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Shoda T, Kaufman KM, Wen T, Caldwell JM, Osswald GA, Purnima P, Zimmermann N, Collins MH, Rehn K, Foote H, Eby MD, Zhang W, Ben-Baruch Morgenstern N, Ballaban AY, Habel JE, Kottyan LC, Abonia JP, Mukkada VA, Putnam PE, Martin LJ, Rothenberg ME. Desmoplakin and periplakin genetically and functionally contribute to eosinophilic esophagitis. Nat Commun 2021; 12:6795. [PMID: 34815391 PMCID: PMC8611043 DOI: 10.1038/s41467-021-26939-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/25/2021] [Indexed: 12/13/2022] Open
Abstract
Eosinophilic esophagitis (EoE) is a chronic allergic inflammatory disease with a complex underlying genetic etiology. Herein, we conduct whole-exome sequencing of a multigeneration EoE pedigree (discovery set) and 61 additional multiplex families with EoE (replication set). A series of rare, heterozygous, missense variants are identified in the genes encoding the desmosome-associated proteins DSP and PPL in 21% of the multiplex families. Esophageal biopsies from patients with these variants retain dilated intercellular spaces and decrease DSP and PPL expression even during disease remission. These variants affect barrier integrity, cell motility and RhoGTPase activity in esophageal epithelial cells and have increased susceptibility to calpain-14-mediated degradation. An acquired loss of esophageal DSP and PPL is present in non-familial EoE. Taken together, herein, we uncover a pathogenic role for desmosomal dysfunction in EoE, providing a deeper mechanistic understanding of tissue-specific allergic responses.
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Affiliation(s)
- Tetsuo Shoda
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 3200 Burnet Avenue, Cincinnati, OH, 45229, USA
- Department of Research, Cincinnati Veterans Affairs Medical Center, 3200 Vine St, Cincinnati, OH, 45220, USA
| | - Ting Wen
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 3200 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Julie M Caldwell
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Garrett A Osswald
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Pathre Purnima
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Nives Zimmermann
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 3200 Burnet Avenue, Cincinnati, OH, 45229, USA
- Division of Pathology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Margaret H Collins
- Department of Pediatrics, University of Cincinnati College of Medicine, 3200 Burnet Avenue, Cincinnati, OH, 45229, USA
- Division of Pathology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Kira Rehn
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Heather Foote
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Michael D Eby
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Wenying Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, 3200 Burnet Avenue, Cincinnati, OH, 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Netali Ben-Baruch Morgenstern
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Adina Y Ballaban
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Jeff E Habel
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Leah C Kottyan
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 3200 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - J Pablo Abonia
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 3200 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Vincent A Mukkada
- Department of Pediatrics, University of Cincinnati College of Medicine, 3200 Burnet Avenue, Cincinnati, OH, 45229, USA
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Philip E Putnam
- Department of Pediatrics, University of Cincinnati College of Medicine, 3200 Burnet Avenue, Cincinnati, OH, 45229, USA
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Lisa J Martin
- Department of Pediatrics, University of Cincinnati College of Medicine, 3200 Burnet Avenue, Cincinnati, OH, 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, 3200 Burnet Avenue, Cincinnati, OH, 45229, USA.
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2
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Azouz NP, Klingler AM, Pathre P, Besse JA, Baruch-Morgenstern NB, Ballaban AY, Osswald GA, Brusilovsky M, Habel JE, Caldwell JM, Ynga-Durand MA, Abonia PJ, Hu YC, Wen T, Rothenberg ME. Functional role of kallikrein 5 and proteinase-activated receptor 2 in eosinophilic esophagitis. Sci Transl Med 2021; 12:12/545/eaaz7773. [PMID: 32461336 DOI: 10.1126/scitranslmed.aaz7773] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/09/2020] [Indexed: 12/12/2022]
Abstract
Eosinophilic esophagitis (EoE) is a chronic, food antigen-driven, inflammatory disease of the esophagus and is associated with impaired barrier function. Evidence is emerging that loss of esophageal expression of the serine peptidase inhibitor, kazal type 7 (SPINK7), is an upstream event in EoE pathogenesis. Here, we provide evidence that loss of SPINK7 mediates its pro-EoE effects via kallikrein 5 (KLK5) and its substrate, protease-activated receptor 2 (PAR2). Overexpression of KLK5 in differentiated esophageal epithelial cells recapitulated the effect of SPINK7 gene silencing, including barrier impairment and loss of desmoglein-1 expression. Conversely, KLK5 deficiency attenuated allergen-induced esophageal protease activity, modified commensal microbiome composition, and attenuated eosinophilia in a murine model of EoE. Inhibition of PAR2 blunted the cytokine production associated with loss of SPINK7 in epithelial cells and attenuated the allergen-induced esophageal eosinophilia in vivo. Clinical samples substantiated dysregulated PAR2 expression in the esophagus of patients with EoE, and delivery of the clinically approved drug α1 antitrypsin (A1AT, a protease inhibitor) inhibited experimental EoE. These findings demonstrate a role for the balance between KLK5 and protease inhibitors in the esophagus and highlight EoE as a protease-mediated disease. We suggest that antagonizing KLK5 and/or PAR2 has potential to be therapeutic for EoE.
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Affiliation(s)
- Nurit P Azouz
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Andrea M Klingler
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Purnima Pathre
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - John A Besse
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Netali Ben Baruch-Morgenstern
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Adina Y Ballaban
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Garrett A Osswald
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Michael Brusilovsky
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Jeff E Habel
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Julie M Caldwell
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Mario A Ynga-Durand
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA.,Laboratorio de Inmunidad de Mucosas, Sección de Investigación y Posgrado, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Pablo J Abonia
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Ting Wen
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA.
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3
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Chim N, Habel JE, Johnston JM, Krieger I, Miallau L, Sankaranarayanan R, Morse RP, Bruning J, Swanson S, Kim H, Kim CY, Li H, Bulloch EM, Payne RJ, Manos-Turvey A, Hung LW, Baker EN, Lott JS, James MNG, Terwilliger TC, Eisenberg DS, Sacchettini JC, Goulding CW. The TB Structural Genomics Consortium: a decade of progress. Tuberculosis (Edinb) 2011; 91:155-72. [PMID: 21247804 DOI: 10.1016/j.tube.2010.11.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/19/2010] [Accepted: 11/26/2010] [Indexed: 01/03/2023]
Abstract
The TB Structural Genomics Consortium is a worldwide organization of collaborators whose mission is the comprehensive structural determination and analyses of Mycobacterium tuberculosis proteins to ultimately aid in tuberculosis diagnosis and treatment. Congruent to the overall vision, Consortium members have additionally established an integrated facilities core to streamline M. tuberculosis structural biology and developed bioinformatics resources for data mining. This review aims to share the latest Consortium developments with the TB community, including recent structures of proteins that play significant roles within M. tuberculosis. Atomic resolution details may unravel mechanistic insights and reveal unique and novel protein features, as well as important protein-protein and protein-ligand interactions, which ultimately lead to a better understanding of M. tuberculosis biology and may be exploited for rational, structure-based therapeutics design.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
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4
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Habel JE, Bursey EH, Rho BS, Kim CY, Segelke BW, Rupp B, Park MS, Terwilliger TC, Hung LW. Structure of Rv1848 (UreA), the Mycobacterium tuberculosis urease gamma subunit. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:781-6. [PMID: 20606272 DOI: 10.1107/s1744309110019536] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 05/25/2010] [Indexed: 11/10/2022]
Abstract
The crystal structure of the urease gamma subunit (UreA) from Mycobacterium tuberculosis, Rv1848, has been determined at 1.8 A resolution. The asymmetric unit contains three copies of Rv1848 arranged into a homotrimer that is similar to the UreA trimer in the structure of urease from Klebsiella aerogenes. Small-angle X-ray scattering experiments indicate that the Rv1848 protein also forms trimers in solution. The observed homotrimer and the organization of urease genes within the M. tuberculosis genome suggest that M. tuberculosis urease has the (alphabetagamma)(3) composition observed for other bacterial ureases. The gamma subunit may be of primary importance for the formation of the urease quaternary structure.
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Affiliation(s)
- Jeff E Habel
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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5
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Deng X, Habel JE, Kabaleeswaran V, Snell EH, Wold MS, Borgstahl GEO. Structure of the full-length human RPA14/32 complex gives insights into the mechanism of DNA binding and complex formation. J Mol Biol 2007; 374:865-76. [PMID: 17976647 DOI: 10.1016/j.jmb.2007.09.074] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2007] [Revised: 09/22/2007] [Accepted: 09/26/2007] [Indexed: 11/16/2022]
Abstract
Replication protein A (RPA) is the ubiquitous, eukaryotic single-stranded DNA (ssDNA) binding protein and is essential for DNA replication, recombination, and repair. Here, crystal structures of the soluble RPA heterodimer, composed of the RPA14 and RPA32 subunits, have been determined for the full-length protein in multiple crystal forms. In all crystals, the electron density for the N-terminal (residues 1-42) and C-terminal (residues 175-270) regions of RPA32 is weak and of poor quality indicating that these regions are disordered and/or assume multiple positions in the crystals. Hence, the RPA32 N terminus, that is hyperphosphorylated in a cell-cycle-dependent manner and in response to DNA damaging agents, appears to be inherently disordered in the unphosphorylated state. The C-terminal, winged helix-loop-helix, protein-protein interaction domain adopts several conformations perhaps to facilitate its interaction with various proteins. Although the ordered regions of RPA14/32 resemble the previously solved protease-resistant core crystal structure, the quaternary structures between the heterodimers are quite different. Thus, the four-helix bundle quaternary assembly noted in the original core structure is unlikely to be related to the quaternary structure of the intact heterotrimer. An organic ligand binding site between subunits RPA14 and RPA32 was identified to bind dioxane. Comparison of the ssDNA binding surfaces of RPA70 with RPA14/32 showed that the lower affinity of RPA14/32 can be attributed to a shallower binding crevice with reduced positive electrostatic charge.
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Affiliation(s)
- Xiaoyi Deng
- The Eppley Institute for Research in Cancer and Allied Diseases, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA
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6
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Liu ZJ, Shah AK, Habel JE, Ng JD, Kataeva I, Xu H, Horanyi P, Yang H, Chang J, Zhao M, Huang L, Chang S, Tempel W, Chen L, Zhou W, Lee D, Lin D, Zhang H, Newton MG, Rose J, Wang BC. Salvaging Pyrococcus furiosus protein targets at SECSG. ACTA ACUST UNITED AC 2006; 6:121-7. [PMID: 16211508 DOI: 10.1007/s10969-005-5242-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Accepted: 04/06/2005] [Indexed: 10/25/2022]
Abstract
Proteins derived from the coding regions of Pyrococcus furiosus are targets for three-dimensional X-ray and NMR structure determination by the Southeast Collaboratory for Structural Genomics (SECSG). Of the 2,200 open reading frames (ORFs) in this organism, 220 protein targets were cloned and expressed in a high-throughput (HT) recombinant system for crystallographic studies. However, only 96 of the expressed proteins could be crystallized and, of these, only 15 have led to structures. To address this issue, SECSG has recently developed a two-tier approach to protein production and crystallization. In this approach, tier-1 efforts are focused on producing protein for new Pfu(italics?) targets using a high-throughput approach. Tier-2 protein production efforts support tier-1 activities by (1) producing additional protein for further crystallization trials, (2) producing modified protein (further purification, methylation, tag removal, selenium labeling, etc) as required and (3) serving as a salvaging pathway for failed tier-1 proteins. In a recent study using this two-tiered approach, nine structures were determined from a set of 50 Pfu proteins, which failed to produce crystals suitable for X-ray diffraction analysis. These results validate this approach and suggest that it has application to other HT crystal structure determination applications.
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Affiliation(s)
- Zhi-Jie Liu
- Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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7
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Xu H, Yang C, Chen L, Kataeva IA, Tempel W, Lee D, Habel JE, Nguyen D, Pflugrath JW, Ferrara JD, Arendall WB, Richardson JS, Richardson DC, Liu ZJ, Newton MG, Rose JP, Wang BC. Away from the edge II: in-house Se-SAS phasing with chromium radiation. Acta Crystallogr D Biol Crystallogr 2005; 61:960-6. [PMID: 15983419 DOI: 10.1107/s0907444905010644] [Citation(s) in RCA: 10] [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] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Accepted: 04/05/2005] [Indexed: 11/11/2022]
Abstract
Recently, the demands of high-throughput macromolecular crystallography have driven continuous improvements in phasing methods, data-collection protocols and many other technologies. Single-wavelength anomalous scattering (SAS) phasing with chromium X-ray radiation opens a new possibility for phasing a protein with data collected in-house and has led to several successful examples of de novo structure solution using only weak anomalous scatterers such as sulfur. To further reduce data-collection time and make SAS phasing more robust, it is natural to combine selenomethionine-derivatized protein (SeMet protein) with Cr Kalpha radiation to take advantage of the larger anomalous scattering signal from selenium (f'' = 2.28 e(-)) compared with sulfur (f'' = 1.14 e(-)). As reported herein, the crystal structure of a putative chorismate mutase from Clostridium thermocellum was determined using Se-SAS with Cr Kalpha radiation. Each protein molecule contains eight selenomethionine residues in 148 amino-acid residues, providing a calculated Bijvoet ratio of about 3.5% at the Cr Kalpha wavelength. A single data set to 2.2 A resolution with approximately ninefold redundancy was collected using an imaging-plate detector coupled with a Cr source. Structure solution, refinement and deposition to the Protein Data Bank were performed within 9 h of the availability of the scaled diffraction data. The procedure used here is applicable to many other proteins and promises to become a routine pathway for in-house high-throughput crystallography.
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Affiliation(s)
- Hao Xu
- Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30605, USA
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8
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Liu ZJ, Tempel W, Ng JD, Lin D, Shah AK, Chen L, Horanyi PS, Habel JE, Kataeva IA, Xu H, Yang H, Chang JC, Huang L, Chang SH, Zhou W, Lee D, Praissman JL, Zhang H, Newton MG, Rose JP, Richardson JS, Richardson DC, Wang BC. The high-throughput protein-to-structure pipeline at SECSG. Acta Crystallogr D Biol Crystallogr 2005; 61:679-84. [PMID: 15930619 DOI: 10.1107/s0907444905013132] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2004] [Accepted: 04/25/2005] [Indexed: 11/10/2022]
Abstract
Using a high degree of automation, the crystallography core at the Southeast Collaboratory for Structural Genomics (SECSG) has developed a high-throughput protein-to-structure pipeline. Various robots and automation procedures have been adopted and integrated into a pipeline that is capable of screening 40 proteins for crystallization and solving four protein structures per week. This pipeline is composed of three major units: crystallization, structure determination/validation and crystallomics. Coupled with the protein-production cores at SECSG, the protein-to-structure pipeline provides a two-tiered approach for protein production at SECSG. In tier 1, all protein samples supplied by the protein-production cores pass through the pipeline using standard crystallization screening and optimization procedures. The protein targets that failed to yield diffraction-quality crystals (resolution better than 3.0 A) become tier 2 or salvaging targets. The goal of tier 2 target salvaging, carried out by the crystallomics core, is to produce the target proteins with increased purity and homogeneity, which would render them more likely to yield well diffracting crystals. This is performed by alternative purification procedures and/or the introduction of chemical modifications to the proteins (such as tag removal, methylation, surface mutagenesis, selenomethionine labelling etc.). Details of the various procedures in the pipeline for protein crystallization, target salvaging, data collection/processing and high-throughput structure determination/validation, as well as some examples, are described.
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Affiliation(s)
- Zhi-Jie Liu
- Southeast Collaboratory for Structural Genomics, Department of Biochechemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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9
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Zhou W, Das A, Habel JE, Liu ZJ, Chang J, Chen L, Lee D, Nguyen D, Chang SH, Tempel W, Rose JP, Ljungdahl LG, Wang BC. Isolation, crystallization and preliminary X-ray analysis of a methanol-induced corrinoid protein from Moorella thermoacetica. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:537-40. [PMID: 16511090 PMCID: PMC1952305 DOI: 10.1107/s1744309105010511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Accepted: 04/04/2005] [Indexed: 05/06/2023]
Abstract
A corrinoid protein was induced and overexpressed in methanol-grown cells of the thermophilic anaerobic bacterium Moorella thermoacetica. The protein was purified from cytosolic extracts. After screening for crystallization conditions and optimization, crystals were obtained that diffracted strongly on a rotating-anode X-ray source. A diffraction data set was collected and processed including reflections to 1.9 A resolution. Reflections were indexed in a primitive orthorhombic cell with unit-cell parameters a = 55.69, b = 62.74, c = 34.54 A. N-terminal amino-acid sequencing indicates that the crystals contain a C-terminal fragment of the protein.
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Affiliation(s)
- Weihong Zhou
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
| | - Amaresh Das
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
| | - Jeff E. Habel
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
| | - Zhi-Jie Liu
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
| | - Jessie Chang
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
| | - Lirong Chen
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
| | - Doowon Lee
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
| | - Duong Nguyen
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
| | - Shu-Huey Chang
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
| | - Wolfram Tempel
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
| | - John P. Rose
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
| | - Lars G. Ljungdahl
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
- Correspondence e-mail: ,
| | - Bi-Cheng Wang
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
- Correspondence e-mail: ,
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10
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Habel JE, Ohren JF, Borgstahl GE. Dynamic light-scattering analysis of full-length human RPA14/32 dimer: purification, crystallization and self-association. Acta Crystallogr D Biol Crystallogr 2001; 57:254-9. [PMID: 11173472 DOI: 10.1107/s0907444900015225] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2000] [Accepted: 10/25/2000] [Indexed: 11/10/2022]
Abstract
Replication protein A (RPA) is a single-stranded DNA-binding protein involved in all aspects of eukaryotic DNA metabolism. A soluble heterodimeric form of RPA is composed of 14 and 32 kDa subunits (RPA14/32). Dynamic light-scattering (DLS) analysis was used to improve the purification, stabilization and crystallization of RPA14/32. Increasing the concentration of reducing agent in the last stage of purification diminished the size of a secondary peak in the anion-exchange chromatograph and promoted a single species in solution. This resulted in decreased polydispersity in the purified protein and enhanced the crystallization time from 9-12 months to 6 d. With this homogeneous preparation, the reversible association of RPA14/32 into a dimer of dimers was demonstrated by DLS. Four different crystal forms of RPA14/32 were obtained for structure determination and complete diffraction data were collected using synchrotron radiation for three of them. Data to 2.4 A resolution was collected from hexagonal crystals (P3(2) or P3(1); a = b = 63.0, c = 272.6 A) and to 2.2 and 1.9 A resolution from two orthorhombic crystal forms (both P2(1)2(1)2(1); form I, a = 61.4, b = 75.2, c = 131.6 A; form II, a = 81.8, b = 140.4, c = 173.1 A).
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Affiliation(s)
- J E Habel
- University of Toledo, Department of Chemistry, 2801 West Bancroft Street, Toledo, OH 43606, USA
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