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Mansouri P, Mansouri P, Behmard E, Najafipour S, Kouhpayeh SA, Farjadfar A. Peptidylarginine deiminase (PAD): A promising target for chronic diseases treatment. Int J Biol Macromol 2024; 278:134576. [PMID: 39127273 DOI: 10.1016/j.ijbiomac.2024.134576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/26/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
In 1958, the presence of citrulline in the structure of the proteins was discovered for the first time. Several years later they found that Arginine converted to citrulline during a post-translational modification process by PAD enzyme. Each PAD is expressed in a certain tissue developing a series of diseases such as inflammation and cancers. Among these, PAD2 and PAD4 play a role in the development of rheumatoid arthritis (RA) by producing citrullinated autoantigens and increasing the production of inflammatory cytokines. PAD4 is also associated with the formation of NET structures and thrombosis. In the crystallographic structure, PAD has several calcium binding sites, and the active site of the enzyme consists of different amino acids. Various PAD inhibitors have been developed divided into pan-PAD and selective PAD inhibitors. F-amidine, Cl-amidine, and BB-Cl-amidine are some of pan-PAD inhibitors. AFM-30a and JBI589 are selective for PAD2 and PAD4, respectively. There is a need to evaluate the effectiveness of existing inhibitors more accurately in the coming years, as well as design and production of novel inhibitors targeting highly specific isoforms.
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Affiliation(s)
- Pegah Mansouri
- Department of Medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran
| | - Pardis Mansouri
- Department of Medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran
| | - Esmaeil Behmard
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Sohrab Najafipour
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Seyed Amin Kouhpayeh
- Department of Pharmacology, Faculty of Medicine, Fasa University of Medical Sciences, Fasa, Iran.
| | - Akbar Farjadfar
- Department of Medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran.
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2
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Zhang X, Bhattacharya A, Pu C, Dai Y, Liu J, Rao L, Tian C. A programmable CRISPR/dCas9-based epigenetic editing system enabling loci-targeted histone citrullination and precise transcription regulation. J Genet Genomics 2024:S1673-8527(24)00123-1. [PMID: 38849111 DOI: 10.1016/j.jgg.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
Histone citrullination, an important post-translational modification mediated by peptidyl arginine deiminases, is essential for many physiological processes and epigenetic regulation. However, the causal relationship between histone citrullination and specific gene regulation remains unresolved. In this study, we develop a programmable epigenetic editor by fusing the peptidyl arginine deiminase PPAD from Porphyromonas gingivalis with dCas9. With the assistance of gRNA, PPAD-dCas9 can recruit peptidyl arginine deiminases to specific genomic loci, enabling direct manipulation of the epigenetic landscape and regulation of gene expression. Our citrullination editor allows for site-specific manipulation of histone H3R2,8,17 and 26 at target human gene loci, resulting in the activation or suppression of different genes in a locus-specific manner. Moreover, the epigenetic effects of the citrullination editor are specific and sustained. This epigenetic editor offers an accurate and efficient tool for exploring gene regulation of histone citrullination.
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Affiliation(s)
- Xiaoya Zhang
- National Technology Innovation Center of Synthetic Biology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; School of Pharmacy, Jilin University, Changchun, Jilin 130012, China
| | - Abhisek Bhattacharya
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chunxiang Pu
- National Technology Innovation Center of Synthetic Biology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yan Dai
- National Technology Innovation Center of Synthetic Biology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jia Liu
- National Technology Innovation Center of Synthetic Biology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Lang Rao
- National Technology Innovation Center of Synthetic Biology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Chaoguang Tian
- National Technology Innovation Center of Synthetic Biology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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3
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Unno M. Modes of PADing. Nat Chem Biol 2024; 20:662-663. [PMID: 38308045 DOI: 10.1038/s41589-023-01506-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Affiliation(s)
- Masaki Unno
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan.
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4
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Zhou X, Kong S, Maker A, Remesh SG, Leung KK, Verba KA, Wells JA. Antibody discovery identifies regulatory mechanisms of protein arginine deiminase 4. Nat Chem Biol 2024; 20:742-750. [PMID: 38308046 PMCID: PMC11142921 DOI: 10.1038/s41589-023-01535-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 12/20/2023] [Indexed: 02/04/2024]
Abstract
Unlocking the potential of protein arginine deiminase 4 (PAD4) as a drug target for rheumatoid arthritis requires a deeper understanding of its regulation. In this study, we use unbiased antibody selections to identify functional antibodies capable of either activating or inhibiting PAD4 activity. Through cryogenic-electron microscopy, we characterized the structures of these antibodies in complex with PAD4 and revealed insights into their mechanisms of action. Rather than steric occlusion of the substrate-binding catalytic pocket, the antibodies modulate PAD4 activity through interactions with allosteric binding sites adjacent to the catalytic pocket. These binding events lead to either alteration of the active site conformation or the enzyme oligomeric state, resulting in modulation of PAD4 activity. Our study uses antibody engineering to reveal new mechanisms for enzyme regulation and highlights the potential of using PAD4 agonist and antagonist antibodies for studying PAD4-dependency in disease models and future therapeutic development.
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Affiliation(s)
- Xin Zhou
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sophie Kong
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Allison Maker
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Soumya G Remesh
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Kliment A Verba
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
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5
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Villanueva-Cañas JL, Fernandez-Fuentes N, Saul D, Kosinsky RL, Teyssier C, Rogalska ME, Pérez FP, Oliva B, Notredame C, Beato M, Sharma P. Evolutionary analysis reveals the role of a non-catalytic domain of peptidyl arginine deiminase 2 in transcriptional regulation. iScience 2024; 27:109584. [PMID: 38623337 PMCID: PMC11016909 DOI: 10.1016/j.isci.2024.109584] [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: 12/21/2023] [Revised: 02/13/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Peptidyl arginine deiminases (PADIs) catalyze protein citrullination, a post-translational conversion of arginine to citrulline. The most widely expressed member of this family, PADI2, regulates cellular processes that impact several diseases. We hypothesized that we could gain new insights into PADI2 function through a systematic evolutionary and structural analysis. Here, we identify 20 positively selected PADI2 residues, 16 of which are structurally exposed and maintain PADI2 interactions with cognate proteins. Many of these selected residues reside in non-catalytic regions of PADI2. We validate the importance of a prominent loop in the middle domain that encompasses PADI2 L162, a residue under positive selection. This site is essential for interaction with the transcription elongation factor (P-TEFb) and mediates the active transcription of the oncogenes c-MYC, and CCNB1, as well as impacting cellular proliferation. These insights could be key to understanding and addressing the role of the PADI2 c-MYC axis in cancer progression.
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Affiliation(s)
- José Luis Villanueva-Cañas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom
| | - Dominik Saul
- Division of Endocrinology, Mayo Clinic, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department of Trauma and Reconstructive Surgery, BG Clinic, University of Tübingen, Tübingen, Germany
| | | | - Catherine Teyssier
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université de Montpellier, Institut Du Cancer de Montpellier (ICM), F-34298 Montpellier, France
| | - Malgorzata Ewa Rogalska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ferran Pegenaute Pérez
- Live-Cell Structural Biology Laboratory, Department of Medicine and Life Sciences, E-08005 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Baldomero Oliva
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Bioinformatics Laboratory (GRIB-IMIM), Department of Medicine and Life Sciences, E-08003 Barcelona, Spain
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Miguel Beato
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Priyanka Sharma
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
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6
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Dejbakht M, Akhzari M, Jalili S, Faraji F, Barazesh M. Multiple Sclerosis: New Insights into Molecular Pathogenesis and Novel Platforms for Disease Treatment. Curr Drug Res Rev 2024; 16:175-197. [PMID: 37724675 DOI: 10.2174/2589977516666230915103730] [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: 01/08/2023] [Revised: 06/23/2023] [Accepted: 07/03/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Multiple sclerosis (MS), a chronic inflammatory disorder, affects the central nervous system via myelin degradation. The cause of MS is not fully known, but during recent years, our knowledge has deepened significantly regarding the different aspects of MS, including etiology, molecular pathophysiology, diagnosis and therapeutic options. Myelin basic protein (MBP) is the main myelin protein that accounts for maintaining the stability of the myelin sheath. Recent evidence has revealed that MBP citrullination or deamination, which is catalyzed by Ca2+ dependent peptidyl arginine deiminase (PAD) enzyme leads to the reduction of positive charge, and subsequently proteolytic cleavage of MBP. The overexpression of PAD2 in the brains of MS patients plays an essential role in new epitope formation and progression of the autoimmune disorder. Some drugs have recently entered phase III clinical trials with promising efficacy and will probably obtain approval in the near future. As different therapeutic platforms develop, finding an optimal treatment for each individual patient will be more challenging. AIMS This review provides a comprehensive insight into MS with a focus on its pathogenesis and recent advances in diagnostic methods and its present and upcoming treatment modalities. CONCLUSION MS therapy alters quickly as research findings and therapeutic options surrounding MS expand. McDonald's guidelines have created different criteria for MS diagnosis. In recent years, ever-growing interest in the development of PAD inhibitors has led to the generation of many reversible and irreversible PAD inhibitors against the disease with satisfactory therapeutic outcomes.
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Affiliation(s)
- Majid Dejbakht
- Department of Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran
| | - Morteza Akhzari
- School of Nursing, Larestan University of Medical Sciences, Larestan, Iran
| | - Sajad Jalili
- Department of Orthopedics, School of Medicine, Ahvaz Jundishapour University of Medical Sciences, Ahvaz, Iran
| | - Fouziyeh Faraji
- Department of Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran
| | - Mahdi Barazesh
- Department of Biotechnology, Cellular and Molecular Research Center, School of Paramedical, Gerash University of Medical Sciences, Gerash, Iran
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7
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James EA, Joglekar AV, Linnemann AK, Russ HA, Kent SC. The beta cell-immune cell interface in type 1 diabetes (T1D). Mol Metab 2023; 78:101809. [PMID: 37734713 PMCID: PMC10622886 DOI: 10.1016/j.molmet.2023.101809] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND T1D is an autoimmune disease in which pancreatic islets of Langerhans are infiltrated by immune cells resulting in the specific destruction of insulin-producing islet beta cells. Our understanding of the factors leading to islet infiltration and the interplay of the immune cells with target beta cells is incomplete, especially in human disease. While murine models of T1D have provided crucial information for both beta cell and autoimmune cell function, the translation of successful therapies in the murine model to human disease has been a challenge. SCOPE OF REVIEW Here, we discuss current state of the art and consider knowledge gaps concerning the interface of the islet beta cell with immune infiltrates, with a focus on T cells. We discuss pancreatic and immune cell phenotypes and their impact on cell function in health and disease, which we deem important to investigate further to attain a more comprehensive understanding of human T1D disease etiology. MAJOR CONCLUSIONS The last years have seen accelerated development of approaches that allow comprehensive study of human T1D. Critically, recent studies have contributed to our revised understanding that the pancreatic beta cell assumes an active role, rather than a passive position, during autoimmune disease progression. The T cell-beta cell interface is a critical axis that dictates beta cell fate and shapes autoimmune responses. This includes the state of the beta cell after processing internal and external cues (e.g., stress, inflammation, genetic risk) that that contributes to the breaking of tolerance by hyperexpression of human leukocyte antigen (HLA) class I with presentation of native and neoepitopes and secretion of chemotactic factors to attract immune cells. We anticipate that emerging insights about the molecular and cellular aspects of disease initiation and progression processes will catalyze the development of novel and innovative intervention points to provide additional therapies to individuals affected by T1D.
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Affiliation(s)
- Eddie A James
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Alok V Joglekar
- Center for Systems Immunology and Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amelia K Linnemann
- Center for Diabetes and Metabolic Diseases, and Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Holger A Russ
- Diabetes Institute, University of Florida, Gainesville, FL, USA; Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - Sally C Kent
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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8
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Harada K, Carr SM, Shrestha A, La Thangue NB. Citrullination and the protein code: crosstalk between post-translational modifications in cancer. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220243. [PMID: 37778382 PMCID: PMC10542456 DOI: 10.1098/rstb.2022.0243] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/05/2023] [Indexed: 10/03/2023] Open
Abstract
Post-translational modifications (PTMs) of proteins are central to epigenetic regulation and cellular signalling, playing an important role in the pathogenesis and progression of numerous diseases. Growing evidence indicates that protein arginine citrullination, catalysed by peptidylarginine deiminases (PADs), is involved in many aspects of molecular and cell biology and is emerging as a potential druggable target in multiple diseases including cancer. However, we are only just beginning to understand the molecular activities of PADs, and their underlying mechanistic details in vivo under both physiological and pathological conditions. Many questions still remain regarding the dynamic cellular functions of citrullination and its interplay with other types of PTMs. This review, therefore, discusses the known functions of PADs with a focus on cancer biology, highlighting the cross-talk between citrullination and other types of PTMs, and how this interplay regulates downstream biological events. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Koyo Harada
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Simon M. Carr
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Amit Shrestha
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Nicholas B. La Thangue
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
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9
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Vikhe Patil K, Meijer M, Mak KHM, Yang W, Falcão AM, Castelo-Branco G, Genander M. Co-expression of PADI isoforms during progenitor differentiation enables functional diversity. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220451. [PMID: 37778375 PMCID: PMC10542451 DOI: 10.1098/rstb.2022.0451] [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: 02/28/2023] [Accepted: 05/02/2023] [Indexed: 10/03/2023] Open
Abstract
Protein isoforms, generated through alternative splicing or promoter usage, contribute to tissue function. Here, we characterize the expression of predicted Padi3α and Padi3β isoforms in hair follicles and describe expression of Padi2β, a hitherto unknown PADI2 isoform, in the oligodendrocyte lineage. Padi2β transcription is initiated from a downstream intronic promoter, generating an N-terminally truncated, unstable, PADI2β. By contrast to the established role of the canonical PADI2 (PADI2α) (Falcao et al. 2019 Cell Rep. 27, 1090-1102.e10. (doi:10.1016/j.celrep.2019.03.108)), PADI2β inhibits oligodendrocyte differentiation, suggesting that PADI2 isoforms exert opposing effects on oligodendrocyte lineage progression. We localize Padi3α and Padi3β to developing hair follicles and find that both transcripts are expressed at low levels in progenitor cells, only to increase in expression concomitant with differentiation. When expressed in vitro, PADI3α and PADI3β are enriched in the cytoplasm and precipitate together. Whereas PADI3β protein stability is low and PADI3β fails to induce protein citrullination, we find that the enzymatic activity and protein stability of PADI3α is reduced in the presence of PADI3β. We propose that PADI3β modulates PADI3α activity by direct binding and heterodimer formation. Here, we establish expression and function of Padi2 and Padi3 isoforms, expanding on the mechanisms in place to regulate citrullination in complex tissues. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Kim Vikhe Patil
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mandy Meijer
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kylie Hin-Man Mak
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Wei Yang
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ana Mendanha Falcão
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's Associate Laboratory, PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Center for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden
| | - Maria Genander
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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Méchin MC, Simon M. Deimination in epidermal barrier and hair formation. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220245. [PMID: 37778378 PMCID: PMC10542453 DOI: 10.1098/rstb.2022.0245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/13/2023] [Indexed: 10/03/2023] Open
Abstract
Peptidylarginine deiminases (PADs) transform a protein arginine residue into the non-standard amino acid citrulline. This calcium-dependent post-translational modification of proteins is called citrullination or deimination. As described in this special issue, PADs play a role in various physiological processes, and PAD deregulations are involved in many human diseases. Three PADs are expressed in the epidermis, where their roles begin to be deciphered. PAD1 and PAD3 are involved in keratinocyte differentiation, particularly in the epidermal barrier function, keratins, filaggrin and filaggrin-related proteins being the most abundant deiminated epidermal proteins. Reduced amounts of deiminated proteins and PAD1 expression may be involved in the pathogenesis of psoriasis and atopic dermatitis, two very frequent and chronic skin inflammatory diseases. The trichohyalin/PAD3/transglutaminase three pathway is important for hair shaft formation. Mutations of the PADI3 gene, leading to a decreased activity or abnormal localization of the corresponding isotype, are the cause of a rare hair disorder called uncombable hair syndrome, and are associated with the central centrifugal cicatricial alopecia, a frequent alopecia mainly affecting women of African ancestry. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Marie-Claire Méchin
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, University Paul Sabatier, 31024 Toulouse, France
| | - Michel Simon
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, University Paul Sabatier, 31024 Toulouse, France
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11
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Williams JPC, Walport LJ. PADI6: What we know about the elusive fifth member of the peptidyl arginine deiminase family. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220242. [PMID: 37778376 PMCID: PMC10542454 DOI: 10.1098/rstb.2022.0242] [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: 01/31/2023] [Accepted: 03/05/2023] [Indexed: 10/03/2023] Open
Abstract
Peptidyl arginine deiminase 6 (PADI6) is a maternal factor that is vital for early embryonic development. Deletion and mutations of its encoding gene in female mice or women lead to early embryonic developmental arrest, female infertility, maternal imprinting defects and hyperproliferation of the trophoblast. PADI6 is the fifth and least well-characterized member of the peptidyl arginine deiminases (PADIs), which catalyse the post-translational conversion of arginine to citrulline. It is less conserved than the other PADIs, and currently has no reported catalytic activity. While there are many suggested functions of PADI6 in the early mouse embryo, including in embryonic genome activation, cytoplasmic lattice formation, maternal mRNA and ribosome regulation, and organelle distribution, the molecular mechanisms of its function remain unknown. In this review, we discuss what is known about the function of PADI6 and highlight key outstanding questions that must be answered if we are to understand the crucial role it plays in early embryo development and female fertility. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
| | - Louise J. Walport
- Imperial College of Science Technology and Medicine, London, W12 0BZ, UK
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Zhang X, Shen M, Zhu H, Zhang J, Yang M, Su K, Zhang Y, Fu W, Ke X, Qu Y. Small molecule activates citrullination through targeting PAD2. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220248. [PMID: 37778388 PMCID: PMC10542452 DOI: 10.1098/rstb.2022.0248] [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: 02/15/2023] [Accepted: 06/11/2023] [Indexed: 10/03/2023] Open
Abstract
Citrullination is a post-translational modification catalysed by peptidyl arginine deiminase (PAD) enzymes, and dysregulation of protein citrullination is involved in various pathological disorders. During the past decade, a panel of citrullination inhibitors has been developed, while small molecules activating citrullination have rarely been reported so far. In this study, we screened citrullination activator using an antibody against citrullinated histone H3 (cit-H3), and a natural compound demethoxycurcumin (DMC) significantly activated citrullination. The requirement of PAD2 for DMC-activated citrullination was confirmed by a loss of function assay. Notably, DMC directly engaged with PAD2, and showed binding selectivity among PAD family enzymes. Point mutation assay indicated that residue E352 is essential for DMC targeting PAD2. Consistently, DMC induced typical phenotypes of cells with dysregulation of PAD2 activity, including citrullination-associated cell apoptosis and DNA damage. Overall, our study not only presents a strategy for rationally screening citrullination activators, but also provides a chemical approach for activating protein citrullination. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Xue Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
| | - Mengzhen Shen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
| | - Huimin Zhu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
| | - Junjie Zhang
- School of pharmacy, Fudan University, Shanghai 201203, People's Republic of China
| | - Min Yang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
| | - Kaiyan Su
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, People's Republic of China
| | - Yirong Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
| | - Wei Fu
- School of pharmacy, Fudan University, Shanghai 201203, People's Republic of China
| | - Xisong Ke
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
| | - Yi Qu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
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13
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Barasa L, Thompson PR. Protein citrullination: inhibition, identification and insertion. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220240. [PMID: 37778377 PMCID: PMC10542963 DOI: 10.1098/rstb.2022.0240] [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: 04/14/2023] [Accepted: 06/26/2023] [Indexed: 10/03/2023] Open
Abstract
Protein citrullination is a post-translational modification (PTM) that is catalysed by the protein arginine deiminase (PAD) family of enzymes. This PTM involves the transformation of an arginine residue into citrulline. Protein citrullination is associated with several physiological processes, including the epigenetic regulation of gene expression, neutrophil extracellular trap formation and DNA damage-induced apoptosis. Aberrant protein citrullination is relevant to several autoimmune and neurodegenerative diseases and certain forms of cancer. PAD inhibitors have shown remarkable efficacy in a range of diseases including rheumatoid arthritis (RA), lupus, atherosclerosis and ulcerative colitis. In RA, anti-citrullinated protein antibodies can be detected prior to disease onset and are thus a valuable diagnostic tool for RA. Notably, citrullinated proteins may serve more generally as biomarkers of specific disease states; however, the identification of citrullinated protein residues remains challenging owing to the small 1 Da mass change that occurs upon citrullination. Herein, we highlight the progress made so far in the development of pan-PAD and isozyme selective inhibitors as well as the identification of citrullinated proteins and the site-specific incorporation of citrulline into proteins. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Leonard Barasa
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Paul R. Thompson
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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14
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Kim HJ, Shin HR, Yoon H, Park MS, Kim BG, Moon JI, Kim WJ, Park SG, Kim KT, Kim HN, Choi JY, Ryoo HM. Peptidylarginine deiminase 2 plays a key role in osteogenesis by enhancing RUNX2 stability through citrullination. Cell Death Dis 2023; 14:576. [PMID: 37648716 PMCID: PMC10468518 DOI: 10.1038/s41419-023-06101-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Peptidylarginine deiminase (PADI) 2 catalyzes the post-translational conversion of peptidyl-arginine to peptidyl-citrulline in a process called citrullination. However, the precise functions of PADI2 in bone formation and homeostasis remain unknown. In this study, our objective was to elucidate the function and regulatory mechanisms of PADI2 in bone formation employing global and osteoblast-specific Padi2 knockout mice. Our findings demonstrate that Padi2 deficiency leads to the loss of bone mass and results in a cleidocranial dysplasia (CCD) phenotype with delayed calvarial ossification and clavicular hypoplasia, due to impaired osteoblast differentiation. Mechanistically, Padi2 depletion significantly reduces RUNX2 levels, as PADI2-dependent stabilization of RUNX2 protected it from ubiquitin-proteasomal degradation. Furthermore, we discovered that PADI2 binds to RUNX2 and citrullinates it, and identified ten PADI2-induced citrullination sites on RUNX2 through high-resolution LC-MS/MS analysis. Among these ten citrullination sites, the R381 mutation in mouse RUNX2 isoform 1 considerably reduces RUNX2 levels, underscoring the critical role of citrullination at this residue in maintaining RUNX2 protein stability. In conclusion, these results indicate that PADI2 plays a distinct role in bone formation and osteoblast differentiation by safeguarding RUNX2 against proteasomal degradation. In addition, we demonstrate that the loss-of-function of PADI2 is associated with CCD, thereby providing a new target for the treatment of bone diseases.
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Affiliation(s)
- Hyun-Jung Kim
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Hye-Rim Shin
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Heein Yoon
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Min-Sang Park
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, South Korea
| | - Jae-I Moon
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Woo-Jin Kim
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Seung Gwa Park
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Ki-Tae Kim
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Ha-Neui Kim
- Center for Musculoskeletal Disease Research and Center for Osteoporosis and Metabolic Bone Diseases, Department of Internal Medicine, Division of Endocrinology and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Je-Yong Choi
- Department of Biochemistry and Cell Biology, Cell and Matrix Research Institute, BK21 Plus KNU Biomedical Convergence Program, Skeletal Disease Analysis Center, Korea Mouse Phenotyping Center, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Hyun-Mo Ryoo
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea.
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15
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Green RM, Thompson PR. Current insights into the role of citrullination in thrombosis. Curr Opin Chem Biol 2023; 75:102313. [PMID: 37148643 PMCID: PMC10523988 DOI: 10.1016/j.cbpa.2023.102313] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/22/2023] [Accepted: 04/01/2023] [Indexed: 05/08/2023]
Abstract
Protein citrullination is a post-translational modification of arginine that controls a diverse array of cellular processes, including gene regulation, protein stability, and neutrophil extracellular trap (NET) formation. Histone citrullination promotes chromatin decondensation and NET formation, a pro-inflammatory form of cell death that is aberrantly increased in numerous immune disorders. This review will provide insights into NETosis and how this novel form of cell death contributes to inflammatory diseases, with a particular emphasis on its role in thrombosis. We will also discuss recent efforts to develop PAD-specific inhibitors.
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Affiliation(s)
- R Madison Green
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Paul R Thompson
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
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16
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Yeh CY, Izaguirre JA, Greisman JB, Willmore L, Maragakis P, Shaw DE. A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. J Chem Inf Model 2023. [PMID: 37378552 DOI: 10.1021/acs.jcim.3c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator of the insulin and leptin signaling pathways, making it a highly attractive target for the treatment of type II diabetes. For PTP1B to perform its enzymatic function, a loop referred to as the "WPD loop" must transition between open (catalytically incompetent) and closed (catalytically competent) conformations, which have both been resolved by X-ray crystallography. Although prior studies have established this transition as the rate-limiting step for catalysis, the transition mechanism for PTP1B and other PTPs has been unclear. Here we present an atomically detailed model of WPD loop transitions in PTP1B based on unbiased, long-timescale molecular dynamics simulations and weighted ensemble simulations. We found that a specific WPD loop region─the PDFG motif─acted as the key conformational switch, with structural changes to the motif being necessary and sufficient for transitions between long-lived open and closed states of the loop. Simulations starting from the closed state repeatedly visited open states of the loop that quickly closed again unless the infrequent conformational switching of the motif stabilized the open state. The functional importance of the PDFG motif is supported by the fact that it is well conserved across PTPs. Bioinformatic analysis shows that the PDFG motif is also conserved, and adopts two distinct conformations, in deiminases, and the related DFG motif is known to function as a conformational switch in many kinases, suggesting that PDFG-like motifs may control transitions between structurally distinct, long-lived conformational states in multiple protein families.
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Affiliation(s)
- Christine Y Yeh
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - Jack B Greisman
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - Paul Maragakis
- D. E. Shaw Research, New York, New York 10036, United States
| | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, United States
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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17
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Tillotson J, Aryal B, Lai L, Beaver JA, Rao VA. Differential Protein Citrullination in Human ER- and ER+ Tumor and Adjacent Healthy Breast Tissue. Biochemistry 2023; 62:893-898. [PMID: 36757899 PMCID: PMC9948284 DOI: 10.1021/acs.biochem.2c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Post-translational modification of arginine to citrulline is catalyzed by members of the peptidylarginine deiminase (PAD) family. Dysregulation of this catalysis is a significant driver of the pathogenesis of numerous inflammatory diseases, including cancer. However, dysregulation of PAD activity has not been examined in breast cancer with respect to hormone receptor status. In this study, we measured PAD enzyme levels using Western blotting and investigated protein citrullination using a mass spectrometry-based proteomics approach in primary estrogen receptor negative (ER-) or positive (ER+) breast tumor and matched adjacent normal tissue. Our findings reveal 72 and 41 citrullinated proteins in ER- tumor and adjacent healthy tissue, respectively, where 20 of these proteins are common between the two groups. We detected 64 and 49 citrullinated proteins in ER+ tumor and adjacent healthy tissue, respectively, where 32 proteins are common. Interestingly, upon comparison of ER- and ER+ tumor tissue, only 32 citrullinated proteins are shared between the two and the rest are unique to the tumor's receptor status. Using the STRING database for protein-protein interaction network analysis, these proteins are involved in protein-folding events (i.e., heat shock proteins) in ER- samples and blood-clotting events (i.e., fibulin) in ER+ samples. Constituents of the extracellular matrix structure (i.e., collagen and fibrinogen) were found in both. Herein, we establish evidence that supports the role of this unique post-translational modification in breast cancer biology. Finally, to aid drug discovery against citrullination, we developed a liquid chromatography-ultraviolet method to measure PAD enzymatic activity and optimized glucagon-like peptide II to quantitatively measure the ability of PADs to citrullinate its substrate.
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Affiliation(s)
- Joseph Tillotson
- Laboratory
of Applied Biochemistry, Division of Biotechnology Review and Research
III, Office of Biotechnology Products, Center for Drug Evaluation
and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Baikuntha Aryal
- Laboratory
of Applied Biochemistry, Division of Biotechnology Review and Research
III, Office of Biotechnology Products, Center for Drug Evaluation
and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Lo Lai
- Laboratory
of Applied Biochemistry, Division of Biotechnology Review and Research
III, Office of Biotechnology Products, Center for Drug Evaluation
and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Julia A. Beaver
- Oncology
Center of Excellence and Center for Drug Evaluation and Research,
Office of Oncologic Diseases, U.S. Food
and Drug Administration, Silver
Spring, Maryland 20993, United States
| | - V. Ashutosh Rao
- Laboratory
of Applied Biochemistry, Division of Biotechnology Review and Research
III, Office of Biotechnology Products, Center for Drug Evaluation
and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States,
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18
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Christensen AO, Li G, Young CH, Snow B, Khan SA, DeVore SB, Edwards S, Bouma GJ, Navratil AM, Cherrington BD, Rothfuss HM. Peptidylarginine deiminase enzymes and citrullinated proteins in female reproductive physiology and associated diseases†. Biol Reprod 2022; 107:1395-1410. [PMID: 36087287 PMCID: PMC10248218 DOI: 10.1093/biolre/ioac173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 09/15/2023] Open
Abstract
Citrullination, the post-translational modification of arginine residues, is catalyzed by the four catalytically active peptidylarginine deiminase (PAD or PADI) isozymes and alters charge to affect target protein structure and function. PADs were initially characterized in rodent uteri and, since then, have been described in other female tissues including ovaries, breast, and the lactotrope and gonadotrope cells of the anterior pituitary gland. In these tissues and cells, estrogen robustly stimulates PAD expression resulting in changes in levels over the course of the female reproductive cycle. The best-characterized targets for PADs are arginine residues in histone tails, which, when citrullinated, alter chromatin structure and gene expression. Methodological advances have allowed for the identification of tissue-specific citrullinomes, which reveal that PADs citrullinate a wide range of enzymes and structural proteins to alter cell function. In contrast to their important physiological roles, PADs and citrullinated proteins are also involved in several female-specific diseases including autoimmune disorders and reproductive cancers. Herein, we review current knowledge regarding PAD expression and function and highlight the role of protein citrullination in both normal female reproductive tissues and associated diseases.
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Affiliation(s)
- Amanda O Christensen
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Guangyuan Li
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Coleman H Young
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Bryce Snow
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | | | - Stanley B DeVore
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Sydney Edwards
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Gerrit J Bouma
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Amy M Navratil
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Brian D Cherrington
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Heather M Rothfuss
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
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19
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Zhu D, Lu Y, Wang Y, Wang Y. PAD4 and Its Inhibitors in Cancer Progression and Prognosis. Pharmaceutics 2022; 14:2414. [PMID: 36365233 PMCID: PMC9699117 DOI: 10.3390/pharmaceutics14112414] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/28/2022] [Accepted: 11/06/2022] [Indexed: 07/24/2023] Open
Abstract
The systemic spread of malignancies and the risk of cancer-associated thrombosis are major clinical challenges in cancer therapy worldwide. As an important post-translational modification enzyme, peptidyl arginine deiminase 4 (PAD4) could mediate the citrullination of protein in different components (including nucleus and cytoplasm, etc.) of a variety of cells (tumor cells, neutrophils, macrophages, etc.), thus participating in gene regulation, neutrophil extracellular trap (NET) and macrophage extracellular trap (MET). Thereby, PAD4 plays an important role in enhancing the growth of primary tumors and facilitating the distant metastasis of cancer cells. In addition, it is related to the formation of cancer-associated thrombosis. Therefore, the development of PAD4-specific inhibitors may be a promising strategy for treating cancer, and it may improve patient prognosis. In this review, we describe PAD4 involvement in gene regulation, protein citrullination, and NET formation. We also discuss its potential role in cancer and cancer-associated thrombosis, and we summarize the development and application of PAD4 inhibitors.
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Affiliation(s)
- Di Zhu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, China
| | - Yu Lu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, China
| | - Yanming Wang
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yuji Wang
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, China
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20
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Hemmati-Dinarvand M, Kheirandish S, Khodadadian A, Mostafazadeh M, Seghatoleslam A. Blockage of Wnt/β-catenin Signaling Pathway in Colorectal Cancer Resistant Cells by Nitazoxanide Effects on Peptidylarginine Deiminases Expression. Asian Pac J Cancer Prev 2022; 23:3215-3222. [PMID: 36172687 PMCID: PMC9810304 DOI: 10.31557/apjcp.2022.23.9.3215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Multidrug resistance (MDR) is a major cause of unsuccessful cancer treatment in which drugs are not effective. Therefore, it is necessary to identify the critical mechanisms of the development of MDR and target those with novel compounds. Accordingly, the current study is the first to investigate the combination effect and molecular mechanism of nitazoxanide (NTZ) and oxaliplatin (OXP) on LS174T/OXP-resistant cells. METHODS The effect of NTZ on OXP cytotoxicity in LS174T and LS174T/OXP cell lines was evaluated by MTT assay. Changes in expression levels of MDR1, MRP1, CTNNB1, peptidylarginine deiminase (PAD)2, and PAD4 genes and proteins were evaluated by RT-qPCR and western blotting methods, respectively. Lastly, the apoptosis assay was performed by flow cytometer. RESULTS OXP resistant and sensitive cells were identified based on the IC50 values (11567 nM vs. 1745 nM, p<0.05 for 24 h treatment; and 5161 nM vs. 882 nM, p<0.05 for 48 h incubation). The combination of NTZ and OXP for 48 h led to a reduction in IC50 values in resistant cells (2154 nM, p<0.05). The effect of NTZ plus OXP significantly decreased the expression of MDR1 (p<0.001), MRP1 (p<0.05), and CTNNB1 (p<0.001), while PAD2 and PAD4 expression was significantly increased (p<0.001). This combination therapy enhanced the percentage of the sub-G1 population (apoptosed) compared to other groups. CONCLUSION The results showed that NTZ leads to notable upregulation of PAD2 and PAD4, which can disrupt the Wnt/β-catenin signaling pathway and reverse the MDR by reducing MDR1 and MRP1 expression.
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Affiliation(s)
- Mohsen Hemmati-Dinarvand
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
| | - Shahnaz Kheirandish
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Ali Khodadadian
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Mostafa Mostafazadeh
- Department of Clinical Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Atefeh Seghatoleslam
- Department of Clinical Biochemistry, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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21
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Sawata M, Shima H, Murayama K, Matsui T, Igarashi K, Funabashi K, Ite K, Kizawa K, Takahara H, Unno M. Autocitrullination and Changes in the Activity of Peptidylarginine Deiminase 3 Induced by High Ca 2+ Concentrations. ACS OMEGA 2022; 7:28378-28387. [PMID: 35990454 PMCID: PMC9386831 DOI: 10.1021/acsomega.2c02972] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/18/2022] [Indexed: 05/22/2023]
Abstract
Peptidylarginine deiminases (PADs) are enzymes that catalyze the Ca2+-dependent conversion of arginine residues into proteins to citrulline residues. Five PAD isozymes have been identified in mammals. Several studies have shown that the active-site pockets of these isozymes are formed when Ca2+ ions are properly bound. We previously characterized the structures of PAD3 in six states. Among these, we identified a "nonproductive" form of PAD3 in which the active site was disordered even though five Ca2+ ions were bound. This strange structure was probably obtained as a result of either high Ca2+ concentration (∼260 mM)-induced denaturation during the crystallization process or high Ca2+-concentration-induced autocitrullination. While autocitrullination has been reported in PAD2 and PAD4 for some time, only a single report on PAD3 has been published recently. In this study, we investigated whether PAD3 catalyzes the autocitrullination reaction and identified autocitrullination sites. In addition to the capacity of PAD3 for autocitrullination, the autocitrullination sites increased depending on the Ca2+ concentration and reaction time. These findings suggest that some of the arginine residues in the "nonproductive" form of PAD3 would be autocitrullinated. Furthermore, most of the autocitrullinated sites in PAD3 were located near the substrate-binding site. Given the high Ca2+ concentration in the crystallization condition, it is likely that Arg372 was citrullinated in the "nonproductive" PAD3 structure, the structure was slightly altered from the active form by citrulline residues, and probably inhibited Ca2+-ion binding at the proper position. Following Arg372 citrullination, PAD3 enters an inactive form; however, the Arg372-citrullinated PAD3 are considered minor components in autocitrullinated PAD3 (CitPAD3), and CitPAD3 does not significantly decrease the enzyme activity. Autocitrullination of PAD3 could not be confirmed at the low Ca2+ concentrations seen in vivo. Future experiments using cells and animals are needed to verify the effect of Ca2+ on the PAD3 structure and functions in vivo.
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Affiliation(s)
- Mizuki Sawata
- Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Kazutaka Murayama
- Graduate School of Biomedical Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Toshitaka Matsui
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Kazumasa Funabashi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Kenji Ite
- Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Kenji Kizawa
- Kao Corporation, Biological Science Research Laboratory, Odawara 250-0002, Japan
| | - Hidenari Takahara
- College of Agriculture, Ibaraki University, Ami, Inashiki 300-0393, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan
| | - Masaki Unno
- Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan
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22
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Gómez-Bañuelos E, Konig MF, Andrade F. Microbial pathways to subvert host immunity generate citrullinated neoantigens targeted in rheumatoid arthritis. Curr Opin Struct Biol 2022; 75:102423. [PMID: 35834948 PMCID: PMC9668488 DOI: 10.1016/j.sbi.2022.102423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 11/03/2022]
Abstract
The specific association between antibodies to citrullinated proteins and rheumatoid arthritis (RA) has centered interest on understanding why citrullinated proteins become immunogenic in this disease, which is believed to inform the origins of autoimmunity in RA. Since citrullination is a physiologic post-translational modification (PTM), one theory is that conditions promoting abnormal citrullination are initiators of self-reactive immune responses to citrullinated proteins in RA. Foremost candidates that dysregulate the normal balance of citrullination are microbial agents, which can exploit citrullination as an effector mechanism to subvert host antimicrobial activities and maximize their progeny. Here, we will use the host-pathogen interface as a unifying model to link microbe-induced citrullination and the loss of immunological tolerance to citrullinated antigens in RA.
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Affiliation(s)
- Eduardo Gómez-Bañuelos
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA. https://twitter.com/@Eduardo95668787
| | - Maximilian F Konig
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA. https://twitter.com/@MaxKonigMD
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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23
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Cicek E, Monard G, Sungur FA. Molecular Mechanism of Protein Arginine Deiminase 2: A Study Involving Multiple Microsecond Long Molecular Dynamics Simulations. Biochemistry 2022; 61:1286-1297. [PMID: 35737372 PMCID: PMC9260958 DOI: 10.1021/acs.biochem.2c00158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidylarginine deiminase 2 (PAD2) is a Ca2+-dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. This kind of structural modification in histone molecules may affect gene regulation, leading to effects that may trigger several diseases, including breast cancer, which makes PAD2 an attractive target for anticancer drug development. To design new effective inhibitors to control activation of PAD2, improving our understanding of the molecular mechanisms of PAD2 using up-to-date computational techniques is essential. We have designed five different PAD2-substrate complex systems based on varying protonation states of the active site residues. To search the conformational space broadly, multiple independent molecular dynamics simulations of the complexes have been performed. In total, 50 replica simulations have been performed, each of 1 μs, yielding a total simulation time of 50 μs. Our findings identify that the protonation states of Cys647, Asp473, and His471 are critical for the binding and localization of the N-α-benzoyl-l-arginine ethyl ester substrate within the active site. A novel mechanism for enzyme activation is proposed according to near attack conformers. This represents an important step in understanding the mechanism of citrullination and developing PAD2-inhibiting drugs for the treatment of breast cancer.
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Affiliation(s)
- Erdem Cicek
- Informatics Institute, Computational Science and Engineering, Istanbul Technical University, TR-34469 Istanbul, Turkey
| | - Gerald Monard
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Fethiye Aylin Sungur
- Informatics Institute, Computational Science and Engineering, Istanbul Technical University, TR-34469 Istanbul, Turkey
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24
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Young C, Russell JR, Van De Lagemaat LN, Lawson H, Mapperley C, Kranc KR, Christophorou MA. Intrinsic function of the peptidylarginine deiminase PADI4 is dispensable for normal haematopoiesis. Biol Open 2022; 11:bio059143. [PMID: 35603697 PMCID: PMC9212077 DOI: 10.1242/bio.059143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
Peptidylarginine deiminases (PADIs) are strongly associated with the development of autoimmunity, neurodegeneration and cancer but their physiological roles are ill-defined. The nuclear deiminase PADI4 regulates pluripotency in the mammalian pre-implantation embryo but its function in tissue development is unknown. PADI4 is primarily expressed in the bone marrow, as part of a self-renewal-associated gene signature. It has been shown to regulate the proliferation of multipotent haematopoietic progenitors and proposed to impact on the differentiation of haematopoietic stem cells (HSCs), suggesting that it controls haematopoietic development or regeneration. Using conditional in vivo models of steady state and acute Padi4 ablation, we examined the role of PADI4 in the development and function of the haematopoietic system. We found that PADI4 loss does not significantly affect HSC self-renewal or differentiation potential upon injury or serial transplantation, nor does it lead to HSC exhaustion or premature ageing. Thus PADI4 is dispensable for cell-autonomous HSC maintenance, differentiation and haematopoietic regeneration. This work represents the first study of PADI4 in tissue development and indicates that pharmacological PADI4 inhibition may be tolerated without adverse effects.
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Affiliation(s)
- Christine Young
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
| | - John R. Russell
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Louie N. Van De Lagemaat
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
- Laboratory of Haematopoietic Stem Cell & Leukaemia Biology, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M6BQ, United Kingdom
| | - Hannah Lawson
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
- Laboratory of Haematopoietic Stem Cell & Leukaemia Biology, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M6BQ, United Kingdom
| | - Christopher Mapperley
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
- Laboratory of Haematopoietic Stem Cell & Leukaemia Biology, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M6BQ, United Kingdom
| | - Kamil R. Kranc
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
- Laboratory of Haematopoietic Stem Cell & Leukaemia Biology, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M6BQ, United Kingdom
| | - Maria A. Christophorou
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
- Epiegetics, Babraham Institute, Cambridge CB22 3AT, United Kingdom
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25
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Christophorou MA. The virtues and vices of protein citrullination. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220125. [PMID: 35706669 PMCID: PMC9174705 DOI: 10.1098/rsos.220125] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/16/2022] [Indexed: 05/03/2023]
Abstract
The post-translational modification of proteins expands the regulatory scope of the proteome far beyond what is achievable through genome regulation. The field of protein citrullination has seen significant progress in the last two decades. The small family of peptidylarginine deiminase (PADI or PAD) enzymes, which catalyse citrullination, have been implicated in virtually all facets of molecular and cell biology, from gene transcription and epigenetics to cell signalling and metabolism. We have learned about their association with a remarkable array of disease states and we are beginning to understand how they mediate normal physiological functions. However, while the biochemistry of PADI activation has been worked out in exquisite detail in vitro, we still lack a clear mechanistic understanding of the processes that regulate PADIs within cells, under physiological and pathophysiological conditions. This review summarizes and discusses the current knowledge, highlights some of the unanswered questions of immediate importance and gives a perspective on the outlook of the citrullination field.
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26
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Sarnik J, Makowska J. Citrullination good or bad guy? Immunobiology 2022; 227:152233. [DOI: 10.1016/j.imbio.2022.152233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 04/11/2022] [Accepted: 05/21/2022] [Indexed: 11/16/2022]
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27
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Citrullination in the pathology of inflammatory and autoimmune disorders: recent advances and future perspectives. Cell Mol Life Sci 2022; 79:94. [PMID: 35079870 PMCID: PMC8788905 DOI: 10.1007/s00018-022-04126-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 02/06/2023]
Abstract
Numerous
post-translational modifications (PTMs) govern the collective metabolism of a cell through altering the structure and functions of proteins. The action of the most prevalent PTMs, encompassing phosphorylation, methylation, acylations, ubiquitination and glycosylation is well documented. A less explored protein PTM, conversion of peptidylarginine to citrulline, is the subject of this review. The process of citrullination is catalysed by peptidylarginine deiminases (PADs), a family of conserved enzymes expressed in a variety of human tissues. Accumulating evidence suggest that citrullination plays a significant role in regulating cellular metabolism and gene expression by affecting a multitude of pathways and modulating the chromatin status. Here, we will discuss the biochemical nature of arginine citrullination, the enzymatic machinery behind it and also provide information on the pathological consequences of citrullination in the development of inflammatory diseases (rheumatoid arthritis, multiple sclerosis, psoriasis, systemic lupus erythematosus, periodontitis and COVID-19), cancer and thromboembolism. Finally, developments on inhibitors against protein citrullination and recent clinical trials providing a promising therapeutic approach to inflammatory disease by targeting citrullination are discussed.
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28
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Vikhe Patil K, Mak KHM, Genander M. A Hairy Cituation - PADIs in Regeneration and Alopecia. Front Cell Dev Biol 2021; 9:789676. [PMID: 34966743 PMCID: PMC8710808 DOI: 10.3389/fcell.2021.789676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/23/2021] [Indexed: 02/04/2023] Open
Abstract
In this Review article, we focus on delineating the expression and function of Peptidyl Arginine Delminases (PADIs) in the hair follicle stem cell lineage and in inflammatory alopecia. We outline our current understanding of cellular processes influenced by protein citrullination, the PADI mediated posttranslational enzymatic conversion of arginine to citrulline, by exploring citrullinomes from normal and inflamed tissues. Drawing from other stem cell lineages, we detail the potential function of PADIs and specific citrullinated protein residues in hair follicle stem cell activation, lineage specification and differentiation. We highlight PADI3 as a mediator of hair shaft differentiation and display why mutations in PADI3 are linked to human alopecia. Furthermore, we propose mechanisms of PADI4 dependent fine-tuning of the hair follicle lineage progression. Finally, we discuss citrullination in the context of inflammatory alopecia. We present how infiltrating neutrophils establish a citrullination-driven self-perpetuating proinflammatory circuitry resulting in T-cell recruitment and activation contributing to hair follicle degeneration. In summary, we aim to provide a comprehensive perspective on how citrullination modulates hair follicle regeneration and contributes to inflammatory alopecia.
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Affiliation(s)
- Kim Vikhe Patil
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kylie Hin-Man Mak
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maria Genander
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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29
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Grant J, Kimmel BR, Szymczak LC, Roll J, Mrksich M. Characterizing Enzyme Cooperativity with Imaging SAMDI-MS. Chemistry 2021; 28:e202103807. [PMID: 34890480 DOI: 10.1002/chem.202103807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Indexed: 11/11/2022]
Abstract
This paper describes a method that combines a microfluidic device and self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI) mass spectrometry to calculate the cooperativity in binding of calcium ions to peptidylarginine deiminase type 2 (PAD2). This example uses only 120 µL of enzyme solution and three fluidic inputs. This microfluidic device incorporates a self-assembled monolayer that is functionalized with a peptide substrate for PAD2. The enzyme and different concentrations of calcium ions are flowed through each of eight channels, where the position along the channel corresponds to reaction time and position across the channel corresponds to the concentration of Ca2+. Imaging SAMDI (iSAMDI) is then used to determine the yield for the enzyme reaction at each 200 µm pixel on the monolayer, providing a time course for the reactions. Analysis of the peptide conversion as a function of position and time gives the degree of cooperativity (n) and the concentration of ligand required for half maximal activity (K0.5) for the Ca2+ - dependent activation of PAD2. This work establishes a high-throughput and label-free method for studying enzyme-ligand binding interactions and widens the applicability of microfluidics and matrix-assisted laser desorption/ionization mass spectrometry (MALDI) imaging mass spectrometry.
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Affiliation(s)
| | - Blaise R Kimmel
- Northwestern University, Chemical and Biological Engineering, UNITED STATES
| | | | - Juliet Roll
- Northwestern University, Biomedical Engineering, UNITED STATES
| | - Milan Mrksich
- Northwestern University, Department of Chemistry, 2145 Sheridan Road, 60208, Evanston, UNITED STATES
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30
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Wang L, Chen H, Tang J, Guo Z, Wang Y. Peptidylarginine Deiminase and Alzheimer's Disease. J Alzheimers Dis 2021; 85:473-484. [PMID: 34842193 DOI: 10.3233/jad-215302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptidylarginine deiminases (PADs) are indispensable enzymes for post-translational modification of proteins, which can convert Arg residues on the surface of proteins to citrulline residues. The PAD family has five isozymes, PAD1, 2, 3, 4, and 6, which have been found in multiple tissues and organs. PAD2 and PAD4 were detected in cerebral cortex and hippocampus from human and rodent brain. In the central nervous system, abnormal expression and activation of PADs are involved in the pathological changes and pathogenesis of Alzheimer's disease (AD). This article reviews the classification, distribution, and function of PADs, with an emphasis on the relationship between the abnormal activation of PADs and AD pathogenesis, diagnosis, and the therapeutic potential of PADs as drug targets for AD.
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Affiliation(s)
- Lai Wang
- Epigenetics & Translational Medicine Laboratory, School of Life Sciences, Henan University, Kaifeng, Henan Province, P.R. China
| | - Hongyang Chen
- Epigenetics & Translational Medicine Laboratory, School of Life Sciences, Henan University, Kaifeng, Henan Province, P.R. China
| | - Jing Tang
- Epigenetics & Translational Medicine Laboratory, School of Life Sciences, Henan University, Kaifeng, Henan Province, P.R. China
| | - Zhengwei Guo
- Epigenetics & Translational Medicine Laboratory, School of Life Sciences, Henan University, Kaifeng, Henan Province, P.R. China
| | - Yanming Wang
- Epigenetics & Translational Medicine Laboratory, School of Life Sciences, Henan University, Kaifeng, Henan Province, P.R. China
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31
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Mamsa SSA, Meloni BP. Arginine and Arginine-Rich Peptides as Modulators of Protein Aggregation and Cytotoxicity Associated With Alzheimer's Disease. Front Mol Neurosci 2021; 14:759729. [PMID: 34776866 PMCID: PMC8581540 DOI: 10.3389/fnmol.2021.759729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/29/2021] [Indexed: 01/10/2023] Open
Abstract
A substantial body of evidence indicates cationic, arginine-rich peptides (CARPs) are effective therapeutic compounds for a range of neurodegenerative pathologies, with beneficial effects including the reduction of excitotoxic cell death and mitochondrial dysfunction. CARPs, therefore, represent an emergent class of promising neurotherapeutics with multimodal mechanisms of action. Arginine itself is a known chaotrope, able to prevent misfolding and aggregation of proteins. The putative role of proteopathies in chronic neurodegenerative diseases such as Alzheimer's disease (AD) warrants investigation into whether CARPs could also prevent the aggregation and cytotoxicity of amyloidogenic proteins, particularly amyloid-beta and tau. While monomeric arginine is well-established as an inhibitor of protein aggregation in solution, no studies have comprehensively discussed the anti-aggregatory properties of arginine and CARPs on proteins associated with neurodegenerative disease. Here, we review the structural, physicochemical, and self-associative properties of arginine and the guanidinium moiety, to explore the mechanisms underlying the modulation of protein aggregation by monomeric and multimeric arginine molecules. Arginine-rich peptide-based inhibitors of amyloid-beta and tau aggregation are discussed, as well as further modulatory roles which could reduce proteopathic cytotoxicity, in the context of therapeutic development for AD.
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Affiliation(s)
- Somayra S A Mamsa
- School of Molecular Sciences, Faculty of Science, The University of Western Australia, Perth, WA, Australia.,Perron Institute for Neurological and Translational Science, QEII Medical Centre, Perth, WA, Australia
| | - Bruno P Meloni
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Perth, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Crawley, WA, Australia.,Department of Neurology, Sir Charles Gairdner Hospital, QEII Medical Centre, Perth, WA, Australia
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32
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Wu Z, Li P, Tian Y, Ouyang W, Ho JWY, Alam HB, Li Y. Peptidylarginine Deiminase 2 in Host Immunity: Current Insights and Perspectives. Front Immunol 2021; 12:761946. [PMID: 34804050 PMCID: PMC8599989 DOI: 10.3389/fimmu.2021.761946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
Peptidylarginine deiminases (PADs) are a group of enzymes that catalyze post-translational modifications of proteins by converting arginine residues into citrullines. Among the five members of the PAD family, PAD2 and PAD4 are the most frequently studied because of their abundant expression in immune cells. An increasing number of studies have identified PAD2 as an essential factor in the pathogenesis of many diseases. The successes of preclinical research targeting PAD2 highlights the therapeutic potential of PAD2 inhibition, particularly in sepsis and autoimmune diseases. However, the underlying mechanisms by which PAD2 mediates host immunity remain largely unknown. In this review, we will discuss the role of PAD2 in different types of cell death signaling pathways and the related immune disorders contrasted with functions of PAD4, providing novel therapeutic strategies for PAD2-associated pathology.
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Affiliation(s)
- Zhenyu Wu
- Department of Surgery, University of Michigan Hospital, Ann Arbor, MI, United States,Department of Infectious Diseases, Xiangya 2 Hospital, Central South University, Changsha, China
| | - Patrick Li
- Department of Surgery, University of Michigan Hospital, Ann Arbor, MI, United States,Department of Internal Medicine, New York University (NYU) Langone Health, New York, NY, United States
| | - Yuzi Tian
- Department of Surgery, University of Michigan Hospital, Ann Arbor, MI, United States,Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, China
| | - Wenlu Ouyang
- Department of Surgery, University of Michigan Hospital, Ann Arbor, MI, United States,Department of Infectious Diseases, Xiangya 2 Hospital, Central South University, Changsha, China
| | - Jessie Wai-Yan Ho
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Hasan B. Alam
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Yongqing Li
- Department of Surgery, University of Michigan Hospital, Ann Arbor, MI, United States,*Correspondence: Yongqing Li,
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33
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Cummings TFM, Gori K, Sanchez-Pulido L, Gavriilidis G, Moi D, Wilson AR, Murchison E, Dessimoz C, Ponting CP, Christophorou MA. Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria. Mol Biol Evol 2021; 39:6420225. [PMID: 34730808 PMCID: PMC8826395 DOI: 10.1093/molbev/msab317] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Protein posttranslational modifications add great sophistication to biological systems. Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is enigmatic from an evolutionary perspective. Although the citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates, they are absent from yeast, worms, and flies. Based on this distribution PADIs were proposed to have been horizontally transferred, but this has been contested. Here, we map the evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologs. The animal and cyanobacterial PADI proteins share functionally relevant primary and tertiary synapomorphic sequences that are distinct from a second PADI type present in fungi and actinobacteria. Molecular clock calculations and sequence divergence analyses using the fossil record estimate the last common ancestor of the cyanobacterial and animal PADIs to be less than 1 billion years old. Additionally, under an assumption of vertical descent, PADI sequence change during this evolutionary time frame is anachronistically low, even when compared with products of likely endosymbiont gene transfer, mitochondrial proteins, and some of the most highly conserved sequences in life. The consilience of evidence indicates that PADIs were introduced from cyanobacteria into animals by horizontal gene transfer (HGT). The ancestral cyanobacterial PADI is enzymatically active and can citrullinate eukaryotic proteins, suggesting that the PADI HGT event introduced a new catalytic capability into the regulatory repertoire of animals. This study reveals the unusual evolution of a pleiotropic protein modification.
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Affiliation(s)
- Thomas F M Cummings
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom,Corresponding authors: E-mails: ;
| | - Kevin Gori
- Transmissible Cancer Group, Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Luis Sanchez-Pulido
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Gavriil Gavriilidis
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - David Moi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abigail R Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Elizabeth Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland,Swiss Institute of Bioinformatics, Lausanne, Switzerland,Department of Genetics Evolution and Environment, University College London, London, United Kingdom,Department of Computer Science, University College London, London, United Kingdom
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Maria A Christophorou
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom,Epigenetics Department, The Babraham Institute, Cambridge, United Kingdom,Corresponding authors: E-mails: ;
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34
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Rechiche O, Lee TV, Lott JS. Structural characterization of human peptidyl-arginine deiminase type III by X-ray crystallography. Acta Crystallogr F Struct Biol Commun 2021; 77:334-340. [PMID: 34605437 PMCID: PMC8488854 DOI: 10.1107/s2053230x21009195] [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: 03/04/2021] [Accepted: 09/04/2021] [Indexed: 11/10/2022] Open
Abstract
The Ca2+-dependent enzyme peptidyl-arginine deiminase type III (PAD3) catalyses the deimination of arginine residues to form citrulline residues in proteins such as keratin, filaggrin and trichohyalin. This is an important post-translation modification that is required for normal hair and skin formation in follicles and keratocytes. The structure of apo human PAD3 was determined by X-ray crystallography to a resolution of 2.8 Å. The structure of PAD3 revealed a similar overall architecture to other PAD isoforms: the N-terminal and middle domains of PAD3 show sequence and structural variety, whereas the sequence and structure of the C-terminal catalytic domain is highly conserved. Structural analysis indicates that PAD3 is a dimer in solution, as is also the case for the PAD2 and PAD4 isoforms but not the PAD1 isoform.
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Affiliation(s)
- Othman Rechiche
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Althouse Laboratory, Science Drive, State College, PA 16801, USA
| | - T. Verne Lee
- School of Biological Sciences, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| | - J. Shaun Lott
- School of Biological Sciences, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
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35
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Maurais AJ, Salinger AJ, Tobin M, Shaffer SA, Weerapana E, Thompson PR. A Streamlined Data Analysis Pipeline for the Identification of Sites of Citrullination. Biochemistry 2021; 60:2902-2914. [PMID: 34491035 DOI: 10.1021/acs.biochem.1c00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Citrullination is an enzyme-catalyzed post-translational modification (PTM) that is essential for a host of biological processes, including gene regulation, programmed cell death, and organ development. While this PTM is required for normal cellular functions, aberrant citrullination is a hallmark of autoimmune disorders as well as cancer. Although aberrant citrullination is linked to human pathology, the exact role of citrullination in disease remains poorly characterized, in part because of the challenges associated with identifying the specific arginine residues that are citrullinated. Tandem mass spectrometry is the most precise method for uncovering sites of citrullination; however, due to the small mass shift (+0.984 Da) that results from citrullination, current database search algorithms commonly misannotate spectra, leading to a high number of false-positive assignments. To address this challenge, we developed an automated workflow to rigorously and rapidly mine proteomic data to unambiguously identify the sites of citrullination from complex peptide mixtures. The crux of this streamlined workflow is the ionFinder software program, which classifies citrullination sites with high confidence on the basis of the presence of diagnostic fragment ions. These diagnostic ions include the neutral loss of isocyanic acid, which is a dissociative event that is unique to citrulline residues. Using the ionFinder program, we have mapped the sites of autocitrullination on purified protein arginine deiminases (PAD1-4) and mapped the global citrullinome in a PAD2-overexpressing cell line. The ionFinder algorithm is a highly versatile, user-friendly, and open-source program that is agnostic to the type of instrument and mode of fragmentation that are used.
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Affiliation(s)
- Aaron J Maurais
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Ari J Salinger
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States.,Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Micaela Tobin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Scott A Shaffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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36
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Funabashi K, Sawata M, Nagai A, Akimoto M, Mashimo R, Takahara H, Kizawa K, Thompson PR, Ite K, Kitanishi K, Unno M. Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design. Arch Biochem Biophys 2021; 708:108911. [PMID: 33971157 DOI: 10.1016/j.abb.2021.108911] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 11/29/2022]
Abstract
Peptidylarginine deiminase type III (PAD3) is an isozyme belonging to the PAD enzyme family that converts arginine to citrulline residue(s) within proteins. PAD3 is expressed in most differentiated keratinocytes of the epidermis and hair follicles, while S100A3, trichohyalin, and filaggrin are its principal substrates. In this study, the X-ray crystal structures of PAD3 in six states, including its complex with the PAD inhibitor Cl-amidine, were determined. This structural analysis identified a large space around Gly374 in the PAD3-Ca2+-Cl-amidine complex, which may be used to develop novel PAD3-selective inhibitors. In addition, similarities between PAD3 and PAD4 were found based on the investigation of PAD4 reactivity with S100A3 in vitro. A comparison of the structures of PAD1, PAD2, PAD3, and PAD4 implied that the flexibility of the structures around the active site may lead to different substrate selectivity among these PAD isozymes.
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Affiliation(s)
- Kazumasa Funabashi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan
| | - Mizuki Sawata
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan
| | - Anna Nagai
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai Naka, Japan
| | - Megumi Akimoto
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai Naka, Japan
| | - Ryutaro Mashimo
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai Naka, Japan
| | - Hidenari Takahara
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai Naka, Japan; College of Agriculture, Ibaraki University, Ami Inashiki, Japan
| | - Kenji Kizawa
- Kao Corporation, Biological Science Research Laboratory, Odawara, Japan
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Kenji Ite
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai Naka, Japan
| | - Kenichi Kitanishi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan; Tokyo University of Science, Faculty of Science Division I, Tokyo, Japan
| | - Masaki Unno
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai Naka, Japan.
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Guzmán-Guzmán IP, Ramírez-Vélez CI, Falfán-Valencia R, Navarro-Zarza JE, Gutiérrez-Pérez IA, Zaragoza-García O, Ramírez M, Castro-Alarcón N, Parra-Rojas I. PADI2 Polymorphisms Are Significantly Associated With Rheumatoid Arthritis, Autoantibodies Serologic Status and Joint Damage in Women from Southern Mexico. Front Immunol 2021; 12:718246. [PMID: 34421923 PMCID: PMC8371707 DOI: 10.3389/fimmu.2021.718246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/19/2021] [Indexed: 12/29/2022] Open
Abstract
The enzymes of the family peptidylarginine deiminases (PADs) have an important role in the pathogenesis of rheumatoid arthritis (RA) due to their association with the anti-citrullinated protein antibodies (ACPA) production. To evaluate the association between single-nucleotide polymorphisms (SNPs) in the PADI2 gene and RA susceptibility, related clinical parameters, and the serologic status of autoantibodies in a women population with RA from southern Mexico, a case-control study was conducted (case n=229; control n=333). Sociodemographic characteristics were evaluated, along with clinical parameters, inflammation markers, the levels of ACPAs as anti-cyclic citrullinated peptides (anti-CCPs), anti-modified citrullinated vimentin (anti-MCV), and rheumatoid factor (RF). Genomic DNA was extracted from peripheral blood, and three SNPs of the PADI2 gene (rs1005753, rs2057094, and rs2235926) were performed by qPCR using TaqMan probes. The data analysis reveals that the carriers of the T allele for rs2057094 and rs2235926 presented an earlier onset of the disease (β= -3.26; p = 0.03 and β = -4.13; p = 0.015, respectively) while the carriers of the T allele for rs1005753 presented higher levels of anti-CCPs (β= 68.3; p = 0.015). Additionally, the T allele of rs2235926 was associated with a positive RF (OR = 2.90; p = 0.04), anti-MCV (OR = 2.92; p = 0.05), and with the serologic status anti-CCP+/anti-MCV+ (OR = 3.02; p = 0.03), and anti-CCP+/anti-MCV+/RF+ (OR = 3.79; p = 0.004). The haplotypes GTT (OR =1.52; p = 0.027) and TTT (OR = 1.32; p = 0.025) were associated with the presence of RA. In addition, in this study the haplotype TTT is linked to the presence of radiographic joint damage defined by a Sharp-van der Heijde score (SHS) ≥2 (OR = 1.97; p = 0.0021) and SHS ≥3 (OR = 1.94; p = 0.011). The haplotype TTT of SNPs rs1005753, rs2057094, and rs2235926 of the PADI2 gene confers genetic susceptibility to RA and radiographic joint damage in women from southern Mexico. The evidence reveals that SNPs of the PADI2 gene favors the presence of a positive serologic status in multiple autoantibodies and the clinical manifestations of RA at an early onset age.
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Affiliation(s)
| | | | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - José Eduardo Navarro-Zarza
- Department of Rheumatology and Internal Medicine, Hospital General de Chilpancingo Dr. Raymundo Abarca Alarcón, Guerrero, Mexico
| | | | - Oscar Zaragoza-García
- Faculty of Chemical-Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | - Mónica Ramírez
- Consejo Nacional de Ciencia y Tecnología, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | | | - Isela Parra-Rojas
- Faculty of Chemical-Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
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Yang ML, Sodré FMC, Mamula MJ, Overbergh L. Citrullination and PAD Enzyme Biology in Type 1 Diabetes - Regulators of Inflammation, Autoimmunity, and Pathology. Front Immunol 2021; 12:678953. [PMID: 34140951 PMCID: PMC8204103 DOI: 10.3389/fimmu.2021.678953] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023] Open
Abstract
The generation of post-translational modifications (PTMs) in human proteins is a physiological process leading to structural and immunologic variety in proteins, with potentially altered biological functions. PTMs often arise through normal responses to cellular stress, including general oxidative changes in the tissue microenvironment and intracellular stress to the endoplasmic reticulum or immune-mediated inflammatory stresses. Many studies have now illustrated the presence of 'neoepitopes' consisting of PTM self-proteins that induce robust autoimmune responses. These pathways of inflammatory neoepitope generation are commonly observed in many autoimmune diseases including systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and type 1 diabetes (T1D), among others. This review will focus on one specific PTM to self-proteins known as citrullination. Citrullination is mediated by calcium-dependent peptidylarginine deiminase (PAD) enzymes, which catalyze deimination, the conversion of arginine into the non-classical amino acid citrulline. PADs and citrullinated peptides have been associated with different autoimmune diseases, notably with a prominent role in the diagnosis and pathology of rheumatoid arthritis. More recently, an important role for PADs and citrullinated self-proteins has emerged in T1D. In this review we will provide a comprehensive overview on the pathogenic role for PADs and citrullination in inflammation and autoimmunity, with specific focus on evidence for their role in T1D. The general role of PADs in epigenetic and transcriptional processes, as well as their crucial role in histone citrullination, neutrophil biology and neutrophil extracellular trap (NET) formation will be discussed. The latter is important in view of increasing evidence for a role of neutrophils and NETosis in the pathogenesis of T1D. Further, we will discuss the underlying processes leading to citrullination, the genetic susceptibility factors for increased recognition of citrullinated epitopes by T1D HLA-susceptibility types and provide an overview of reported autoreactive responses against citrullinated epitopes, both of T cells and autoantibodies in T1D patients. Finally, we will discuss recent observations obtained in NOD mice, pointing to prevention of diabetes development through PAD inhibition, and the potential role of PAD inhibitors as novel therapeutic strategy in autoimmunity and in T1D in particular.
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Affiliation(s)
- Mei-Ling Yang
- Section of Rheumatology, Allergy and Clinical Immunology, Department of Internal Medicine, Yale University, New Haven, CT, United States
| | - Fernanda M C Sodré
- Department of Chronic Diseases, Metabolism and Ageing, Laboratory of Clinical and Experimental Endocrinology (CEE), KU Leuven, Leuven, Belgium
| | - Mark J Mamula
- Section of Rheumatology, Allergy and Clinical Immunology, Department of Internal Medicine, Yale University, New Haven, CT, United States
| | - Lut Overbergh
- Department of Chronic Diseases, Metabolism and Ageing, Laboratory of Clinical and Experimental Endocrinology (CEE), KU Leuven, Leuven, Belgium
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Bruggeman Y, Sodré FMC, Buitinga M, Mathieu C, Overbergh L, Kracht MJL. Targeting citrullination in autoimmunity: insights learned from preclinical mouse models. Expert Opin Ther Targets 2021; 25:269-281. [PMID: 33896351 DOI: 10.1080/14728222.2021.1918104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Aberrant citrullination and excessive peptidylarginine deiminase (PAD) activity are detected in numerous challenging autoimmune diseases such as rheumatoid arthritis, inflammatory bowel diseases, systemic lupus erythematosus, multiple sclerosis, and type 1 diabetes. Because excessive PAD activity is a common denominator in these diseases, PADs are interesting potential therapeutic targets for future therapies. AREAS COVERED This review summarizes the advances made in the design of PAD inhibitors, their utilization and therapeutic potential in preclinical mouse models of autoimmunity. Relevant literature encompasses studies from 1994 to 2021 that are available on PubMed.gov. EXPERT OPINION Pan-PAD inhibition is a promising therapeutic strategy for autoimmune diseases. Drugs achieving pan-PAD inhibition were capable of ameliorating, reversing, and preventing clinical symptoms in preclinical mouse models. However, the implications for PADs in key biological processes potentially present a high risk for clinical complications and could hamper the translation of PAD inhibitors to the clinic. We envisage that PAD isozyme-specific inhibitors will improve the understanding the role of PAD isozymes in disease pathology, reduce the risk of side-effects and enhance prospects for future clinical translation.
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Affiliation(s)
- Ylke Bruggeman
- Department of Chronic Diseases and Metabolism, Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Fernanda M C Sodré
- Department of Chronic Diseases and Metabolism, Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Mijke Buitinga
- Department of Chronic Diseases and Metabolism, Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium.,Department of Nutrition and Movement Sciences, Maastricht University, Maastricht, The Netherlands.,Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Chantal Mathieu
- Department of Chronic Diseases and Metabolism, Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Lut Overbergh
- Department of Chronic Diseases and Metabolism, Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Maria J L Kracht
- Department of Chronic Diseases and Metabolism, Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
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40
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Wang X, Zhang X, Peng C, Shi Y, Li H, Xu Z, Zhu W. D3DistalMutation: a Database to Explore the Effect of Distal Mutations on Enzyme Activity. J Chem Inf Model 2021; 61:2499-2508. [PMID: 33938221 DOI: 10.1021/acs.jcim.1c00318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzyme activity is affected by amino acid mutations, particularly mutations near the active site. Increasing evidence has shown that distal mutations more than 10 Å away from the active site may significantly affect enzyme activity. However, it is difficult to study the enzyme regulation mechanism of distal mutations due to the lack of a systematic collection of three-dimensional (3D) structures, highlighting distal mutation site and the corresponding enzyme activity change. Therefore, we constructed a distal mutation database, namely, D3DistalMutation, which relates the distal mutation to enzyme activity. As a result, we observed that approximately 80% of distal mutations could affect enzyme activity and 72.7% of distal mutations would decrease or abolish enzyme activity in D3DistalMutation. Only 6.6% of distal mutations in D3DistalMutation could increase enzyme activity, which have great potential to the industrial field. Among these mutations, the Y to F, S to D, and T to D mutations are most likely to increase enzyme activity, which sheds some light on industrial catalysis. Distal mutations decreasing enzyme activity in the allosteric pocket play an indispensable role in allosteric drug design. In addition, the pockets in the enzyme structures are provided to explore the enzyme regulation mechanism of distal mutations. D3DistalMutation is accessible free of charge at https://www.d3pharma.com/D3DistalMutation/index.php.
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Affiliation(s)
- Xiaoyu Wang
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Xinben Zhang
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Peng
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yulong Shi
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Huiyu Li
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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41
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Mondal S, Thompson PR. Chemical biology of protein citrullination by the protein A arginine deiminases. Curr Opin Chem Biol 2021; 63:19-27. [PMID: 33676233 DOI: 10.1016/j.cbpa.2021.01.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/19/2021] [Accepted: 01/31/2021] [Indexed: 12/25/2022]
Abstract
Citrullination is a post-translational modification (PTM) that converts peptidyl-arginine into peptidyl-citrulline; citrullination is catalyzed by the protein arginine deiminases (PADs). This PTM is associated with several physiological processes, including the epigenetic regulation of gene expression, neutrophil extracellular trap formation, and DNA-damage induced apoptosis. Notably, aberrant protein citrullination is relevant to several autoimmune and neurodegenerative diseases and certain forms of cancer. As such, the PADs are promising therapeutic targets. In this review, we discuss recent advances in the development of PAD inhibitors and activity-based probes, the development and use of citrulline-specific probes in chemoproteomic applications, and methods to site-specifically incorporate citrulline into proteins.
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Affiliation(s)
- Santanu Mondal
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, MA, 01605, USA; Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, MA, 01605, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, MA, 01605, USA; Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, MA, 01605, USA.
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42
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Site-specific incorporation of citrulline into proteins in mammalian cells. Nat Commun 2021; 12:45. [PMID: 33398026 PMCID: PMC7782748 DOI: 10.1038/s41467-020-20279-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/20/2020] [Indexed: 12/02/2022] Open
Abstract
Citrullination is a post-translational modification (PTM) of arginine that is crucial for several physiological processes, including gene regulation and neutrophil extracellular trap formation. Despite recent advances, studies of protein citrullination remain challenging due to the difficulty of accessing proteins homogeneously citrullinated at a specific site. Herein, we report a technology that enables the site-specific incorporation of citrulline (Cit) into proteins in mammalian cells. This approach exploits an engineered E. coli-derived leucyl tRNA synthetase-tRNA pair that incorporates a photocaged-citrulline (SM60) into proteins in response to a nonsense codon. Subsequently, SM60 is readily converted to Cit with light in vitro and in living cells. To demonstrate the utility of the method, we biochemically characterize the effect of incorporating Cit at two known autocitrullination sites in Protein Arginine Deiminase 4 (PAD4, R372 and R374) and show that the R372Cit and R374Cit mutants are 181- and 9-fold less active than the wild-type enzyme. This technology possesses the potential to decipher the biology of citrullination. Citrullination of arginine is crucial for several physiological processes. Here the authors report the site-specific incorporation of citrulline into proteins in mammalian cells using an engineered tRNA synthetase/tRNA pair and a photocaged-citrulline.
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Barasa L, Yong A, Yoganathan S. An Efficient Chemo‐Selective N‐Alkylation Methodology for the Structure Diversification of Indolylbenzimidazoles. ChemistrySelect 2020. [DOI: 10.1002/slct.201904745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Leonard Barasa
- Department of Pharmaceutical SciencesMedicinal Chemistry DivisionCollege of Pharmacy and Health SciencesSt. John's University 8000 Utopia Pkwy, Queens NY 11439
| | - Alison Yong
- Department of Pharmaceutical SciencesMedicinal Chemistry DivisionCollege of Pharmacy and Health SciencesSt. John's University 8000 Utopia Pkwy, Queens NY 11439
| | - Sabesan Yoganathan
- Department of Pharmaceutical SciencesMedicinal Chemistry DivisionCollege of Pharmacy and Health SciencesSt. John's University 8000 Utopia Pkwy, Queens NY 11439
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Beato M, Sharma P. Peptidyl Arginine Deiminase 2 (PADI2)-Mediated Arginine Citrullination Modulates Transcription in Cancer. Int J Mol Sci 2020; 21:ijms21041351. [PMID: 32079300 PMCID: PMC7072959 DOI: 10.3390/ijms21041351] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/12/2022] Open
Abstract
Protein arginine deimination leading to the non-coded amino acid citrulline remains a key question in the field of post-translational modifications ever since its discovery by Rogers and Simmonds in 1958. Citrullination is catalyzed by a family of enzymes called peptidyl arginine deiminases (PADIs). Initially, increased citrullination was associated with autoimmune diseases, including rheumatoid arthritis and multiple sclerosis, as well as other neurological disorders and multiple types of cancer. During the last decade, research efforts have focused on how citrullination contributes to disease pathogenesis by modulating epigenetic events, pluripotency, immunity and transcriptional regulation. However, our knowledge regarding the functional implications of citrullination remains quite limited, so we still do not completely understand its role in physiological and pathological conditions. Here, we review the recently discovered functions of PADI2-mediated citrullination of the C-terminal domain of RNA polymerase II in transcriptional regulation in breast cancer cells and the proposed mechanisms to reshape the transcription regulatory network that promotes cancer progression.
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Affiliation(s)
- Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Correspondence: (M.B.); (P.S.)
| | - Priyanka Sharma
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Correspondence: (M.B.); (P.S.)
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45
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Mahneva O, Risley MG, John C, Milton SL, Dawson-Scully K, Ja WW. In vivo expression of peptidylarginine deiminase in Drosophila melanogaster. PLoS One 2020; 15:e0227822. [PMID: 31940417 PMCID: PMC6961906 DOI: 10.1371/journal.pone.0227822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 12/30/2019] [Indexed: 11/18/2022] Open
Abstract
Peptidylarginine deiminase (PAD) modifies peptidylarginine and converts it to peptidylcitrulline in the presence of elevated calcium. Protein modification can lead to severe changes in protein structure and function, and aberrant PAD activity is linked to human pathologies. While PAD homologs have been discovered in vertebrates-as well as in protozoa, fungi, and bacteria-none have been identified in Drosophila melanogaster, a simple and widely used animal model for human diseases. Here, we describe the development of a human PAD overexpression model in Drosophila. We established fly lines harboring human PAD2 or PAD4 transgenes for ectopic expression under control of the GAL4/UAS system. We show that ubiquitous or nervous system expression of PAD2 or PAD4 have minimal impact on fly lifespan, fecundity, and the response to acute heat stress. Although we did not detect citrullinated proteins in fly homogenates, fly-expressed PAD4-but not PAD2-was active in vitro upon Ca2+ supplementation. The transgenic fly lines may be valuable in future efforts to develop animal models of PAD-related disorders and for investigating the biochemistry and regulation of PAD function.
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Affiliation(s)
- Olena Mahneva
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Monica G. Risley
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
- International Max Planck Research School (IMPRS) for Brain and Behavior, Boca Raton, Florida, United States of America
| | - Ciny John
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Sarah L. Milton
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Ken Dawson-Scully
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - William W. Ja
- Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida, United States of America
- Center on Aging, The Scripps Research Institute, Jupiter, Florida, United States of America
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46
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Méchin MC, Takahara H, Simon M. Deimination and Peptidylarginine Deiminases in Skin Physiology and Diseases. Int J Mol Sci 2020; 21:ijms21020566. [PMID: 31952341 PMCID: PMC7014782 DOI: 10.3390/ijms21020566] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/10/2020] [Accepted: 01/12/2020] [Indexed: 01/06/2023] Open
Abstract
Deimination, also known as citrullination, corresponds to the conversion of the amino acid arginine, within a peptide sequence, into the non-standard amino acid citrulline. This post-translational modification is catalyzed by a family of calcium-dependent enzymes called peptidylarginine deiminases (PADs). Deimination is implicated in a growing number of physiological processes (innate and adaptive immunity, gene regulation, embryonic development, etc.) and concerns several human diseases (rheumatoid arthritis, neurodegenerative diseases, female infertility, cancer, etc.). Here, we update the involvement of PADs in both the homeostasis of skin and skin diseases. We particularly focus on keratinocyte differentiation and the epidermal barrier function, and on hair follicles. Indeed, alteration of PAD activity in the hair shaft is responsible for two hair disorders, the uncombable hair syndrome and a particular form of inflammatory scarring alopecia, mainly affecting women of African ancestry.
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Affiliation(s)
- Marie-Claire Méchin
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université Paul Sabatier, Université de Toulouse Midi-Pyrénées, U1056, 31059 Toulouse, France;
| | - Hidenari Takahara
- University of Ibaraki, School of Agriculture, Ibaraki 300-0393, Japan;
| | - Michel Simon
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université Paul Sabatier, Université de Toulouse Midi-Pyrénées, U1056, 31059 Toulouse, France;
- Correspondence: ; Tel.: +33-5-6115-8427
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Alghamdi M, Al Ghamdi KA, Khan RH, Uversky VN, Redwan EM. An interplay of structure and intrinsic disorder in the functionality of peptidylarginine deiminases, a family of key autoimmunity-related enzymes. Cell Mol Life Sci 2019; 76:4635-4662. [PMID: 31342121 PMCID: PMC11105357 DOI: 10.1007/s00018-019-03237-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 12/21/2022]
Abstract
Citrullination is a post-translation modification of proteins, where the proteinaceous arginine residues are converted to non-coded citrulline residues. The immune tolerance to such citrullinated protein can be lost, leading to inflammatory and autoimmune diseases. Citrullination is a chemical reaction mediated by peptidylarginine deiminase enzymes (PADs), which are a family of calcium-dependent cysteine hydrolase enzymes that includes five isotypes: PAD1, PAD2, PAD3, PAD4, and PAD6. Each PAD has specific substrates and tissue distribution, where it modifies the arginine to produce a citrullinated protein with altered structure and function. All mammalian PADs have a sequence similarity of about 70-95%, whereas in humans, they are 50-55% homologous in their structure and amino acid sequences. Being calcium-dependent hydrolases, PADs are inactive under the physiological level of calcium, but could be activated due to distortions in calcium homeostasis, or when the cellular calcium levels are increased. In this article, we analyze some of the currently available data on the structural properties of human PADs, the mechanisms of their calcium-induced activation, and show that these proteins contain functionally important regions of intrinsic disorder. Citrullination represents an important trigger of multiple physiological and pathological processes, and as a result, PADs are recognized to play a number of important roles in autoimmune diseases, cancer, and neurodegeneration. Therefore, we also review the current state of the art in the development of PAD inhibitors with good potency and selectivity.
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Affiliation(s)
- Mohammed Alghamdi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
- Laboratory Department, University Medical Services Center, King Abdulaziz University, P.O. Box 80200, Jeddah, 21589, Saudi Arabia
| | - Khaled A Al Ghamdi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
| | - Rizwan H Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP, India
| | - Vladimir N Uversky
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia.
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 7 Institutskaya Str., 142290, Pushchino, Moscow region, Russia.
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Elrashdy M Redwan
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia.
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, Alexandria, 21934, Egypt.
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48
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Martinez-Prat L, Palterer B, Vitiello G, Parronchi P, Robinson WH, Mahler M. Autoantibodies to protein-arginine deiminase (PAD) 4 in rheumatoid arthritis: immunological and clinical significance, and potential for precision medicine. Expert Rev Clin Immunol 2019; 15:1073-1087. [DOI: 10.1080/1744666x.2020.1668778] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Laura Martinez-Prat
- Research and Development, Inova Diagnostics, San Diego, CA, USA
- Department of Experimental Science, Francisco de Vitoria University, Madrid, Spain
| | - Boaz Palterer
- specialist in Allergy and Clinical Immunology, Experimental and Clinical Medicine Department, University of Florence, Florence, Italy
| | - Gianfranco Vitiello
- resident in Allergy and Clinical Immunology, Experimental and Clinical Medicine Department, University of Florence, Florence, Italy
| | - Paola Parronchi
- (Allergy and Clinical Immunology), Laboratory Head, Experimental and Clinical Medicine Department, University of Florence, Florence, Italy
| | - William H. Robinson
- (Immunology and Rheumatology), Division of Immunology and Rheumatology, Stanford University, Stanford, CA, USA
- Geriatric Research Education and Clinical [GRECC] Division, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Michael Mahler
- Research and Development, Inova Diagnostics, San Diego, CA, USA
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49
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Liu XR, Rempel DL, Gross ML. Composite Conformational Changes of Signaling Proteins upon Ligand Binding Revealed by a Single Approach: Calcium-Calmodulin Study. Anal Chem 2019; 91:12560-12567. [PMID: 31487155 DOI: 10.1021/acs.analchem.9b03491] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Signaling proteins exemplified by calmodulin usually bind cooperatively to multiple ligands. Intermediate states and allosteric behavior are difficult to characterize. Here we extend a recently reported mass spectrometry (MS)-based method named LITPOMS (ligand titration, fast photochemical oxidation of proteins and mass spectrometry) that characterizes complex binding systems typically found as signaling proteins. As reported previously, calmodulin's response to binding four Ca2+ can be determined by LITPOMS to reveal binding sites, binding order, and most importantly composite binding behavior. Modeling this behavior provides site-specific binding affinities. In this article, we dissect the composite, peptide-level conformational changes at several regions either by digestion with a different protease or by tandem MS of LITPOMS behavior at the amino-acid residue level. Such dissection greatly elevates spatial resolution and increases the confidence of binding-order assignment. These complementary views of complex protein conformational change recapitulate the cumulative understanding via a single approach, providing new insights on poorly understood yet important allostery and underpin an approach applicable for exploring other signaling systems.
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Affiliation(s)
- Xiaoran Roger Liu
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Don L Rempel
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Michael L Gross
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive , St. Louis , Missouri 63130 , United States
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50
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Mondal S, Gong X, Zhang X, Salinger AJ, Zheng L, Sen S, Weerapana E, Zhang X, Thompson PR. Halogen Bonding Increases the Potency and Isozyme Selectivity of Protein Arginine Deiminase 1 Inhibitors. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Santanu Mondal
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical School 364 Plantation street Worcester MA 01605 USA
| | - Xuefeng Gong
- State Key Laboratory of Reproductive MedicineNanjing Medical University Nanjing 211166 China
| | - Xiaoqian Zhang
- State Key Laboratory of Reproductive MedicineNanjing Medical University Nanjing 211166 China
| | - Ari J. Salinger
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical School 364 Plantation street Worcester MA 01605 USA
- Department of ChemistryBoston College Chestnut Hill MA 02467 USA
| | - Li Zheng
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical School 364 Plantation street Worcester MA 01605 USA
| | - Sudeshna Sen
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical School 364 Plantation street Worcester MA 01605 USA
| | | | - Xuesen Zhang
- State Key Laboratory of Reproductive MedicineNanjing Medical University Nanjing 211166 China
| | - Paul R. Thompson
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical School 364 Plantation street Worcester MA 01605 USA
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