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Umumararungu T, Gahamanyi N, Mukiza J, Habarurema G, Katandula J, Rugamba A, Kagisha V. Proline, a unique amino acid whose polymer, polyproline II helix, and its analogues are involved in many biological processes: a review. Amino Acids 2024; 56:50. [PMID: 39182198 PMCID: PMC11345334 DOI: 10.1007/s00726-024-03410-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 08/06/2024] [Indexed: 08/27/2024]
Abstract
Proline is a unique amino acid in that its side-chain is cyclised to the backbone, thus giving proline an exceptional rigidity and a considerably restricted conformational space. Polyproline forms two well-characterized helical structures: a left-handed polyproline helix (PPII) and a right-handed polyproline helix (PPI). Usually, sequences made only of prolyl residues are in PPII conformation, but even sequences not rich in proline but which are rich in glycine, lysine, glutamate, or aspartate have also a tendency to form PPII helices. Currently, the only way to study unambiguously PPII structure in solution is to use spectroscopies based on optical activity such as circular dichroism, vibrational circular dichroism and Raman optical activity. The importance of the PPII structure is emphasized by its ubiquitous presence in different organisms from yeast to human beings where proline-rich motifs and their binding domains are believed to be involved in vital biological processes. Some of the domains that are bound by proline-rich motifs include SH3 domains, WW domains, GYF domains and UEV domains, etc. The PPII structure has been demonstrated to be essential to biological activities such as signal transduction, transcription, cell motility, and immune response.
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Affiliation(s)
- Théoneste Umumararungu
- Department of Industrial Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.
| | - Noël Gahamanyi
- Department of Biology, School of Science, College of Science and Technology, University of Rwanda, Kigali, Rwanda
- Rwanda Biomedical Center, Microbiology Unit, National Reference Laboratory, Kigali, Rwanda
| | - Janvier Mukiza
- Rwanda Food and Drugs Authority, Nyarutarama Plaza, KG 9 Avenue, Kigali, Rwanda
| | - Gratien Habarurema
- Department of Chemistry, School of Science, College of Science and Technology, University of Rwanda, Kigali, Rwanda
| | - Jonathan Katandula
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Alexis Rugamba
- Department of Biochemistry, Molecular Biology and Genetics, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Vedaste Kagisha
- Department of Pharmaceuticals and Biomolecules Analysis, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
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2
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Stražar M, Park J, Abelin JG, Taylor HB, Pedersen TK, Plichta DR, Brown EM, Eraslan B, Hung YM, Ortiz K, Clauser KR, Carr SA, Xavier RJ, Graham DB. HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery. Immunity 2023; 56:1681-1698.e13. [PMID: 37301199 PMCID: PMC10519123 DOI: 10.1016/j.immuni.2023.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/08/2023] [Accepted: 05/11/2023] [Indexed: 06/12/2023]
Abstract
CD4+ T cell responses are exquisitely antigen specific and directed toward peptide epitopes displayed by human leukocyte antigen class II (HLA-II) on antigen-presenting cells. Underrepresentation of diverse alleles in ligand databases and an incomplete understanding of factors affecting antigen presentation in vivo have limited progress in defining principles of peptide immunogenicity. Here, we employed monoallelic immunopeptidomics to identify 358,024 HLA-II binders, with a particular focus on HLA-DQ and HLA-DP. We uncovered peptide-binding patterns across a spectrum of binding affinities and enrichment of structural antigen features. These aspects underpinned the development of context-aware predictor of T cell antigens (CAPTAn), a deep learning model that predicts peptide antigens based on their affinity to HLA-II and full sequence of their source proteins. CAPTAn was instrumental in discovering prevalent T cell epitopes from bacteria in the human microbiome and a pan-variant epitope from SARS-CoV-2. Together CAPTAn and associated datasets present a resource for antigen discovery and the unraveling genetic associations of HLA alleles with immunopathologies.
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Affiliation(s)
- Martin Stražar
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jihye Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Hannah B Taylor
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas K Pedersen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Basak Eraslan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yuan-Mao Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kayla Ortiz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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3
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Amundarain MJ, Vietri A, Dodero VI, Costabel MD. IDP Force Fields Applied to Model PPII-Rich 33-mer Gliadin Peptides. J Phys Chem B 2023; 127:2407-2417. [PMID: 36884001 DOI: 10.1021/acs.jpcb.3c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The 33-mer gliadin peptide and its deamidated metabolite, 33-mer DGP, are the immunodominant peptides responsible for the adaptive immune response in celiac disease (CD). CD is a complex autoimmune chronic disorder triggered by gluten ingestion that affects the small intestine and affects ∼1% of the global population. The 33-mers are polyproline II-rich (PPII) and intrinsically disordered peptides (IDPs), whose structures remain elusive. We sampled the conformational ensembles of both 33-mer peptides via molecular dynamics simulations employing two force fields (FFs) (Amber ff03ws and Amber ff99SB-disp) specifically validated for other IDPs. Our results show that both FFs allow the extensive exploration of the conformational landscape, which was not possible with the standard FF GROMOS53A6 reported before. Clustering analysis of the trajectories showed that the five largest clusters (78-88% of the total structures) present elongated, semielongated, and curved conformations in both FFs. Large average radius of gyration and solvent-exposed surfaces characterized these structures. While the structures sampled are similar, the Amber ff99SB-disp trajectories explored folded conformations with a higher probability. In addition, PPII secondary structure was preserved throughout the trajectories (58-73%) together with a non-negligible content of β structures (11-23%), in agreement with previous experimental results. This work represents the initial step in studying further the interaction of these peptides with other biologically relevant molecules, which could lead to finally disclose the molecular events that lead to CD.
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Affiliation(s)
- María J Amundarain
- Departamento de Física, Instituto de Física del Sur (IFISUR), Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
- Department of Chemistry, Organic Chemistry III, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Agustín Vietri
- Departamento de Física, Instituto de Física del Sur (IFISUR), Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Verónica I Dodero
- Department of Chemistry, Organic Chemistry III, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Marcelo D Costabel
- Departamento de Física, Instituto de Física del Sur (IFISUR), Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
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Becht DC, Leavens MJ, Zeng B, Rothfuss MT, Briknarová K, Bowler BE. Residual Structure in the Denatured State of the Fast-Folding UBA(1) Domain from the Human DNA Excision Repair Protein HHR23A. Biochemistry 2022; 61:767-784. [PMID: 35430812 PMCID: PMC9150713 DOI: 10.1021/acs.biochem.2c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of the first ubiquitin-associated domain from HHR23A, UBA(1), was determined by X-ray crystallography at a 1.60 Å resolution, and its stability, folding kinetics, and residual structure under denaturing conditions have been investigated. The concentration dependence of thermal denaturation and size-exclusion chromatography indicate that UBA(1) is monomeric. Guanidine hydrochloride (GdnHCl) denaturation experiments reveal that the unfolding free energy, ΔGu°'(H2O), of UBA(1) is 2.4 kcal mol-1. Stopped-flow folding kinetics indicates sub-millisecond folding with only proline isomerization phases detectable at 25 °C. The full folding kinetics are observable at 4 °C, yielding a folding rate constant, kf, in the absence of a denaturant of 13,000 s-1 and a Tanford β-value of 0.80, consistent with a compact transition state. Evaluation of the secondary structure via circular dichroism shows that the residual helical structure in the denatured state is replaced by polyproline II structure as the GdnHCl concentration increases. Analysis of NMR secondary chemical shifts for backbone 15NH, 13CO, and 13Cα atoms between 4 and 7 M GdnHCl shows three islands of residual helical secondary structure that align in sequence with the three native-state helices. Extrapolation of the NMR data to 0 M GdnHCl demonstrates that helical structure would populate to 17-33% in the denatured state under folding conditions. Comparison with NMR data for a peptide corresponding to helix 1 indicates that this helix is stabilized by transient tertiary interactions in the denatured state of UBA(1). The high helical content in the denatured state, which is enhanced by transient tertiary interactions, suggests a diffusion-collision folding mechanism.
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Affiliation(s)
- Dustin C Becht
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Moses J Leavens
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Baisen Zeng
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Michael T Rothfuss
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Klára Briknarová
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
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5
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He W, Chen N, Yu Z, Sun Q, He Q, Zeng W. Effect of tea polyphenols on the quality of Chinese steamed bun and the action mechanism. J Food Sci 2022; 87:1500-1513. [DOI: 10.1111/1750-3841.16120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Wen‐Jing He
- Antioxidant Polyphenols Team Department of Food Engineering, Sichuan University Chengdu P. R. China
| | - Nan Chen
- The Key Laboratory of Food Science and Technology of Sichuan Province of Education Sichuan University Chengdu P. R. China
| | - Zhi‐Long Yu
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences McGill University Saint‐Anne‐de‐Bellevue Quebec Canada
| | - Qun Sun
- The Key Laboratory of Food Science and Technology of Sichuan Province of Education Sichuan University Chengdu P. R. China
| | - Qiang He
- The Key Laboratory of Food Science and Technology of Sichuan Province of Education Sichuan University Chengdu P. R. China
| | - Wei‐Cai Zeng
- Antioxidant Polyphenols Team Department of Food Engineering, Sichuan University Chengdu P. R. China
- The Key Laboratory of Food Science and Technology of Sichuan Province of Education Sichuan University Chengdu P. R. China
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6
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Gliadin proteolytical resistant peptides: the interplay between structure and self-assembly in gluten-related disorders. Biophys Rev 2022; 13:1147-1154. [PMID: 35047092 PMCID: PMC8724473 DOI: 10.1007/s12551-021-00856-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022] Open
Abstract
In recent years, the evaluation of the structural properties of food has become of crucial importance in the understanding of food-related disorders. One of the most exciting systems is gliadin, a protein in wheat gluten, that plays a protagonist role in gluten-related disorders with a worldwide prevalence of 5%, including autoimmune celiac disease (CeD) (1%) and non-celiac wheat sensitivity (0.5–13%). It is accepted that gliadin is not fully digested by humans, producing large peptides that reach the gut mucosa. The gliadin peptides cross the lamina propria eliciting different immune responses in susceptible patients. Many clinical and biomedical efforts aim to diagnose and understand gluten-related disorders; meanwhile, the early stages of the inflammatory events remain elusive. Interestingly, although the primary sequence of many gliadin peptides is well known, it was only recently revealed the self-assembly capability of two pathogenic gliadin fragments and their connection to the early stage of diseases. This review is dedicated to the most relevant biophysical characterization of the complex gliadin digest and the two most studied gliadin fragments, the immunodominant 33-mer peptide and the toxic p31-43 in connection with inflammation and innate immune response. Here, we want to emphasize that combining different biophysical methods with cellular and in vivo models is of key importance to get an integrative understanding of a complex biological problem, as discussed here.
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7
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Woldemariam KY, Yuan J, Wan Z, Yu Q, Cao Y, Mao H, Liu Y, Wang J, Li H, Sun B. Celiac Disease and Immunogenic Wheat Gluten Peptides and the Association of Gliadin Peptides with HLA DQ2 and HLA DQ8. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2021.1907755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Kalekristos Yohannes Woldemariam
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Juanli Yuan
- School of Pharmacy, Nanchang University, Nanchang, China
| | - Zhen Wan
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Qinglin Yu
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Yating Cao
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Huijia Mao
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Yingli Liu
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Jing Wang
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Hongyan Li
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Baoguo Sun
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
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8
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Gliadin Sequestration as a Novel Therapy for Celiac Disease: A Prospective Application for Polyphenols. Int J Mol Sci 2021; 22:ijms22020595. [PMID: 33435615 PMCID: PMC7826989 DOI: 10.3390/ijms22020595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
Celiac disease is an autoimmune disorder characterized by a heightened immune response to gluten proteins in the diet, leading to gastrointestinal symptoms and mucosal damage localized to the small intestine. Despite its prevalence, the only treatment currently available for celiac disease is complete avoidance of gluten proteins in the diet. Ongoing clinical trials have focused on targeting the immune response or gluten proteins through methods such as immunosuppression, enhanced protein degradation and protein sequestration. Recent studies suggest that polyphenols may elicit protective effects within the celiac disease milieu by disrupting the enzymatic hydrolysis of gluten proteins, sequestering gluten proteins from recognition by critical receptors in pathogenesis and exerting anti-inflammatory effects on the system as a whole. This review highlights mechanisms by which polyphenols can protect against celiac disease, takes a critical look at recent works and outlines future applications for this potential treatment method.
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Falcigno L, Calvanese L, Conte M, Nanayakkara M, Barone MV, D’Auria G. Structural Perspective of Gliadin Peptides Active in Celiac Disease. Int J Mol Sci 2020; 21:E9301. [PMID: 33291297 PMCID: PMC7731278 DOI: 10.3390/ijms21239301] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022] Open
Abstract
Gluten fragments released in gut of celiac individuals activate the innate or adaptive immune systems. The molecular mechanisms associated with the adaptive response involve a series of immunodominant gluten peptides which are mainly recognized by human leucocyte antigen (HLA)-DQ2.5 and HLA-DQ8. Other peptides, such as A-gliadin P31-43, are not recognized by HLA and trigger innate responses by several routes not yet well detailed. Among the gluten fragments known to be active in Celiac disease, here we focus on the properties of all gluten peptides with known tri-dimensional structure either those locked into HLA-DQ complexes whose crystals were X-ray analyzed or characterized in solution as free forms. The aim of this work was to find the structural reasons why some gluten peptides prompt the adaptive immune systems while others do not, by apparently involving just the innate immune routes. We propose that P31-43 is a non-adaptive prompter because it is not a good ligand for HLA-DQ. Even sharing a similar ability to adopt polyproline II structure with the adaptive ones, the way in which the proline residues are located along the sequence disfavors a productive P31-43-HLA-DQ binding.
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Affiliation(s)
- Lucia Falcigno
- Department of Pharmacy, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy;
| | - Luisa Calvanese
- Department of Pharmacy, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy;
| | - Mariangela Conte
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, 80131 Naples, Italy; (M.C.); (M.N.); (M.V.B.)
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, 80131 Naples, Italy
| | - Merlin Nanayakkara
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, 80131 Naples, Italy; (M.C.); (M.N.); (M.V.B.)
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, 80131 Naples, Italy
| | - Maria Vittoria Barone
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, 80131 Naples, Italy; (M.C.); (M.N.); (M.V.B.)
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, 80131 Naples, Italy
| | - Gabriella D’Auria
- Department of Pharmacy, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy;
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Amundarain MJ, Herrera MG, Zamarreño F, Viso JF, Costabel MD, Dodero VI. Molecular mechanisms of 33-mer gliadin peptide oligomerisation. Phys Chem Chem Phys 2019; 21:22539-22552. [DOI: 10.1039/c9cp02338k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The 33-mer gliadin peptide oligomerizes driven by its non-ionic polar character, flexible PPII secondary structure and stable glutamine H-bonds.
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Affiliation(s)
- María Julia Amundarain
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | | | - Fernando Zamarreño
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | - Juan Francisco Viso
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | - Marcelo D. Costabel
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | - Verónica I. Dodero
- Universität Bielefeld
- Fakultät für Chemie
- Organische Chemie
- 33615 Bielefeld
- Germany
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11
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Abstract
Gluten‐related disorders are a complex group of diseases that involve the activation of the immune system triggered by the ingestion of gluten. Among these, celiac disease, with a prevalence of 1 %, is the most investigated, but recently, a new pathology, named nonceliac gluten sensitivity, was reported with a general prevalence of 7 %. Finally, there other less‐prevalent gluten‐related diseases such as wheat allergy, gluten ataxia, and dermatitis herpetiformis (with an overall prevalence of less than 0.1 %). As mentioned, the common molecular trigger is gluten, a complex mixture of storage proteins present in wheat, barley, and a variety of oats that are not fully degraded by humans. The most‐studied protein related to disease is gliadin, present in wheat, which possesses in its sequence many pathological fragments. Despite a lot of effort to treat these disorders, the only effective method is a long‐life gluten‐free diet. This Review summarizes the actual knowledge of gluten‐related disorders from a translational chemistry point of view. We discuss what is currently known from the literature about the interaction of gluten with the gut and the critical host responses it evokes and, finally, connect them to our current and novel molecular understanding of the supramolecular organization of gliadin and the 33‐mer gliadin peptide fragment under physiological conditions.
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Affiliation(s)
- Karen M Lammers
- Laboratory Immunogenetics, Department of Medical Microbiology and Infection Control VU University Medical Center 1081 Amsterdam Netherlands
| | - Maria G Herrera
- Faculty of Pharmacy and Biochemistry Institute of biological chemistry and Physicochemical CONICET-University of Buenos Aires Junín 956 C1113AAD Buenos Aires Argentina
| | - Veronica I Dodero
- Department of Chemistry, Organic Chemistry III Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany
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12
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Darewicz M, Dziuba J, Minkiewicz P. Computational Characterisation and Identification of Peptides for in silico Detection of Potentially Celiac-Toxic Proteins. FOOD SCI TECHNOL INT 2016. [DOI: 10.1177/1082013207077954] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This work reports on in silico analysis of celiac-toxic peptide occurrence in proteins. The toxic properties of celiac disease are linked to the presence of specific amino acid sequences and the properties of their environment. The analysed celiac-toxic peptides were found to be predominated by unordered structures of random coil and β-turns. Proline and glutamine-rich amino acid sequences from hydrophilic β-turns were exposed on the surface of the precursor proteins. The sequence motifs represented by gluten peptide epitopes or tetrapeptides with surroundings seem to represent an immunodominant structure. The application of MS BLAST software enabled identification of a few fragments with high degrees of identity to the toxic peptides in one protein sequence. Rich sources of celiac-disease-potentiating peptides were wheat gliadins, barley hordeins and rye secalins as well as low-molecular weight fractions of glutenin. In addition, amino acid sequences with a high degree of identity to the toxic peptides examined were detected in maize zein, oat avenin, protein of rice, yeast and chicken muscles, as well as β-casein and galanin.
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Affiliation(s)
- M. Darewicz
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Pl. Cieszyński 1, 10-726 Olsztyn, Poland
| | - J. Dziuba
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Pl. Cieszyński 1, 10-726 Olsztyn, Poland,
| | - P. Minkiewicz
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Pl. Cieszyński 1, 10-726 Olsztyn, Poland
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13
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Herrera MG, Zamarreño F, Costabel M, Ritacco H, Hütten A, Sewald N, Dodero VI. Circular dichroism and electron microscopy studies in vitro of 33-mer gliadin peptide revealed secondary structure transition and supramolecular organization. Biopolymers 2016; 101:96-106. [PMID: 23703327 DOI: 10.1002/bip.22288] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/07/2013] [Accepted: 05/09/2013] [Indexed: 12/17/2022]
Abstract
Gliadin, a protein present in wheat, rye, and barley, undergoes incomplete enzymatic degradation during digestion, producing an immunogenic 33-mer peptide, LQLQPF(PQPQLPY)3 PQPQPF. The special features of 33-mer that provoke a break in its tolerance leading to gliadin sensitivity and celiac disease remains elusive. Herein, it is reported that 33-mer gliadin peptide was not only able to fold into polyproline II secondary structure but also depending on concentration resulted in conformational transition and self-assembly under aqueous condition, pH 7.0. A 33-mer dimer is presented as one initial possible step in the self-assembling process obtained by partial electrostatics charge distribution calculation and molecular dynamics. In addition, electron microscopy experiments revealed supramolecular organization of 33-mer into colloidal nanospheres. In the presence of 1 mM sodium citrate, 1 mM sodium borate, 1 mM sodium phosphate buffer, 15 mM NaCl, the nanospheres were stabilized, whereas in water, a linear organization and formation of fibrils were observed. It is hypothesized that the self-assembling process could be the result of the combination of hydrophobic effect, intramolecular hydrogen bonding, and electrostatic complementarity due to 33-mer's high content of proline and glutamine amino acids and its calculated nonionic amphiphilic character. Although, performed in vitro, these experiments have revealed new features of the 33-mer gliadin peptide that could represent an important and unprecedented event in the early stage of 33-mer interaction with the gut mucosa prior to onset of inflammation. Moreover, these findings may open new perspectives for the understanding and treatment of gliadin intolerance disorders.
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Affiliation(s)
- María G Herrera
- Department of Chemistry, INQUISUR, National University of South, CONICET, Av. Alem 1253, 8000 Bahía Blanca, Argentina
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14
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Bruun SW, Josefsen K, Tanassi JT, Marek A, Pedersen MHF, Sidenius U, Haupt-Jorgensen M, Antvorskov JC, Larsen J, Heegaard NH, Buschard K. Large Gliadin Peptides Detected in the Pancreas of NOD and Healthy Mice following Oral Administration. J Diabetes Res 2016; 2016:2424306. [PMID: 27795959 PMCID: PMC5067331 DOI: 10.1155/2016/2424306] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/10/2016] [Indexed: 12/20/2022] Open
Abstract
Gluten promotes type 1 diabetes in nonobese diabetic (NOD) mice and likely also in humans. In NOD mice and in non-diabetes-prone mice, it induces inflammation in the pancreatic lymph nodes, suggesting that gluten can initiate inflammation locally. Further, gliadin fragments stimulate insulin secretion from beta cells directly. We hypothesized that gluten fragments may cross the intestinal barrier to be distributed to organs other than the gut. If present in pancreas, gliadin could interact directly with the immune system and the beta cells to initiate diabetes development. We orally and intravenously administered 33-mer and 19-mer gliadin peptide to NOD, BALB/c, and C57BL/6 mice and found that the peptides readily crossed the intestinal barrier in all strains. Several degradation products were found in the pancreas by mass spectroscopy. Notably, the exocrine pancreas incorporated large amounts of radioactive label shortly after administration of the peptides. The study demonstrates that, even in normal animals, large gliadin fragments can reach the pancreas. If applicable to humans, the increased gut permeability in prediabetes and type 1 diabetes patients could expose beta cells directly to gliadin fragments. Here they could initiate inflammation and induce beta cell stress and thus contribute to the development of type 1 diabetes.
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MESH Headings
- Administration, Oral
- Animals
- Chromatography, Liquid
- Diabetes Mellitus, Type 1/immunology
- Electrophoresis, Polyacrylamide Gel
- Gliadin/immunology
- Gliadin/pharmacokinetics
- Inflammation
- Insulin/metabolism
- Insulin Secretion
- Insulin-Secreting Cells/immunology
- Insulin-Secreting Cells/metabolism
- Intestinal Mucosa/metabolism
- Male
- Mass Spectrometry
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Pancreas/metabolism
- Pancreas, Exocrine/metabolism
- Peptide Fragments/pharmacokinetics
- Permeability
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Affiliation(s)
| | - Knud Josefsen
- The Bartholin Institute, Rigshospitalet, Copenhagen N, Denmark
- *Knud Josefsen:
| | - Julia T. Tanassi
- Clinical Biochemistry, Immunology & Genetics, Statens Serum Institut, Copenhagen S, Denmark
| | - Aleš Marek
- The Hevesy Laboratory, DTU Nutech, Technical University of Denmark, Roskilde, Denmark
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
| | - Martin H. F. Pedersen
- The Hevesy Laboratory, DTU Nutech, Technical University of Denmark, Roskilde, Denmark
| | - Ulrik Sidenius
- Enzyme Purification and Characterization, Novozymes A/S, Bagsværd, Denmark
| | | | | | - Jesper Larsen
- The Bartholin Institute, Rigshospitalet, Copenhagen N, Denmark
| | - Niels H. Heegaard
- Clinical Biochemistry, Immunology & Genetics, Statens Serum Institut, Copenhagen S, Denmark
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15
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Fraccalvieri D, Motta S, Galliani G, Cavaletti L, Bonati L. Design of gliadin peptide analogues with low affinity for the celiac disease associated HLA–DQ2 protein. ACTA ACUST UNITED AC 2014; 10:2064-73. [DOI: 10.1039/c4mb00085d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A computational study on the binding of celiac disease relevant epitopes and their analogues identified the di-hydroxylation of Pro residues as a promising functionalization to lower the affinity for HLA–DQ2.5.
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Affiliation(s)
- Domenico Fraccalvieri
- Department of Earth and Environmental Sciences
- University of Milano-Bicocca
- 20126 Milano, Italy
| | - Stefano Motta
- Department of Earth and Environmental Sciences
- University of Milano-Bicocca
- 20126 Milano, Italy
| | | | - Linda Cavaletti
- FIIRV
- Fondazione Istituto Insubrico di Ricerca per la Vita
- 21040 Gerenzano, Italy
| | - Laura Bonati
- Department of Earth and Environmental Sciences
- University of Milano-Bicocca
- 20126 Milano, Italy
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16
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Unudurthi SD, Hotta K, Kim CY. Engineering the polyproline II propensity of a class II major histocompatibility complex ligand peptide. ACS Chem Biol 2013; 8:2383-7. [PMID: 24001370 DOI: 10.1021/cb400594q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Our immune system constantly samples peptides found inside the body as a means to detect foreign pathogens, infected cells, and tumorous cells. T cells, which carry out the critical task of distinguishing self from nonself peptides, can only survey peptides that are presented by the major histocompatibility complex protein. We investigated how the secondary structure of a peptide, namely, the polyproline II helix content, influences major histocompatibility complex binding. We synthesized 12 analogues of the wheat gluten derived α-I-gliadin peptide and tested their binding to the celiac disease associated HLA-DQ2 protein. Our analogue library represents a broad spectrum of polyproline II propensities, ranging from random coil structure to high polyproline II helix content. Overall, there was no noticeable correlation between the peptide polyproline II helix content and HLA-DQ2 binding. One analogue peptide, which has low polyproline II helix content, showed a 4.5-fold superior binding compared to native α-I-gliadin.
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Affiliation(s)
- Sathya Dev Unudurthi
- Department of Biological
Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
| | - Kinya Hotta
- Department of Biological
Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
| | - Chu-Young Kim
- Department of Biological
Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
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17
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Byrne C, Miclet E, Broutin I, Gallo D, Pelekanou V, Kampa M, Castanas E, Leclercq G, Jacquot Y. Identification of polyproline II regions derived from the proline-rich nuclear receptor coactivators PNRC and PNRC2: new insights for ERα coactivator interactions. Chirality 2013; 25:628-42. [PMID: 23925889 DOI: 10.1002/chir.22188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 04/12/2013] [Indexed: 11/07/2022]
Abstract
Protein-protein interactions are crucial for signal transductions required for cell differentiation and proliferation. Their modulation is therefore key to the development of therapeutic alternatives, particularly in the context of cancer. According to literature data, the polyproline-rich nuclear receptor coactivators PNRC and PNRC2 interact with estrogen receptor (ERα) through their PxxP SH3-binding motifs. In a search to identify the molecular features governing this interaction, we explored using electronic circular dichroism (ECD) spectroscopy and molecular dynamics (MD) calculations, the capacity of a range of putative biologically active peptides derived from these proteins and containing this PxxP motif(s) to form polyproline II (PPII) domains. An additional more exhaustive structural study on a lead PPII peptide was also performed using 2D nuclear magnetic resonance (NMR) spectroscopy. With the exception of one of all the investigated peptides (PNRC-D), binding assays failed to detect any affinity for Grb2 SH3 domains, suggesting that PPII motifs issued from Grb2 antagonists have a binding mode distinct from those derived from Grb2 agonists. Instead, the peptides revealed a competitive binding ability against a synthetic peptide (ERα17p) with a putative PPII-cognate domain located within a coregulator recruitment region of ERα (AF-2 site). Our work, which constitutes the first structure-related interaction study concerning PNRC and PNRC2, supports not only the existence of PxxP-induced PPII sequences in these coregulators, but also confirms the presence of a PPII recognition site in the AF-2 of the steroid receptor ERα, a region important for transcription regulation.
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Affiliation(s)
- C Byrne
- Laboratoire des BioMolécules (LBM), CNRS - UMR 7203, Ecole Normale Supérieure / Université Pierre et Marie Curie 24, rue Lhomond, 75231, Paris Cedex 05, France; Fondation Pierre-Gilles de Gennes pour la Recherche, 29, rue d'Ulm, 75005, Paris, France
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18
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Chaubet G, Coursindel T, Morelli X, Betzi S, Roche P, Guari Y, Lebrun A, Toupet L, Collette Y, Parrot I, Martinez J. Stereoselective synthesis of original spirolactams displaying promising folded structures. Org Biomol Chem 2013; 11:4719-26. [DOI: 10.1039/c3ob40643a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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19
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Buchko GW, Bekhazi J, Cort JR, Valentine NB, Snead ML, Shaw WJ. 1H, 13C, and 15N resonance assignments of murine amelogenin, an enamel biomineralization protein. BIOMOLECULAR NMR ASSIGNMENTS 2008; 2:89-91. [PMID: 19081741 PMCID: PMC2600544 DOI: 10.1007/s12104-008-9092-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Amelogenin is the predominant matrix protein in developing dental enamel. Making extensive use of residue specific 15N-labeled amino acids samples, the majority of the main and side chain resonances for murine amelogenin were assigned in 2% aqueous acetic acid at pH 3.0.
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Affiliation(s)
- Garry W. Buchko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jacky Bekhazi
- Chemical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Mail-Stop K2-57, Richland, WA 99352, USA
| | - John R. Cort
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Nancy B. Valentine
- Chemical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Mail-Stop K2-57, Richland, WA 99352, USA
| | - Malcolm L. Snead
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Wendy J. Shaw
- Chemical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Mail-Stop K2-57, Richland, WA 99352, USA
- e-mail:
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20
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Eri R, Kodumudi KN, Summerlin DJ, Srinivasan M. Suppression of colon inflammation by CD80 blockade: evaluation in two murine models of inflammatory bowel disease. Inflamm Bowel Dis 2008; 14:458-70. [PMID: 18186109 DOI: 10.1002/ibd.20344] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND Human inflammatory bowel disease (IBD) is a chronic condition mediated by aberrant immune responses to the luminal antigens by activated CD4+ T cells. The CD80/CD86:CD28/CD152 costimulatory pathways transmit signals critical for T cell activation and suppression. Macrophages and epithelial cells are the chief antigen-presenting cells in the gut. Macrophages from the IBD colon express significantly elevated levels of CD80 and CD86 costimulatory molecules. The CD28-CD80 interaction primarily participates in breaking the tolerance and inducing the immune response in murine models of colitis. Blockade of CD80-costimulatory axis is an attractive strategy in the treatment of IBD. METHODS Incorporating the structural information of the CD80:CD152 complex together with the preferences of interface residues to form polyproline type II helix, we designed novel peptide agents that selectively blocked CD80 receptor interactions. RESULTS Administration of CD80 blocking agent at the time of adoptive transfer prevented the SCID mice from CD4+CD45Rb(high) T-cell mediated colitis. Significantly, CD80-CAP (competitive antagonist peptide) treatment suppressed established inflammation in TNBS-induced colitis, a model for Th1-mediated Crohn's disease. The colons of the mice receiving the CD80 blocking agent appeared unaffected macroscopically and exhibited negligible microscopic inflammation. The CD80-CAP treatment was associated with significantly reduced Th1 cytokines in the colon. CONCLUSIONS The CD80 blocking peptide appeared to mediate protection against colitis by inducing Th2 skewing of the cytokine response.
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Affiliation(s)
- Rajaraman Eri
- Department of Oral Pathology, Medicine and Radiology, School of Dentistry, Indiana University Purdue University at Indianapolis, Indianapolis, Indiana 46202, USA
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21
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Tunheim G, Schjetne KW, Rasmussen IB, Sollid LM, Sandlie I, Bogen B. Recombinant antibodies for delivery of antigen: a single loop between -strands in the constant region can accommodate long, complex and tandem T cell epitopes. Int Immunol 2008; 20:295-306. [DOI: 10.1093/intimm/dxm141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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22
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Chugh J, Sharma S, Hosur RV. Pockets of short-range transient order and restricted topological heterogeneity in the guanidine-denatured state ensemble of GED of dynamin. Biochemistry 2007; 46:11819-32. [PMID: 17910478 DOI: 10.1021/bi701280p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nature and variety in the denatured state of a protein, a non-native state under a given set of conditions, has been a subject of intense debate. Here, using multidimensional NMR, we have characterized the 6 M Gdn-HCl-denatured state of GED, the assembly domain of dynamin. Even under such strongly denaturing conditions, we detected the presence of conformations in slow exchange on the NMR chemical shift time scale. Although the GED oligomer as well as the SDS-denatured monomeric GED were seen to be predominantly helical [Chugh et al. (2006) FEBS J. 273, 388-397], the 6 M Gdn-HCl-denatured GED has largely beta-structural preferences. However, against such a background, we could detect the presence of a population with a short helical stretch (Arg42-Ile47) in the ensemble. The 1H-1H NOEs suggested presence of pockets of transient short-range order along the chain. Put together these segments may lead to a rather small number of interconverting topologically distinguishable ensembles. Spectral density analysis of 15N relaxation rates and {1H}-15N NOE, measured at 600 and 800 MHz, and comparison of J(0) with hydrophobic patches calculated using AABUF approach, indicated presence of four domains of slow motions. These coincided to a large extent with those showing significant Rex. Additionally, a proline residue in the connection between two of these domains seems to cause a fast hinge motion. These observations help enhance our understanding of protein denatured states, and of folding concepts, in general.
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Affiliation(s)
- Jeetender Chugh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
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23
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Lakshminarayanan R, Fan D, Du C, Moradian-Oldak J. The role of secondary structure in the entropically driven amelogenin self-assembly. Biophys J 2007; 93:3664-74. [PMID: 17704165 PMCID: PMC2072069 DOI: 10.1529/biophysj.107.113936] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Amelogenin, the major extracellular enamel matrix protein, plays critical roles in controlling enamel mineralization. This generally hydrophobic protein self-assembles to form nanosphere structures under certain solution conditions. To gain clearer insight into the mechanisms of amelogenin self-assembly, we first investigated the occurrences of secondary structures within its sequence. By applying isothermal titration calorimetry (ITC), we determined the thermodynamic parameters associated with protein-protein interactions and with conformational changes during self-assembly. The recombinant porcine full length (rP172) and a truncated amelogenin lacking the hydrophilic C-terminal (rP148) were used. Circular dichroism (CD) measurements performed at low concentrations (<5 microM) revealed the presence of the polyproline-type II (PPII) conformation in both amelogenins in addition to alpha-helix and unordered conformations. Structural transition from PPII/unordered to beta-sheet was observed for both proteins at higher concentrations (>62.5 microM) and upon self-assembly. ITC measurements indicated that the self-assembly of rP172 and rP148 is entropically driven (+DeltaS(A)) and energetically favorable (-DeltaG(A)). The magnitude of enthalpy (DeltaH(A)) and entropy changes of assembly (DeltaS(A)) were smaller for rP148 than rP172, whereas the Gibbs free energy change of assembly (DeltaG(A)) was not significantly different. It was found that rP172 had higher PPII content than rP148, and the monomer-multimer equilibrium for rP172 was observed in a narrower protein concentration range when compared to rP148. The large positive enthalpy and entropy changes in both cases are attributed to the release of ordered water molecules and the associated entropy gain (due to the hydrophobic effect). These findings suggest that PPII conformation plays an important role in amelogenin self-assembly and that rP172 assembly is more favorable than rP148. The data are direct evidence for the notion that hydrophobic interactions are the main driving force for amelogenin self-assembly.
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Affiliation(s)
- Rajamani Lakshminarayanan
- University of Southern California, School of Dentistry, Center for Craniofacial Molecular Biology, Los Angeles, California 90033, USA
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24
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Keresztessy Z, Csosz E, Hársfalvi J, Csomós K, Gray J, Lightowlers RN, Lakey JH, Balajthy Z, Fésüs L. Phage display selection of efficient glutamine-donor substrate peptides for transglutaminase 2. Protein Sci 2007; 15:2466-80. [PMID: 17075129 PMCID: PMC2242420 DOI: 10.1110/ps.051818406] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Understanding substrate specificity and identification of natural targets of transglutaminase 2 (TG2), the ubiquitous multifunctional cross-linking enzyme, which forms isopeptide bonds between protein-linked glutamine and lysine residues, is crucial in the elucidation of its physiological role. As a novel means of specificity analysis, we adapted the phage display technique to select glutamine-donor substrates from a random heptapeptide library via binding to recombinant TG2 and elution with a synthetic amine-donor substrate. Twenty-six Gln-containing sequences from the second and third biopanning rounds were susceptible for TG2-mediated incorporation of 5-(biotinamido)penthylamine, and the peptides GQQQTPY, GLQQASV, and WQTPMNS were modified most efficiently. A consensus around glutamines was established as pQX(P,T,S)l, which is consistent with identified substrates listed in the TRANSDAB database. Database searches showed that several proteins contain peptides similar to the phage-selected sequences, and the N-terminal glutamine-rich domain of SWI1/SNF1-related chromatin remodeling proteins was chosen for detailed analysis. MALDI/TOF and tandem mass spectrometry-based studies of a representative part of the domain, SGYGQQGQTPYYNQQSPHPQQQQPPYS (SnQ1), revealed that Q(6), Q(8), and Q(22) are modified by TG2. Kinetic parameters of SnQ1 transamidation (K(M)(app) = 250 microM, k(cat) = 18.3 sec(-1), and k(cat)/K(M)(app) = 73,200) classify it as an efficient TG2 substrate. Circular dichroism spectra indicated that SnQ1 has a random coil conformation, supporting its accessibility in the full-length parental protein. Added together, here we report a novel use of the phage display technology with great potential in transglutaminase research.
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Affiliation(s)
- Zsolt Keresztessy
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
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25
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Abstract
Celiac disease (CD) is an (auto)immunologically mediated intestinal intolerance against proteins from wheat (gluten) and related cereal proteins. Tissue transglutaminase (tTG) has been identified as the autoantigen in CD. Although ultimate diagnosis is based on histological analysis of small intestinal mucosa obtained via tissue biopsy, assessment of autoantibodies can provide substantial help in the evaluation of CD. Gliadin antibodies are directed against the native disease-provoking cereal proteins. Despite their initial usefulness, these antibodies have lost diagnostic importance due to their poor specificity and sensitivity as CD markers. Recently, it was found, however, that gliadin antibodies from sera of patients with active CD preferentially recognized deamidated gliadin peptides. The use of deamidated gliadin peptides in immunoassays has significantly improved the usefulness of gliadin antibodies in diagnosis of CD to that observed with autoantibody assay methods (endomysium antibodies, antibodies against tTG). The antibody epitopes (B-cell epitopes) reflect substrate specificity of tTG and resemble peptide sequences known to be strongly T-cell stimulatory (T-cell epitopes) in CD. The assay applying deamidated gliadin peptides measures a new species of antibodies, which is different from conventional gliadin antibodies as well as from autoantibodies and will likely provide new information on pathophysiological mechanisms of CD.
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Affiliation(s)
- Thomas Mothes
- Institute for Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital and Medical Faculty of the University, Leipzig, Germany
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26
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Affiliation(s)
- Zhengshuang Shi
- Department of Chemistry, New York University, 100 Washington Place, New York, New York 10003-5180, USA
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27
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Kumar A, Srivastava S, Mishra RK, Mittal R, Hosur RV. Local structural preferences and dynamics restrictions in the urea-denatured state of SUMO-1: NMR characterization. Biophys J 2006; 90:2498-509. [PMID: 16415059 PMCID: PMC1403170 DOI: 10.1529/biophysj.105.071746] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2005] [Accepted: 12/29/2005] [Indexed: 12/31/2022] Open
Abstract
We have investigated by multidimensional NMR the structural and dynamic characteristics of the urea-denatured state of activated SUMO-1, a 97-residue protein belonging to the growing family of ubiquitin-like proteins involved in post-translational modifications. Complete backbone amide and 15N resonance assignments were obtained in the denatured state by using HNN and HN(C)N experiments. These enabled other proton assignments from TOCSY-HSQC spectra. Secondary Halpha chemical shifts and 1H-1H NOE indicate that the protein chain in the denatured state has structural preferences in the broad beta-domain for many residues. Several of these are seen to populate the (phi,psi) space belonging to polyproline II structure. Although there is no evidence for any persistent structures, many contiguous stretches of three or more residues exhibit structural propensities suggesting possibilities of short-range transient structure formation. The hetero-nuclear 1H-15N NOEs are extremely weak for most residues, except for a few at the C-terminal, and the 15N relaxation rates show sequence-wise variation. Some of the regions of slow motions coincide with those of structural preferences and these are interspersed by highly flexible residues. The implications of these observations for the early folding events starting from the urea-denatured state of activated SUMO-1 have been discussed.
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Affiliation(s)
- Ashutosh Kumar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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28
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Satheshkumar PS, Gayathri P, Prasad K, Savithri HS. "Natively unfolded" VPg is essential for Sesbania mosaic virus serine protease activity. J Biol Chem 2005; 280:30291-300. [PMID: 15944159 DOI: 10.1074/jbc.m504122200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Polyprotein processing is a major strategy used by many plant and animal viruses to maximize the number of protein products obtainable from a single open reading frame. In Sesbania mosaic virus, open reading frame-2 codes for a polyprotein that is cleaved into different functional proteins in cis by the N-terminal serine protease domain. The soluble protease domain lacking 70-amino-acid residues from the N terminus (deltaN70Pro, where Pro is protease) was not active in trans. Interestingly, the protease domain exhibited trans-catalytic activity when VPg (viral protein genome-linked) was present at the C terminus. Bioinformatic analysis of VPg primary structure suggested that it could be a disordered protein. Biophysical studies validated this observation, and VPg resembled "natively unfolded" proteins. CD spectral analysis showed that the deltaN70Pro-VPg fusion protein had a characteristic secondary structure with a 230 nm positive CD peak. Mutation of Trp-43 in the VPg domain to phenylalanine abrogated the positive peak with concomitant loss in cis- and trans-proteolytic activity of the deltaN70Pro domain. Further, deletion of VPg domain from the polyprotein completely abolished proteolytic processing. The results suggested a novel mechanism of activation of the protease, wherein the interaction between the natively unfolded VPg and the protease domains via aromatic amino acid residues alters the conformation of the individual domains and the active site of the protease. Thus, VPg is an activator of protease in Sesbania mosaic virus, and probably by this mechanism, the polyprotein processing could be regulated in planta.
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29
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Srinivasan M, Lu D, Eri R, Brand DD, Haque A, Blum JS. CD80 binding polyproline helical peptide inhibits T cell activation. J Biol Chem 2004; 280:10149-55. [PMID: 15598660 DOI: 10.1074/jbc.m409521200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The critical role played by the CD28/CD152-CD80/CD86 costimulatory molecules in mediating T cell activation and suppression provides attractive targets for therapeutic strategies. CD28 and CD152 share a conserved polyproline motif in the ligand-binding region. Similar proline-rich regions in globular domains preferentially adopt a polyproline type II (PP) helical conformation and are involved in transient (II)protein-protein interactions. Interestingly, in the human CD80-CD152 complex, Pro(102) of CD152 restricts the preceding proline to PP(II) helix in the binding orientation in relation to the shallow binding pocket of CD80. Peptide agents derived from binding sites of receptors that mimic the bioactive conformation have been shown to block receptor-ligand interactions. Contact preferences of the interface amino acids at the protein-protein interaction sites and the propensity of each residue to form PP(II) helix were integrated in the design of novel peptide agents referred to as CD80 competitive antagonist peptides. Structural and functional studies suggest potential therapeutic value for select CD80 competitive antagonist peptides.
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MESH Headings
- Animals
- Antigens, CD/chemistry
- Antigens, Differentiation/chemistry
- Arthritis, Experimental
- B7-1 Antigen/chemistry
- B7-1 Antigen/metabolism
- B7-2 Antigen
- Binding, Competitive
- CD28 Antigens/chemistry
- CTLA-4 Antigen
- Cell Proliferation
- Circular Dichroism
- Collagen/metabolism
- Dose-Response Relationship, Drug
- Enzyme-Linked Immunosorbent Assay
- Humans
- Ligands
- Lymph Nodes/pathology
- Lymphocyte Activation
- Membrane Glycoproteins/chemistry
- Mice
- Mice, Inbred BALB C
- Mice, Inbred DBA
- Models, Molecular
- Peptides/chemistry
- Proline/chemistry
- Protein Binding
- Protein Conformation
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Structure-Activity Relationship
- T-Lymphocytes/metabolism
- Time Factors
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Affiliation(s)
- Mythily Srinivasan
- Department of Oral Pathology, School of Dentistry, 1121 W. Michigan St., Indianapolis 46202, USA.
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Kim CY, Quarsten H, Bergseng E, Khosla C, Sollid LM. Structural basis for HLA-DQ2-mediated presentation of gluten epitopes in celiac disease. Proc Natl Acad Sci U S A 2004; 101:4175-9. [PMID: 15020763 PMCID: PMC384714 DOI: 10.1073/pnas.0306885101] [Citation(s) in RCA: 296] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2003] [Indexed: 01/05/2023] Open
Abstract
Celiac disease, also known as celiac sprue, is a gluten-induced autoimmune-like disorder of the small intestine, which is strongly associated with HLA-DQ2. The structure of DQ2 complexed with an immunogenic epitope from gluten, QLQPFPQPELPY, has been determined to 2.2-A resolution by x-ray crystallography. The glutamate at P6, which is formed by tissue transglutaminase-catalyzed deamidation, is an important anchor residue as it participates in an extensive hydrogen-bonding network involving Lys-beta71 of DQ2. The gluten peptide-DQ2 complex retains critical hydrogen bonds between the MHC and the peptide backbone despite the presence of many proline residues in the peptide that are unable to participate in amide-mediated hydrogen bonds. Positioning of proline residues such that they do not interfere with backbone hydrogen bonding results in a reduction in the number of registers available for gluten peptides to bind to MHC class II molecules and presumably impairs the likelihood of establishing favorable side-chain interactions. The HLA association in celiac disease can be explained by a superior ability of DQ2 to bind the biased repertoire of proline-rich gluten peptides that have survived gastrointestinal digestion and that have been deamidated by tissue transglutaminase. Finally, surface-exposed proline residues in the proteolytically resistant ligand were replaced with functionalized analogs, thereby providing a starting point for the design of orally active agents for blocking gluten-induced toxicity.
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Affiliation(s)
- Chu-Young Kim
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
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31
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Tamburro AM, Bochicchio B, Pepe A. Dissection of human tropoelastin: exon-by-exon chemical synthesis and related conformational studies. Biochemistry 2004; 42:13347-62. [PMID: 14609345 DOI: 10.1021/bi034837t] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polypeptide sequences encoding the single exons of human tropoelastin were synthesized and their conformations were studied in different solvents and at different temperatures by CD and (1)H NMR. The results demonstrated the presence of labile conformations such as poly-proline II helix (PPII) and beta-turns whose stability is strongly dependent on the microenvironment. Stable, periodic structures, such as alpha-helices, are only present in the poly-alanine cross-linking domains. These findings give a strong experimental basis to the understanding of the molecular mechanism of elasticity of elastin. In particular, they strongly support the description of the native relaxed state of the protein in terms of trans-conformational equilibria between extended and folded structures as previously proposed [Debelle, L., and Tamburro, A. M. (1999) Int. J. Biochem. Cell. Biol. 31, 261-272].
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Affiliation(s)
- Antonio M Tamburro
- Department of Chemistry, Università della Basilicata, Via N. Sauro 85, 85100 Potenza, Italy.
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