lead compounds for the development of C. difficile specific antibiotics.
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Affiliation(s)
- Kiira Ratia
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Samuel H. Light
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Aleksandar Antanasijevic
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
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45
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Abstract
Arabinose 5-phosphate (A5P) is the aldopentose version of the ketohexose fructose 6-phosphate (F6P), having identical stereochemistry but lacking atoms corresponding to the 1-carbon and 1-hydroxyl. Despite structural similarity and conservation of the reactive portion of F6P, F6P acts as a substrate whereas A5P is reported to be an inhibitor of transaldolase. To address the lack of A5P reactivity we determined a crystal structure of the Francisella tularensis transaldolase in complex with A5P. This structure reveals that like F6P, A5P forms a covalent Schiff base with active site Lys135. Unlike F6P, A5P binding fails to displace an ordered active site water molecule. Retaining this water necessitates conformational changes at the A5P-protein linkage that possibly hinder reactivity. The findings presented here show the basis of A5P inhibition and suggest an unusual mechanism of competitive, reversible-covalent transaldolase regulation.
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Affiliation(s)
- Samuel H Light
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
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46
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Light SH, Minasov G, Duban ME, Anderson WF. Adherence to Bürgi-Dunitz stereochemical principles requires significant structural rearrangements in Schiff-base formation: insights from transaldolase complexes. Acta Crystallogr D Biol Crystallogr 2014; 70:544-52. [PMID: 24531488 PMCID: PMC3940192 DOI: 10.1107/s1399004713030666] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/08/2013] [Indexed: 11/10/2022]
Abstract
The Bürgi-Dunitz angle (αBD) describes the trajectory of approach of a nucleophile to an electrophile. The adoption of a stereoelectronically favorable αBD can necessitate significant reactive-group repositioning over the course of bond formation. In the context of enzyme catalysis, interactions with the protein constrain substrate rotation, which could necessitate structural transformations during bond formation. To probe this theoretical framework vis-à-vis biocatalysis, Schiff-base formation was analysed in Francisella tularensis transaldolase (TAL). Crystal structures of wild-type and Lys→Met mutant TAL in covalent and noncovalent complexes with fructose 6-phosphate and sedoheptulose 7-phosphate clarify the mechanism of catalysis and reveal that substrate keto moieties undergo significant conformational changes during Schiff-base formation. Structural changes compelled by the trajectory considerations discussed here bear relevance to bond formation in a variety of constrained enzymic/engineered systems and can inform the design of covalent therapeutics.
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Affiliation(s)
- Samuel H. Light
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mark-Eugene Duban
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Chemistry and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60201, USA
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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47
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Light SH, Antanasijevic A, Krishna SN, Caffrey M, Anderson WF, Lavie A. Crystal structures of type I dehydroquinate dehydratase in complex with quinate and shikimate suggest a novel mechanism of Schiff base formation. Biochemistry 2014; 53:872-80. [PMID: 24437575 PMCID: PMC3985847 DOI: 10.1021/bi4015506] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
A component of the shikimate biosynthetic
pathway, dehydroquinate
dehydratase (DHQD) catalyzes the dehydration of 3-dehydroquniate (DHQ)
to 3-dehydroshikimate. In the type I DHQD reaction mechanism a lysine
forms a Schiff base intermediate with DHQ. The Schiff base acts as
an electron sink to facilitate the catalytic dehydration. To address
the mechanism of Schiff base formation, we determined structures of
the Salmonella enterica wild-type DHQD in complex
with the substrate analogue quinate and the product analogue shikimate.
In addition, we determined the structure of the K170M mutant (Lys170
being the Schiff base forming residue) in complex with quinate. Combined
with nuclear magnetic resonance and isothermal titration calorimetry
data that revealed altered binding of the analogue to the K170M mutant,
these structures suggest a model of Schiff base formation characterized
by the dynamic interplay of opposing forces acting on either side
of the substrate. On the side distant from the substrate 3-carbonyl
group, closure of the enzyme’s β8−α8 loop
is proposed to guide DHQ into the proximity of the Schiff base-forming
Lys170. On the 3-carbonyl side of the substrate, Lys170 sterically
alters the position of DHQ’s reactive ketone, aligning it at
an angle conducive for nucleophilic attack. This study of a type I
DHQD reveals the interplay between the enzyme and substrate required
for the correct orientation of a functional group constrained within
a cyclic substrate.
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Affiliation(s)
- Samuel H Light
- Center for Structural Genomics of Infectious Diseases and Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University , Chicago, Illinois 60611, United States
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48
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Kuhn ML, Prachi P, Minasov G, Shuvalova L, Ruan J, Dubrovska I, Winsor J, Giraldi M, Biagini M, Liberatori S, Savino S, Bagnoli F, Anderson WF, Grandi G. Structure and protective efficacy of the Staphylococcus aureus autocleaving protease EpiP. FASEB J 2014; 28:1780-93. [PMID: 24421400 DOI: 10.1096/fj.13-241737] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [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: 01/27/2023]
Abstract
Despite the global medical needs associated with Staphylococcus aureus infections, no licensed vaccines are currently available. We identified and characterized a protein annotated as an epidermin leader peptide processing serine protease (EpiP), as a novel S. aureus vaccine candidate. In addition, we determined the structure of the recombinant protein (rEpiP) by X-ray crystallography. The crystal structure revealed that rEpiP was cleaved somewhere between residues 95 and 100, and we found that the cleavage occurs through an autocatalytic intramolecular mechanism. The protein expressed by S. aureus cells also appeared to undergo a similar processing event. To determine whether the protein acts as a serine protease, we mutated the hypothesized catalytic serine 393 residue to alanine, generating rEpiP-S393A. The crystal structure of this mutant protein showed that the polypeptide chain was not cleaved and was not interacting stably with the active site. Indeed, rEpiP-S393A was shown to be impaired in its protease activity. Mice vaccinated with rEpiP were protected from S. aureus infection (34% survival, P=0.0054). Moreover, the protective efficacy generated by rEpiP and rEpiP-S393A was comparable, implying that the noncleaving mutant could be used for vaccination purposes.
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Affiliation(s)
- Misty L Kuhn
- 2G.G., Novartis Vaccines, via Fiorentina 1, 53100, Siena, Italy.
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Abstract
The fluorescence thermal shift (FTS) method is a biophysical technique that can improve productivity in a structural genomics pipeline and provide a fast and easy platform for identifying ligands in protein function or drug discovery screening. The technique has gained widespread popularity in recent years due to its broad-scale applicability, throughput, and functional relevance. FTS is based on the principle that a protein unfolds at a critical temperature that depends upon its intrinsic stability. A probe that will fluoresce when bound to hydrophobic surfaces is used to monitor protein unfolding as temperature is increased. In this manner, conditions or small molecules that affect the thermal stability of a protein can be identified. Herein, principles, protocols, data analysis, and special considerations of FTS screening as performed for the Center for Structural Genomics of Infectious Diseases (CSGID) pipeline are described in detail. The CSGID FTS screen is designed as a high-throughput 384-well assay to be performed on a robotic platform; however, all protocols can be adapted to a 96-well format that can be assembled manually. Data analysis can be performed using a simple curve fitting of the fluorescent signal using a Boltzmann or double Boltzmann equation. A case study of 100 proteins screened against Emerald Biosystem's ADDit™ library is included as discussion.
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Affiliation(s)
- Chi-Hao Luan
- High-Throughput Analysis Laboratory, Department of Molecular Biosciences, Center for Structural Genomics of Infectious Diseases, Northwestern University, Evanston, IL, 60208, USA
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50
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Anderson WF. Abstract ES05-2: Divergent trends in breast cancer subtypes, a manifestation of cancer heterogeneity. Cancer Res 2013. [DOI: 10.1158/0008-5472.sabcs13-es05-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent studies in the United States show an unexpected divergence of ER positive and ER negative breast cancer incidence rates (JNCI 103: 1397-1402, 2011). ER positive cancers have risen while ER negative cancers have declined over the long-term. Divergent ER-specific trends might reflect statistical anomalies, lower assay thresholds for classifying breast cancers as ER positive, and/or the implementation of widespread screening mammography with increased sensitivity for ER positive cancers. However, the analysis of secular trends in Denmark, where there was better control of these potentially confounding factors, showed similar trends as in the United States (IJC 133: 2201-2206, 2013). ER positive cancers had increased among middle-aged and older Danish women in earlier birth-cohorts (or generations), implying a confluence of risk factor exposures during the peri- and the post-menopausal time periods of a woman's lifetime. In contrast, ER negative cancers had decreased among younger women in more recent birth-cohorts during the premenopausal time periods.
Divergent ER-specific trends among different birth-cohorts in younger and older generations is consistent with breast cancer heterogeneity due to distinct etiologic pathways for ER positive and ER negative breast cancers, which could be due to trends in environmental and lifestyle risk factors with dual effects by ER expression. Two such possible risk factors are pregnancy (or parity) and obesity, which are decreasing and increasing, respectively, in both the United States and Denmark. For example, parity tends to reduce breast cancer risk for ER positive cancer and to increase risk for ER negative cancers. In fact, new breast cancer cases appear to be rising worldwide due to the consequences of changing reproductive, hormonal, and dietary risk factors. For this reason, it is plausible that the same risk factors or at the least risk factors acting through common mechanisms in the United States and Denmark may foreshadow a common pattern worldwide. This is good news since ER negative breast cancers are the most difficult to treat subtypes of breast cancer, especially the so-called triple negative cancers.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr ES05-2.
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