1
|
Zhuang J, Shang Q, Rastinejad F, Wu D. Decoding Allosteric Control in Hypoxia-Inducible Factors. J Mol Biol 2024; 436:168352. [PMID: 37935255 DOI: 10.1016/j.jmb.2023.168352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/10/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
The mammalian family of basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) transcription factors possess the ability to sense and respond to diverse environmental and physiological cues. These proteins all share a common structural framework, comprising a bHLH domain, two PAS domains, and transcriptional activation or repression domain. To function effectively as transcription factors, members of the family must form dimers, bringing together bHLH segments to create a functional unit that allows for DNA response element binding. The significance of bHLH-PAS family is underscored by their involvement in many major human diseases, offering potential avenues for therapeutic intervention. Notably, the clear identification of ligand-binding cavities within their PAS domains enables the development of targeted small molecules. Two examples are Belzutifan, targeting hypoxia-inducible factor (HIF)-2α, and Tapinarof, targeting the aryl hydrocarbon receptor (AHR), both of which have gained regulatory approval recently. Here, we focus on the HIF subfamily. The crystal structures of all three HIF-α proteins have been elucidated, revealing their bHLH and tandem PAS domains are used to engage their dimerization partner aryl hydrocarbon receptor nuclear translocator (ARNT, also called HIF-1β). A broad range of recent findings point to a shared allosteric modulation mechanism among these proteins, whereby small-molecules at the PAS-B domains exert direct influence over the HIF-α transcriptional functions. As our understanding of the architectural and allosteric mechanisms of bHLH-PAS proteins continues to advance, the possibility of discovering new therapeutic drugs becomes increasingly promising.
Collapse
Affiliation(s)
- Jingjing Zhuang
- Marine College, Shandong University, Weihai 264209, China; Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qinghong Shang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Fraydoon Rastinejad
- Target Discovery Institute, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford OX3 7FZ, UK.
| | - Dalei Wu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| |
Collapse
|
2
|
Vergouwen DPC, Ten Berge JC, Guzel C, van den Bosch TPP, Verdijk RM, Rothova A, Luider TM, Schreurs MWJ. Scleral Proteome in Noninfectious Scleritis Unravels Upregulation of Filaggrin-2 and Signs of Neovascularization. Invest Ophthalmol Vis Sci 2023; 64:27. [PMID: 36930145 PMCID: PMC10036950 DOI: 10.1167/iovs.64.3.27] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Purpose Scleritis is a severe inflammatory ocular disorder with unknown pathogenesis. We investigated healthy sclera as well as sclera affected by noninfectious scleritis for differentially expressed proteins using a mass spectrometry approach. Methods We collected scleral samples of enucleated eyes due to severe noninfectious scleritis (n = 3), and control scleral tissues (n = 5), all exenterated eyes for eyelid carcinomas (n = 4), or choroidal melanoma (n = 1) without scleral invasion. Samples were prepared for the nano liquid-chromatography mass spectrometer (LC-MS), data were analyzed using proteomics software (Scaffold), and is available via ProteomeXchange (identifier PXD038727). Samples were also stained for immuno-histopathological evaluation. Results Mass spectrometry identified 629 proteins within the healthy and diseased scleral tissues, whereof collagen type XII, VI, and I were the most abundantly expressed protein. Collagen type II-XII was also present. Filaggrin-2, a protein that plays a crucial role in epidermal barrier function, was found upregulated in all scleritis cases. In addition, other epithelial associated proteins were upregulated (such as keratin 33b, 34, and 85, epiplakin, transglutaminase-3, galectin 7, and caspase-14) in scleritis. Further, upregulated proteins involved in regulation of the cytoskeleton (vinculin and myosin 9), and housekeeping proteins were found (elongation factor-2 and cytoplasmic dynein 1) in our study. Upregulation of filaggrin-2 and myosin-9 was confirmed with immunohistochemistry, the latter protein showing co-localization with the endothelial cell marker ETC-related gene (ERG), indicating neovascularization in scleral tissue affected by scleritis. Conclusions We found upregulation of filaggrin-2 and signs of neovascularization in scleral tissue of patients with noninfectious scleritis. Further research, ideally including more scleritis cases, is needed to validate our findings.
Collapse
Affiliation(s)
- Daphne P C Vergouwen
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Josianne C Ten Berge
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Coskun Guzel
- Department of Neurology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Thierry P P van den Bosch
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Robert M Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Aniki Rothova
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marco W J Schreurs
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| |
Collapse
|
3
|
Su H, Luo Y, Sun J, Liu X, Ling S, Xu B, Zhang Y, Liu J, Li W, Wang B, Yao X. Transglutaminase 3 Promotes Skin Inflammation in Atopic Dermatitis by Activating Monocyte-Derived Dendritic Cells via DC-SIGN. J Invest Dermatol 2020; 140:370-379.e8. [DOI: 10.1016/j.jid.2019.07.703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 07/01/2019] [Accepted: 07/12/2019] [Indexed: 01/15/2023]
|
4
|
Eckert RL. Transglutaminase 2 takes center stage as a cancer cell survival factor and therapy target. Mol Carcinog 2019; 58:837-853. [PMID: 30693974 DOI: 10.1002/mc.22986] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/14/2022]
Abstract
Transglutaminase 2 (TG2) has emerged as a key cancer cell survival factor that drives epithelial to mesenchymal transition, angiogenesis, metastasis, inflammation, drug resistance, cancer stem cell survival and stemness, and invasion and migration. TG2 can exist in a GTP-bound signaling-active conformation or in a transamidase-active conformation. The GTP bound conformation of TG2 contributes to cell survival and the transamidase conformation can contribute to cell survival or death. We present evidence suggesting that TG2 has a role in human cancer, summarize what is known about the TG2 mechanism of action in a range of cancer types, and discuss TG2 as a cancer therapy target.
Collapse
Affiliation(s)
- Richard L Eckert
- Department of Biochemistry and Molecular Biology, Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| |
Collapse
|
5
|
Klöck C, Khosla C. Regulation of the activities of the mammalian transglutaminase family of enzymes. Protein Sci 2012; 21:1781-91. [PMID: 23011841 DOI: 10.1002/pro.2162] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 01/31/2023]
Abstract
Mammalian transglutaminases catalyze post-translational modifications of glutamine residues on proteins and peptides through transamidation or deamidation reactions. Their catalytic mechanism resembles that of cysteine proteases. In virtually every case, their enzymatic activity is modulated by elaborate strategies including controlled gene expression, allostery, covalent modification, and proteolysis. In this review, we focus on our current knowledge of post-translational regulation of transglutaminase activity by physiological as well as synthetic allosteric agents. Our discussion will primarily focus on transglutaminase 2, but will also compare and contrast its regulation with Factor XIIIa as well as transglutaminases 1 and 3. Potential structure-function relationships of known mutations in human transglutaminases are analyzed.
Collapse
Affiliation(s)
- Cornelius Klöck
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | |
Collapse
|
6
|
Prime ME, Andersen OA, Barker JJ, Brooks MA, Cheng RKY, Toogood-Johnson I, Courtney SM, Brookfield FA, Yarnold CJ, Marston RW, Johnson PD, Johnsen SF, Palfrey JJ, Vaidya D, Erfan S, Ichihara O, Felicetti B, Palan S, Pedret-Dunn A, Schaertl S, Sternberger I, Ebneth A, Scheel A, Winkler D, Toledo-Sherman L, Beconi M, Macdonald D, Muñoz-Sanjuan I, Dominguez C, Wityak J. Discovery and structure-activity relationship of potent and selective covalent inhibitors of transglutaminase 2 for Huntington's disease. J Med Chem 2012; 55:1021-46. [PMID: 22224594 DOI: 10.1021/jm201310y] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Tissue transglutaminase 2 (TG2) is a multifunctional protein primarily known for its calcium-dependent enzymatic protein cross-linking activity via isopeptide bond formation between glutamine and lysine residues. TG2 overexpression and activity have been found to be associated with Huntington's disease (HD); specifically, TG2 is up-regulated in the brains of HD patients and in animal models of the disease. Interestingly, genetic deletion of TG2 in two different HD mouse models, R6/1 and R6/2, results in improved phenotypes including a reduction in neuronal death and prolonged survival. Starting with phenylacrylamide screening hit 7d, we describe the SAR of this series leading to potent and selective TG2 inhibitors. The suitability of the compounds as in vitro tools to elucidate the biology of TG2 was demonstrated through mode of inhibition studies, characterization of druglike properties, and inhibition profiles in a cell lysate assay.
Collapse
|
7
|
Király R, Demény M, Fésüs L. Protein transamidation by transglutaminase 2 in cells: a disputed Ca2+-dependent action of a multifunctional protein. FEBS J 2011; 278:4717-39. [PMID: 21902809 DOI: 10.1111/j.1742-4658.2011.08345.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Transglutaminase 2 (TG2) is the first described cellular member of an enzyme family catalyzing Ca(2+)-dependent transamidation of proteins. During the last two decades its additional enzymatic (GTP binding and hydrolysis, protein disulfide isomerase, protein kinase) and non-enzymatic (multiple interactions in protein scaffolds) activities, which do not require Ca(2+) , have been recognized. It became a prevailing view that TG2 is silent as a transamidase, except in extreme stress conditions, in the intracellular environment characterized by low Ca(2+) and high GTP concentrations. To counter this presumption a critical review of the experimental evidence supporting the role of this enzymatic activity in cellular processes is provided. It includes the structural basis of TG2 regulation through non-canonical Ca(2+) binding sites, mechanisms making it sensitive to low Ca(2+) concentrations, techniques developed for the detection of protein transamidation in cells and examples of basic cellular phenomena as well as pathological conditions influenced by this irreversible post-translational protein modification.
Collapse
Affiliation(s)
- Róbert Király
- Department of Biochemistry and Molecular Biology, Apoptosis and Genomics Group of the Hungarian Academy of Sciences, University of Debrecen, Debrecen, Hungary
| | | | | |
Collapse
|
8
|
Walther DJ, Stahlberg S, Vowinckel J. Novel roles for biogenic monoamines: from monoamines in transglutaminase-mediated post-translational protein modification to monoaminylation deregulation diseases. FEBS J 2011; 278:4740-55. [DOI: 10.1111/j.1742-4658.2011.08347.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
9
|
Hoffner G, Vanhoutteghem A, André W, Djian P. Transglutaminase in epidermis and neurological disease or what makes a good cross-linking substrate. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2011; 78:97-160. [PMID: 22220473 DOI: 10.1002/9781118105771.ch3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Guylaine Hoffner
- Unité Propre de Recherche 2228 du Centre National de la Recherche Scientifique, Régulation de la Transcription et Maladies Génétiques, Université Paris Descartes, Paris, France
| | | | | | | |
Collapse
|
10
|
Bergamini CM, Collighan RJ, Wang Z, Griffin M. Structure and regulation of type 2 transglutaminase in relation to its physiological functions and pathological roles. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2011; 78:1-46. [PMID: 22220471 DOI: 10.1002/9781118105771.ch1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Carlo M Bergamini
- Deparment of Biochemistry and Molecular Biology, University of Ferrara, Italy
| | | | | | | |
Collapse
|
11
|
Reiss K, Kirchner E, Gijzen M, Zocher G, Löffelhardt B, Nürnberger T, Stehle T, Brunner F. Structural and phylogenetic analyses of the GP42 transglutaminase from Phytophthora sojae reveal an evolutionary relationship between oomycetes and marine Vibrio bacteria. J Biol Chem 2011; 286:42585-42593. [PMID: 21994936 DOI: 10.1074/jbc.m111.290544] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Transglutaminases (TGases) are ubiquitous enzymes that catalyze selective cross-linking between protein-bound glutamine and lysine residues; the resulting isopeptide bond confers high resistance to proteolysis. Phytophthora sojae, a pathogen of soybean, secretes a Ca(2+)-dependent TGase (GP42) that is activating defense responses in both host and non-host plants. A GP42 fragment of 13 amino acids, termed Pep-13, was shown to be absolutely indispensable for both TGase and elicitor activity. GP42 does not share significant primary sequence similarity with known TGases from mammals or bacteria. This suggests that GP42 has evolved novel structural and catalytic features to support enzymatic activity. We have solved the crystal structure of the catalytically inactive point mutant GP42 (C290S) at 2.95 Å resolution and identified residues involved in catalysis by mutational analysis. The protein comprises three domains that assemble into an elongated structure. Although GP42 has no structural homolog, its core region displays significant similarity to the catalytic core of the Mac-1 cysteine protease from Group A Streptococcus, a member of the papain-like superfamily of cysteine proteases. Proteins that are taxonomically related to GP42 are only present in plant pathogenic oomycetes belonging to the order of the Peronosporales (e.g. Phytophthora, Hyaloperonospora, and Pythium spp.) and in marine Vibrio bacteria. This suggests that a lateral gene transfer event may have occurred between bacteria and oomycetes. Our results offer a basis to design and use highly specific inhibitors of the GP42-like TGase family that may impair the growth of important oomycete and bacterial pathogens.
Collapse
Affiliation(s)
- Kerstin Reiss
- Interfakultäres Institut für Biochemie, Universität Tübingen, 72076 Tübingen, Germany
| | - Eva Kirchner
- Interfakultäres Institut für Biochemie, Universität Tübingen, 72076 Tübingen, Germany
| | - Mark Gijzen
- Agri-Food Canada, London, Ontario N5V 4T3, Canada
| | - Georg Zocher
- Interfakultäres Institut für Biochemie, Universität Tübingen, 72076 Tübingen, Germany
| | - Birgit Löffelhardt
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, 72076 Tübingen, Germany
| | - Thorsten Nürnberger
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, 72076 Tübingen, Germany
| | - Thilo Stehle
- Interfakultäres Institut für Biochemie, Universität Tübingen, 72076 Tübingen, Germany; Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.
| | - Frédéric Brunner
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, 72076 Tübingen, Germany.
| |
Collapse
|
12
|
Transglutaminase 6: a protein associated with central nervous system development and motor function. Amino Acids 2011; 44:161-77. [PMID: 21984379 PMCID: PMC3535377 DOI: 10.1007/s00726-011-1091-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 09/16/2011] [Indexed: 12/20/2022]
Abstract
Transglutaminases (TG) form a family of enzymes that catalyse various post-translational modifications of glutamine residues in proteins and peptides including intra- and intermolecular isopeptide bond formation, esterification and deamidation. We have characterized a novel member of the mammalian TG family, TG6, which is expressed in a human carcinoma cell line with neuronal characteristics and in mouse brain. Besides full-length protein, alternative splicing results in a short variant lacking the second β-barrel domain in man and a variant with truncated β-sandwich domain in mouse. Biochemical data show that TG6 is allosterically regulated by Ca2+ and guanine nucleotides. Molecular modelling indicates that TG6 could have Ca2+ and GDP-binding sites related to those of TG3 and TG2, respectively. Localization of mRNA and protein in the mouse identified abundant expression of TG6 in the central nervous system. Analysis of its temporal and spatial pattern of induction in mouse development indicates an association with neurogenesis. Neuronal expression of TG6 was confirmed by double-labelling of mouse forebrain cells with cell type-specific markers. Induction of differentiation in mouse Neuro 2a cells with NGF or dibutyryl cAMP is associated with an upregulation of TG6 expression. Familial ataxia has recently been linked to mutations in the TGM6 gene. Autoantibodies to TG6 were identified in immune-mediated ataxia in patients with gluten sensitivity. These findings suggest a critical role for TG6 in cortical and cerebellar neurons.
Collapse
|
13
|
Evidences for a role of protein cross-links in transglutaminase-related disease. Amino Acids 2011; 42:975-86. [DOI: 10.1007/s00726-011-1011-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 05/24/2011] [Indexed: 01/13/2023]
|
14
|
Yamane A, Fukui M, Sugimura Y, Itoh M, Alea MP, Thomas V, El Alaoui S, Akiyama M, Hitomi K. Identification of a preferred substrate peptide for transglutaminase 3 and detection of in situ activity in skin and hair follicles. FEBS J 2010; 277:3564-74. [DOI: 10.1111/j.1742-4658.2010.07765.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
15
|
Thibaut S, Cavusoglu N, de Becker E, Zerbib F, Bednarczyk A, Schaeffer C, van Dorsselaer A, Bernard BA. Transglutaminase-3 Enzyme: A Putative Actor in Human Hair Shaft Scaffolding? J Invest Dermatol 2009; 129:449-59. [DOI: 10.1038/jid.2008.231] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
16
|
Inactive and Highly Active, Proteolytically Processed Transglutaminase-5 in Epithelial Cells. J Invest Dermatol 2008; 128:2760-6. [DOI: 10.1038/jid.2008.146] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
17
|
Transglutaminase 2 undergoes a large conformational change upon activation. PLoS Biol 2008; 5:e327. [PMID: 18092889 PMCID: PMC2140088 DOI: 10.1371/journal.pbio.0050327] [Citation(s) in RCA: 347] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Accepted: 11/01/2007] [Indexed: 02/05/2023] Open
Abstract
Human transglutaminase 2 (TG2), a member of a large family of enzymes that catalyze protein crosslinking, plays an important role in the extracellular matrix biology of many tissues and is implicated in the gluten-induced pathogenesis of celiac sprue. Although vertebrate transglutaminases have been studied extensively, thus far all structurally characterized members of this family have been crystallized in conformations with inaccessible active sites. We have trapped human TG2 in complex with an inhibitor that mimics inflammatory gluten peptide substrates and have solved, at 2-Å resolution, its x-ray crystal structure. The inhibitor stabilizes TG2 in an extended conformation that is dramatically different from earlier transglutaminase structures. The active site is exposed, revealing that catalysis takes place in a tunnel, bridged by two tryptophan residues that separate acyl-donor from acyl-acceptor and stabilize the tetrahedral reaction intermediates. Site-directed mutagenesis was used to investigate the acyl-acceptor side of the tunnel, yielding mutants with a marked increase in preference for hydrolysis over transamidation. By providing the ability to visualize this activated conformer, our results create a foundation for understanding the catalytic as well as the non-catalytic roles of TG2 in biology, and for dissecting the process by which the autoantibody response to TG2 is induced in celiac sprue patients. The transglutaminase family of enzymes is best known for crosslinking proteins to form networks that strengthen tissues. Although this enzyme family has been extensively studied, a detailed understanding of the catalytic mechanism has been hampered by the lack of a structure in which the enzyme is active. We have solved, at atomic resolution, the structure of transglutaminase 2 (TG2) in complex with a molecule that mimics a natural substrate. The structure exposes the active site, giving direct insights into the catalytic mechanism. Unexpectedly, we observed a very large conformational change with respect to previous transglutaminase structures. Very few proteins have been observed to undergo this type of large-scale transformation. We propose a role for this structural rearrangement in the early stages of celiac disease, an autoimmune disorder in which TG2 is the principal autoantigen. Besides the fundamental implications, our results should allow for the rational design of better inhibitors of TG2 for pharmacological and therapeutic purposes. By using a chemical biological approach, the authors observed a 12-nanometer conformational change in this ubiquitous and multifunctional protein, revealing its active site. Fundamental, pathological, and pharmacological implications are discussed.
Collapse
|
18
|
Chang CEA, Trylska J, Tozzini V, McCammon JA. Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations. Chem Biol Drug Des 2007; 69:5-13. [PMID: 17313452 DOI: 10.1111/j.1747-0285.2007.00464.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multiscale simulations (coarse-grained Brownian dynamics simulations and all-atom molecular dynamics simulations in implicit solvent) were applied to reveal the binding processes of ligands as they enter the binding site of the HIV-1 protease. The initial structures used for the molecular dynamics simulations were generated based on the Brownian dynamics trajectories, and this is the first molecular dynamics simulation of modeling the association of a ligand with the protease. We found that a protease substrate successfully binds to the protein when the flaps are fully open. Surprisingly, a smaller cyclic urea inhibitor (XK263) can reach the binding site when the flaps are not fully open. However, if the flaps are nearly closed, the inhibitor must rearrange or binding can fail because the inhibitor cannot attain proper conformations to enter the binding site. Both the peptide substrate and XK263 can also affect the protein's internal motion, which may help the flaps to open. Simulations allow us to efficiently study the ligand binding processes and may help those who study drug discovery to find optimal association pathways and to design those ligands with the best binding kinetics.
Collapse
Affiliation(s)
- Chia-En A Chang
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA.
| | | | | | | |
Collapse
|
19
|
Zocchi L, Terrinoni A, Candi E, Ahvazi B, Bagetta G, Corasaniti MT, Lena AM, Melino G. Identification of transglutaminase 3 splicing isoforms. J Invest Dermatol 2007; 127:1791-4. [PMID: 17380116 DOI: 10.1038/sj.jid.5700768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
20
|
Boeshans KM, Mueser TC, Ahvazi B. A three-dimensional model of the human transglutaminase 1: insights into the understanding of lamellar ichthyosis. J Mol Model 2006; 13:233-46. [PMID: 17024410 DOI: 10.1007/s00894-006-0144-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 06/11/2006] [Indexed: 10/24/2022]
Abstract
The stratum corneum, the outer layer of the epidermis, serves as a protective barrier to isolate the skin from the external environment. Keratinocyte transglutaminase 1 (TGase 1) catalyzes amide crosslinking between glutamine and lysine residues on precursor proteins forming the impermeable layers of the epidermal cell envelopes (CE), the highly insoluble membranous structures of the stratum corneum. Patients with the autosomal recessive skin disorder lamellar ichthyosis (LI) appear to have deficient cross-linking of the cell envelope due to mutations identified in TGase 1, linking this enzyme to LI. In the absence of a crystal structure, molecular modeling was used to generate the structure of TGase 1. We have mapped the known mutations of TGase 1 from our survey obtained from a search of PubMed and successfully predicted the impact of these mutations on LI. Furthermore, we have identified Ca(2+) binding sites and propose that Ca(2+) induces a cis to trans isomerization in residues near the active site as part of the enzyme transamidation activation. Docking experiments suggest that substrate binding subsequently induces the reverse cis to trans isomerization, which may be a significant part of the catalytic process. These results give an interpretation at the molecular level of previously reported mutations and lead to further insights into the structural model of TGase 1, providing a new basis for understanding LI.
Collapse
Affiliation(s)
- Karen M Boeshans
- X-ray Crystallography Facility/Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892-8024, USA
| | | | | |
Collapse
|
21
|
Oji V, Hautier JM, Ahvazi B, Hausser I, Aufenvenne K, Walker T, Seller N, Steijlen PM, Küster W, Hovnanian A, Hennies HC, Traupe H. Bathing suit ichthyosis is caused by transglutaminase-1 deficiency: evidence for a temperature-sensitive phenotype. Hum Mol Genet 2006; 15:3083-97. [PMID: 16968736 DOI: 10.1093/hmg/ddl249] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bathing suit ichthyosis (BSI) is a striking and unique clinical form of autosomal recessive congenital ichthyosis characterized by pronounced scaling on the bathing suit areas but sparing of the extremities and the central face. Here we report on a series of 10 BSI patients. Our genetic, ultrastructural and biochemical investigations show that BSI is caused by transglutaminase-1 (TGase-1) deficiency. Altogether, we identified 13 mutations in TGM1-among them seven novel missense mutations and one novel nonsense mutation. Structural modeling for the Tyr276Asn mutation reveals that the residue is buried in the hydrophobic interior of the enzyme and that the hydroxyl side chain of Tyr276 is exposed to solvent in a cavity of the enzyme. Cryosections of healthy skin areas demonstrated an almost normal TGase activity, in contrast to the affected BSI skin, which only showed a cytoplasmic and clearly reduced TGase-1 activity. The distribution of TGase-1 substrates in the epidermis of affected skin corresponded to the situation in TGase-1 deficiency. Interestingly, the expression of TGase-3 and cathepsin D was reduced. Digital thermography validated a striking correlation between warmer body areas and presence of scaling in patients suggesting a decisive influence of the skin temperature. In situ TGase testing in skin of BSI patients demonstrated a marked decrease of enzyme activity when the temperature was increased from 25 to 37 degrees C. We conclude that BSI is caused by TGase-1 deficiency and suggest that it is a temperature-sensitive phenotype.
Collapse
Affiliation(s)
- Vinzenz Oji
- Department of Dermatology, University of Muenster, Von-Esmarch-Str. 58 D-48149, Münster, Germany.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Chang CE, Shen T, Trylska J, Tozzini V, McCammon JA. Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophys J 2006; 90:3880-5. [PMID: 16533835 PMCID: PMC1459512 DOI: 10.1529/biophysj.105.074575] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The internal motions of proteins may serve as a "gate" in some systems, which controls ligand-protein association. This study applies Brownian dynamics simulations in a coarse-grained model to study the gated association rate constants of HIV-1 proteases and drugs. The computed gated association rate constants of three protease mutants, G48V/V82A/I84V/L90M, G48V, and L90M with three drugs, amprenavir, indinavir, and saquinavir, yield good agreements with experiments. The work shows that the flap dynamics leads to "slow gating". The simulations suggest that the flap flexibility and the opening frequency of the wild-type, the G48V and L90M mutants are similar, but the flaps of the variant G48V/V82A/I84V/L90M open less frequently, resulting in a lower gated rate constant. The developed methodology is fast and provides an efficient way to predict the gated association rate constants for various protease mutants and ligands.
Collapse
Affiliation(s)
- Chia-En Chang
- Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, USA.
| | | | | | | | | |
Collapse
|