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Voronina AI, Miroshnichenko YV, Skvortsov VS. Bioinformatic identification of proteins with altered PTM levels in a mouse line established to study the mechanisms of the development of fibromuscular dysplasia. BIOMEDITSINSKAIA KHIMIIA 2024; 70:248-255. [PMID: 39239899 DOI: 10.18097/pbmc20247004248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
Data from a mass spectrometry experiment of a mouse line developed to study the mechanisms of fibromuscular dysplasia and deposited by d'Escamard et al. in ProteomeXchange (PXD051750) have been analyzed. Identification of peptides with post-translational modifications (PTMs) was repeated using more stringent conditions than in the original work. The following modifications were considered during analysis of changes in the PTM levels in experimental and control groups of mice: acetylation of lysine residue and N-terminal protein peptide, ubiquitination of lysine residue, phosphorylation of serine, threonine and tyrosine residues, and deamination of asparagine and glutamine residues. The multistage analysis resulted in selection of 23 proteins with PTMs for which different levels of modification between experimental and control groups could be assumed. These included six proteins with N-terminal protein acetylation, which were particularly interesting: P80318 (T-complex protein 1 subunit gamma), P43274 (Histone H1.4), P97823 (Acyl-protein thioesterase 1), P63242 (Eukaryotic translation initiation factor 5A-1), Q3UMT1 (Protein phosphatase 1 regulatory subunit 12C), Q9D8Y0 (EF-hand domain-containing protein D2). Thus, repeated bioinformatic analysis of the data deposited in the specialized databases resulted in detection of changes in the level of N-terminal acetylation of proteins that might be functionally significant in the mechanisms underlying the development of fibromuscular dysplasia.
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Affiliation(s)
- A I Voronina
- Institute of Biomedical Chemistry, Moscow, Russia
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2
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Chang SS, Cheng CC, Chen YR, Chen FW, Cheng YM, Wang JM. Epithelial CEBPD activates fibronectin and enhances macrophage adhesion in renal ischemia-reperfusion injury. Cell Death Discov 2024; 10:328. [PMID: 39025831 PMCID: PMC11258324 DOI: 10.1038/s41420-024-02082-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 06/14/2024] [Accepted: 06/21/2024] [Indexed: 07/20/2024] Open
Abstract
Ischemia-reperfusion injury (IRI) is a cause of acute kidney injury in patients after renal transplantation and leads to high morbidity and mortality. Damaged kidney resident cells release cytokines and chemokines, which rapidly recruit leukocytes. Fibronectin (FN-1) contributes to immune cell migration, adhesion and growth in inflamed tissues. CCAAT/enhancer-binding protein delta is responsive to inflammatory cytokines and stresses and plays functional roles in cell motility, extracellular matrix production and immune responses. We found that the expression of CCAAT/enhancer-binding protein delta was increased in renal epithelial cells in IRI mice compared with sham mice. Following IRI, the colocalization of FN-1 with the macrophage marker F4/80 was increased in renal injury model wild-type mice but was significantly attenuated in Cebpd-deficient mice. Inactivation of CEBPD can repress hypoxia-induced FN-1 expression in HK-2 cells. Moreover, the inactivation of CEBPD and FN-1 also reduces macrophage accumulation in HK-2 cells. These findings suggest that the involvement of CEBPD in macrophage accumulation through the activation of FN-1 expression and the inhibition of CEBPD can protect against renal IRI.
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Affiliation(s)
- Shen-Shin Chang
- Division of Transplantation, Department of Surgery, National Chung Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Chao-Chun Cheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ying-Ren Chen
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Feng-Wei Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ya-Min Cheng
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan.
- Department of Obstetrics and Gynecology, Kuo General Hospital, Tainan, 700, Taiwan.
| | - Ju-Ming Wang
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan.
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan.
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
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3
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Kalailingam P, Mohd‐Kahliab K, Ngan SC, Iyappan R, Melekh E, Lu T, Zien GW, Sharma B, Guo T, MacNeil AJ, MacPherson REK, Tsiani EL, O'Leary DD, Lim KL, Su IH, Gao Y, Richards AM, Kalaria RN, Chen CP, McCarthy NE, Sze SK. Immunotherapy targeting isoDGR-protein damage extends lifespan in a mouse model of protein deamidation. EMBO Mol Med 2023; 15:e18526. [PMID: 37971164 PMCID: PMC10701600 DOI: 10.15252/emmm.202318526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
Aging results from the accumulation of molecular damage that impairs normal biochemical processes. We previously reported that age-linked damage to amino acid sequence NGR (Asn-Gly-Arg) results in "gain-of-function" conformational switching to isoDGR (isoAsp-Gly-Arg). This integrin-binding motif activates leukocytes and promotes chronic inflammation, which are characteristic features of age-linked cardiovascular disorders. We now report that anti-isoDGR immunotherapy mitigates lifespan reduction of Pcmt1-/- mouse. We observed extensive accumulation of isoDGR and inflammatory cytokine expression in multiple tissues from Pcmt1-/- and naturally aged WT animals, which could also be induced via injection of isoDGR-modified plasma proteins or synthetic peptides into young WT animals. However, weekly injection of anti-isoDGR mAb (1 mg/kg) was sufficient to significantly reduce isoDGR-protein levels in body tissues, decreased pro-inflammatory cytokine concentrations in blood plasma, improved cognition/coordination metrics, and extended the average lifespan of Pcmt1-/- mice. Mechanistically, isoDGR-mAb mediated immune clearance of damaged isoDGR-proteins via antibody-dependent cellular phagocytosis (ADCP). These results indicate that immunotherapy targeting age-linked protein damage may represent an effective intervention strategy in a range of human degenerative disorders.
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Affiliation(s)
| | | | - SoFong Cam Ngan
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Ranjith Iyappan
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Evelin Melekh
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Tian Lu
- iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life SciencesWestlake UniversityHangzhouChina
| | - Gan Wei Zien
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Bhargy Sharma
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Tiannan Guo
- iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life SciencesWestlake UniversityHangzhouChina
| | - Adam J MacNeil
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Rebecca EK MacPherson
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Evangelia Litsa Tsiani
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Deborah D O'Leary
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Kah Leong Lim
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
| | - I Hsin Su
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Yong‐Gui Gao
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - A Mark Richards
- Department of CardiologyNational University Heart CentreSingaporeSingapore
- Department of CardiologyUniversity of OtagoChristchurchNew Zealand
| | - Raj N Kalaria
- Institute of Neuroscience, Campus for Ageing and VitalityNewcastle UniversityNewcastle upon TyneUK
| | - Christopher P Chen
- Memory, Aging and Cognition CentreNational University Health SystemSingaporeSingapore
| | - Neil E McCarthy
- Centre for Immunobiology, The Blizard Institute, Bart's and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Siu Kwan Sze
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
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4
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He Q, Sze SK, Ng KS, Koh CG. Paxillin interactome identified by SILAC and label-free approaches coupled to TurboID sheds light on the compositions of focal adhesions in mouse embryonic stem cells. Biochem Biophys Res Commun 2023; 680:73-85. [PMID: 37725837 DOI: 10.1016/j.bbrc.2023.09.017] [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: 07/09/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
Self-renewal and differentiation of mouse embryonic stem cells (mESCs) are greatly affected by the extracellular matrix (ECM) environment; the composition and stiffness of which are sensed by the cells via integrin-associated focal adhesions (FAs) which link the cells to the ECM. Although FAs have been studied extensively in differentiated cells, their composition and function in mESCs are not as well elucidated. To gain more detailed knowledge of the molecular compositions of FAs in mESCs, we adopted the proximity-dependent biotinylation (BioID) proteomics approach. Paxillin, a known FA protein (FAP), is fused to the promiscuous biotin ligase TurboID as bait. We employed both SILAC- and label-free (LF)-based quantitative proteomics to strengthen as well as complement individual approach. The mass spectrometry data derived from SILAC and LF identified 38 and 443 proteins, respectively, with 35 overlapping candidates. Fifteen of these shared proteins are known FAPs based on literature-curated adhesome and 7 others are among the reported "meta-adhesome", suggesting the components of FAs are largely conserved between mESCs and differentiated cells. Furthermore, the LF data set contained an additional 18 literature-curated FAPs. Notably, the overlapped proteomics data failed to detect LIM-domain proteins such as zyxin family proteins, which suggests that FAs in mESCs are less mature than differentiated cells. Using the LF approach, we are able to identify PDLIM7, a LIM-domain protein, as a FAP in mESCs. This study illustrates the effectiveness of TurboID in mESCs. Importantly, we found that application of both SILAC and LF methods in combination allowed us to analyze the TurboID proteomics data in an unbiased, stringent and yet comprehensive manner.
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Affiliation(s)
- Qianqian He
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Kai Soon Ng
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Cheng-Gee Koh
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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5
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Chandran M, S S, Abhirami, Chandran A, Jaleel A, Plakkal Ayyappan J. Defining atherosclerotic plaque biology by mass spectrometry-based omics approaches. Mol Omics 2023; 19:6-26. [PMID: 36426765 DOI: 10.1039/d2mo00260d] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Atherosclerosis is the principal cause of vascular diseases and one of the leading causes of worldwide death. Even though several insights into its natural course, risk factors and interventions have been identified, it is still an ongoing global pandemic. Since the structure and biochemical composition of the plaques show high heterogeneity, a comprehensive understanding of the intraplaque composition, its microenvironment, and the mechanisms of the progression and instability across different vascular beds at their progression stages is crucial for better risk stratification and treatment modalities. Even though several cell-based studies, animal studies, and extensive multicentric population studies have been conducted concerning cardiovascular diseases for assessing the risk factors and plaque biology, the studies on human clinical samples are very limited. New novel approaches utilize samples from percutaneous coronary interventions, which could possibly gain more access to clinical samples at different stages of the diseases without complex invasive resections. As an emerging technological platform in disease discovery research, mass spectrometry-based omics technologies offer capabilities for a comprehensive understanding of the mechanisms linked to several vascular diseases. Here, we discuss the cellular and molecular processes of atherosclerosis, different mass spectrometry-based omics approaches, and the studies mostly done on clinical samples of atheroma plaque using mass spectrometry-based proteomics, metabolomics and lipidomics approaches.
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Affiliation(s)
- Mahesh Chandran
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India. .,Department of Biotechnology, University of Kerala, Thiruvananthapuram 695034, Kerala, India.,Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695012, India
| | - Sudhina S
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India.
| | - Abhirami
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India.
| | - Akash Chandran
- Department of Nanoscience and Nanotechnology, University of Kerala, Kariavattom, Thiruvananthapuram-695581, Kerala, India
| | - Abdul Jaleel
- Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695012, India
| | - Janeesh Plakkal Ayyappan
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India. .,Department of Biotechnology, University of Kerala, Thiruvananthapuram 695034, Kerala, India.,Department of Nanoscience and Nanotechnology, University of Kerala, Kariavattom, Thiruvananthapuram-695581, Kerala, India.,Centre for Advanced Cancer Research, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India
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6
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Lorca C, Mulet M, Arévalo-Caro C, Sanchez MÁ, Perez A, Perrino M, Bach-Faig A, Aguilar-Martínez A, Vilella E, Gallart-Palau X, Serra A. Plant-derived nootropics and human cognition: A systematic review. Crit Rev Food Sci Nutr 2022; 63:5521-5545. [PMID: 34978226 DOI: 10.1080/10408398.2021.2021137] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Substances with modulatory capabilities on certain aspects of human cognition have been revered as nootropics from the dawn of time. The plant kingdom provides most of the currently available nootropics of natural origin. Here, in this systematic review, we aim to provide state-of-the-art information regarding proven and unproven effects of plant-derived nootropics (PDNs) on human cognition in conditions of health and disease. Six independent searches, one for each neurocognitive domain (NCD), were performed in parallel using three independent scientific library databases: PubMed, Cochrane and Scopus. Only scientific studies and systematic reviews with humans published between January 2000 and November 2021 were reviewed, and 256 papers were included. Ginkgo biloba was the most relevant nootropic regarding perceptual and motor functions. Bacopa monnieri improves language, learning and memory. Withania somnifera (Ashwagandha) modulates anxiety and social-related cognitions. Caffeine enhances attention and executive functions. Together, the results from the compiled studies highlight the nootropic effects and the inconsistencies regarding PDNs that require further research.Supplemental data for this article is available online at https://doi.org/10.1080/10408398.2021.2021137.
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Affiliation(s)
- Cristina Lorca
- IMDEA-Food Research Institute, +Pec Proteomics, Campus of International Excellence UAM + CSIC, Old Cantoblanco Hospital, Madrid, Spain
- Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRB Lleida) - Neuroscience Area - University Hospital Arnau de Vilanova (HUAV) - School of Medicine, University of Lleida (UdL), Lleida, Spain
- Proteored - Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Mulet
- Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRB Lleida) - Neuroscience Area - University Hospital Arnau de Vilanova (HUAV) - School of Medicine, University of Lleida (UdL), Lleida, Spain
| | - Catalina Arévalo-Caro
- Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRB Lleida) - Neuroscience Area - University Hospital Arnau de Vilanova (HUAV) - School of Medicine, University of Lleida (UdL), Lleida, Spain
| | - M Ángeles Sanchez
- IMDEA-Food Research Institute, +Pec Proteomics, Campus of International Excellence UAM + CSIC, Old Cantoblanco Hospital, Madrid, Spain
| | - Ainhoa Perez
- IMDEA-Food Research Institute, +Pec Proteomics, Campus of International Excellence UAM + CSIC, Old Cantoblanco Hospital, Madrid, Spain
| | - María Perrino
- IMDEA-Food Research Institute, +Pec Proteomics, Campus of International Excellence UAM + CSIC, Old Cantoblanco Hospital, Madrid, Spain
| | - Anna Bach-Faig
- FoodLab Research Group (2017SGR 83), Faculty of Health Sciences, Open University of Catalonia (UOC), Barcelona, Spain
- Food and Nutrition Area, Barcelona Official College of Pharmacists, Barcelona, Spain
| | - Alicia Aguilar-Martínez
- FoodLab Research Group (2017SGR 83), Faculty of Health Sciences, Open University of Catalonia (UOC), Barcelona, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata (HUIPM), Institut Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
- Universitat Rovira i Virgili (URV), Reus, Spain
- Centro de investigación Biomédica en Salud Mental CIBERSAM, Instituto de Salud Carlos III, Madrid, Spain
| | - Xavier Gallart-Palau
- Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRB Lleida) - Neuroscience Area - University Hospital Arnau de Vilanova (HUAV) - School of Medicine, University of Lleida (UdL), Lleida, Spain
- Proteored - Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Hospital Universitari Institut Pere Mata (HUIPM), Institut Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
- Centro de investigación Biomédica en Salud Mental CIBERSAM, Instituto de Salud Carlos III, Madrid, Spain
| | - Aida Serra
- IMDEA-Food Research Institute, +Pec Proteomics, Campus of International Excellence UAM + CSIC, Old Cantoblanco Hospital, Madrid, Spain
- Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRB Lleida) - Neuroscience Area - University Hospital Arnau de Vilanova (HUAV) - School of Medicine, University of Lleida (UdL), Lleida, Spain
- Proteored - Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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7
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Zanardi A, Barbariga M, Conti A, Vegliani F, Curnis F, Alessio M. Oxidized/deamidated-ceruloplasmin dysregulates choroid plexus epithelial cells functionality and barrier properties via RGD-recognizing integrin binding. Neurobiol Dis 2021; 158:105474. [PMID: 34384868 DOI: 10.1016/j.nbd.2021.105474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/19/2022] Open
Abstract
Choroid plexus epithelial cells (CPEpiCs) determine the composition of cerebrospinal fluid (CSF) and constitute the blood-CSF barrier (BCSFB), functions that are altered in neurodegenerative diseases. In Parkinson's disease (PD) the pathological environment oxidizes and deamidates the ceruloplasmin, a CSF-resident ferroxidase, which undergoes a gain of RGD-recognizing integrin binding property, that may result in signal transduction. We investigated the effects that oxidized/deamidated ceruloplasmin (Cp-ox/de) may exert on CPEpiCs functions. Through RGD-recognizing integrins binding, Cp-ox/de mediates CPEpiCs adhesion and intracellular signaling, resulting in cell proliferation inhibition and alteration of the secretome profile in terms of proteins related to cell-extracellular matrix interaction. Oxidative conditions, comparable to those found in the CSF of PD patients, induced CPEpiCs barrier leakage, allowing Cp-ox/de to cross it, transducing integrins-mediated signal that further worsens BCSFB integrity. This mechanism might contribute to PD pathological processes altering CSF composition and aggravating the already compromised BCSFB function.
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Affiliation(s)
- Alan Zanardi
- Proteome Biochemistry, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy.
| | - Marco Barbariga
- Proteome Biochemistry, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy
| | - Antonio Conti
- Proteome Biochemistry, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy.
| | - Franco Vegliani
- Proteome Biochemistry, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy
| | - Flavio Curnis
- Tumor Biology and Vascular Targeting, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy.
| | - Massimo Alessio
- Proteome Biochemistry, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy.
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8
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Park JE, JebaMercy G, Pazhanchamy K, Guo X, Ngan SC, Liou KCK, Lynn SE, Ng SS, Meng W, Lim SC, Leow MKS, Richards AM, Pennington DJ, de Kleijn DPV, Sorokin V, Ho HH, McCarthy NE, Sze SK. Aging-induced isoDGR-modified fibronectin activates monocytic and endothelial cells to promote atherosclerosis. Atherosclerosis 2021; 324:58-68. [PMID: 33831670 DOI: 10.1016/j.atherosclerosis.2021.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/24/2021] [Accepted: 03/18/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND AIMS Aging is the primary risk factor for cardiovascular disease (CVD), but the mechanisms underlying age-linked atherosclerosis remain unclear. We previously observed that long-lived vascular matrix proteins can acquire 'gain-of-function' isoDGR motifs that might play a role in atherosclerotic pathology. METHODS IsoDGR-specific mAb were generated and used for ELISA-based measurement of motif levels in plasma samples from patients with coronary artery diseases (CAD) and non-CAD controls. Functional consequences of isoDGR accumulation in age-damaged fibronectin were determined by bioassay for capacity to activate monocytes, macrophages, and endothelial cells (signalling activity, pro-inflammatory cytokine expression, and recruitment/adhesion potential). Mice deficient in the isoDGR repair enzyme PCMT1 were used to assess motif distribution and macrophage localisation in vivo. RESULTS IsoDGR-modified fibronectin and fibrinogen levels in patient plasma were significantly enhanced in CAD and further associated with smoking status. Functional assays demonstrated that isoDGR-modified fibronectin activated both monocytes and macrophages via integrin receptor 'outside in' signalling, triggering an ERK:AP-1 cascade and expression of pro-inflammatory cytokines MCP-1 and TNFα to drive additional recruitment of circulating leukocytes. IsoDGR-modified fibronectin also induced endothelial cell expression of integrin β1 to further enhance cellular adhesion and matrix deposition. Analysis of murine aortic tissues confirmed accumulation of isoDGR-modified proteins co-localised with CD68+ macrophages in vivo. CONCLUSIONS Age-damaged fibronectin features isoDGR motifs that increase binding to integrins on the surface of monocytes, macrophages, and endothelial cells. Subsequent activation of 'outside-in' signalling elicits a range of potent cytokines and chemokines that drive additional leukocyte recruitment to the developing atherosclerotic matrix.
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Affiliation(s)
- Jung Eun Park
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Gnanasekaran JebaMercy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Kalailingam Pazhanchamy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Xue Guo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - SoFong Cam Ngan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Ken Cheng Kang Liou
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Soe EinSi Lynn
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Ser Sue Ng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Wei Meng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Su Chi Lim
- Diabetes Center, Khoo Teck Puat Hospital, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Melvin Khee-Shing Leow
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore; Lee Kong Chian School of Medicine, NTU, Singapore; Department of Endocrinology, Tan Tock Seng Hospital, Singapore
| | - A Mark Richards
- Cardiovascular Research Institute, National University of Singapore, Singapore, 119228; Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch, 8140, New Zealand
| | - Daniel J Pennington
- Centre for Immunobiology, The Blizard Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Dominique P V de Kleijn
- Department of Vascular Surgery, UMC Utrecht, Utrecht University, Utrecht, the Netherlands; Netherlands Heart Institute, Utrecht, the Netherlands
| | - Vitaly Sorokin
- Department of Cardiac, Thoracic and Vascular Surgery, National University Heart Centre, National University Health System, Singapore, 119228
| | - Hee Hwa Ho
- Department of Cardiology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433
| | - Neil E McCarthy
- Centre for Immunobiology, The Blizard Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551.
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9
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Ceruloplasmin Deamidation in Neurodegeneration: From Loss to Gain of Function. Int J Mol Sci 2021; 22:ijms22020663. [PMID: 33440850 PMCID: PMC7827708 DOI: 10.3390/ijms22020663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative disorders can induce modifications of several proteins; one of which is ceruloplasmin (Cp), a ferroxidase enzyme found modified in the cerebrospinal fluid (CSF) of neurodegenerative diseases patients. Cp modifications are caused by the oxidation induced by the pathological environment and are usually associated with activity loss. Together with oxidation, deamidation of Cp was found in the CSF from Alzheimer’s and Parkinson’s disease patients. Protein deamidation is a process characterized by asparagine residues conversion in either aspartate or isoaspartate, depending on protein sequence/structure and cellular environment. Cp deamidation occurs at two Asparagine-Glycine-Arginine (NGR)-motifs which, once deamidated to isoAspartate-Glycine-Arginine (isoDGR), bind integrins, a family of receptors mediating cell adhesion. Therefore, on the one hand, Cp modifications lead to loss of enzymatic activity, while on the other hand, these alterations confer gain of function to Cp. In fact, deamidated Cp binds to integrins and triggers intracellular signaling on choroid plexus epithelial cells, changing cell functioning. Working in concert with the oxidative environment, Cp deamidation could reach different target cells in the brain, altering their physiology and causing detrimental effects, which might contribute to the pathological mechanism.
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Ceruloplasmin oxidized and deamidated by Parkinson's disease cerebrospinal fluid induces epithelial cells proliferation arrest and apoptosis. Sci Rep 2020; 10:15507. [PMID: 32968118 PMCID: PMC7511351 DOI: 10.1038/s41598-020-72447-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
In Parkinson's disease, the ferroxidase ceruloplasmin (Cp) is oxidized and deamidated by the pathological cerebrospinal fluid (CSF) environment. These modifications promote the gain of integrin binding properties, fostered by the deamidation of two NGR-motifs present in the Cp sequence that convert into the isoDGR-motif. Through isoDGR/integrin binding, the oxidized/deamidated-Cp (Cp-ox/de) mediates cell adhesion and transduces an intracellular signal in epithelial cells that seems to be addressed to regulate cell cycle, proliferation and cytoskeletal re-arrangement. However, the effect fostered on cells by integrins engagement via Cp-ox/de is not known. We found that in HaCaT epithelial cells, the incubation with Cp-ox/de resulted in proliferation inhibition mediated by isoDGR, cell cycle arrest and apoptosis induction. Similar proliferation inhibition was induced by treatment with purified Cp previously incubated in the CSF from Parkinson's disease patients, but not by Cp incubated in the CSF from healthy subjects. In human primary choroid plexus epithelial cells, a possible in vivo target of Cp-ox/de generated in pathological CSFs, we found that Cp-ox/de mediated cell adhesion via isoDGR/integrins binding and transduced an intracellular signal, which resulted in cell proliferation inhibition. Thus, the generation of Cp-ox/de in pathological CSFs and the consequent apoptosis induction of epithelial cells facing the liquor, might represent a novel mechanism that contributes to neurodegeneration.
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11
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St. Paul A, Corbett CB, Okune R, Autieri MV. Angiotensin II, Hypercholesterolemia, and Vascular Smooth Muscle Cells: A Perfect Trio for Vascular Pathology. Int J Mol Sci 2020; 21:E4525. [PMID: 32630530 PMCID: PMC7350267 DOI: 10.3390/ijms21124525] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/16/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular disease is the leading cause of morbidity and mortality in the Western and developing world, and the incidence of cardiovascular disease is increasing with the longer lifespan afforded by our modern lifestyle. Vascular diseases including coronary heart disease, high blood pressure, and stroke comprise the majority of cardiovascular diseases, and therefore represent a significant medical and socioeconomic burden on our society. It may not be surprising that these conditions overlap and potentiate each other when we consider the many cellular and molecular similarities between them. These intersecting points are manifested in clinical studies in which lipid lowering therapies reduce blood pressure, and anti-hypertensive medications reduce atherosclerotic plaque. At the molecular level, the vascular smooth muscle cell (VSMC) is the target, integrator, and effector cell of both atherogenic and the major effector protein of the hypertensive signal Angiotensin II (Ang II). Together, these signals can potentiate each other and prime the artery and exacerbate hypertension and atherosclerosis. Therefore, VSMCs are the fulcrum in progression of these diseases and, therefore, understanding the effects of atherogenic stimuli and Ang II on the VSMC is key to understanding and treating atherosclerosis and hypertension. In this review, we will examine studies in which hypertension and atherosclerosis intersect on the VSMC, and illustrate common pathways between these two diseases and vascular aging.
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Affiliation(s)
| | | | | | - Michael V. Autieri
- Department of Physiology, Independence Blue Cross Cardiovascular Research Center, Temple University School of Medicine, Philadelphia, PA 19140, USA; (A.S.P.); (C.B.C.); (R.O.)
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12
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Sze SK, JebaMercy G, Ngan SC. Profiling the 'deamidome' of complex biosamples using mixed-mode chromatography-coupled tandem mass spectrometry. Methods 2020; 200:31-41. [PMID: 32418626 DOI: 10.1016/j.ymeth.2020.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 04/26/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022] Open
Abstract
Deamidation is a spontaneous degenerative protein modification (DPM) that disrupts the structure and function of both endogenous proteins and various therapeutic agents. While deamidation has long been recognized as a critical event in human aging and multiple degenerative diseases, research progress in this field has been restricted by the technical challenges associated with studying this DPM in complex biological samples. Asparagine (Asn) deamidation generates L-aspartic acid (L-Asp), D-aspartic acid (D-Asp), L-isoaspartic acid (L-isoAsp) or D-isoaspartic acid (D-isoAsp) residues at the same position of Asn in the affected protein, but each of these amino acids displays similar hydrophobicity and cannot be effectively separated by reverse phase liquid chromatography. The Asp and isoAsp isoforms are also difficult to resolve using mass spectrometry since they have the same mass and fragmentation pattern in MS/MS. Moreover, the 13C peaks of the amidated peptide are often misassigned as monoisotopic peaks of the corresponding deamidated peptides in protein database searches. Furthermore, typical protein isolation and proteomic sample preparation methods induce artificial deamidation that cannot be distinguished from the physiological forms. To better understand the role of deamidation in biological aging and degenerative pathologies, new technologies are now being developed to address these analytical challenges, including mixed mode electrostatic-interaction modified hydrophilic interaction liquid chromatography (emHILIC). When coupled to high resolution, high accuracy tandem mass spectrometry this technology enables unprecedented, proteome-wide study of the 'deamidome' of complex samples. The current article therefore reviews recent advances in sample preparation methods, emHILIC-MS/MS technology, and MS instrumentation / data processing approaches to achieving accurate and reliable characterization of protein deamidation in complex biological and clinical samples.
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Affiliation(s)
- Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Gnanasekaran JebaMercy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - SoFong Cam Ngan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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13
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Adav SS, Sze SK. Hypoxia-Induced Degenerative Protein Modifications Associated with Aging and Age-Associated Disorders. Aging Dis 2020; 11:341-364. [PMID: 32257546 PMCID: PMC7069466 DOI: 10.14336/ad.2019.0604] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/04/2019] [Indexed: 12/18/2022] Open
Abstract
Aging is an inevitable time-dependent decline of various physiological functions that finally leads to death. Progressive protein damage and aggregation have been proposed as the root cause of imbalance in regulatory processes and risk factors for aging and neurodegenerative diseases. Oxygen is a modulator of aging. The oxygen-deprived conditions (hypoxia) leads to oxidative stress, cellular damage and protein modifications. Despite unambiguous evidence of the critical role of spontaneous non-enzymatic Degenerative Protein Modifications (DPMs) such as oxidation, glycation, carbonylation, carbamylation, and deamidation, that impart deleterious structural and functional protein alterations during aging and age-associated disorders, the mechanism that mediates these modifications is poorly understood. This review summarizes up-to-date information and recent developments that correlate DPMs, aging, hypoxia, and age-associated neurodegenerative diseases. Despite numerous advances in the study of the molecular hallmark of aging, hypoxia, and degenerative protein modifications during aging and age-associated pathologies, a major challenge remains there to dissect the relative contribution of different DPMs in aging (either natural or hypoxia-induced) and age-associated neurodegeneration.
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Affiliation(s)
- Sunil S Adav
- School of Biological Sciences, Nanyang Technological University, Singapore
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore
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14
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Sirtuin-1 and Its Relevance in Vascular Calcification. Int J Mol Sci 2020; 21:ijms21051593. [PMID: 32111067 PMCID: PMC7084838 DOI: 10.3390/ijms21051593] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 12/16/2022] Open
Abstract
Vascular calcification (VC) is highly associated with cardiovascular disease and all-cause mortality in patients with chronic kidney disease. Dysregulation of endothelial cells and vascular smooth muscle cells (VSMCs) is related to VC. Sirtuin-1 (Sirt1) deacetylase encompasses a broad range of transcription factors that are linked to an extended lifespan. Sirt1 enhances endothelial NO synthase and upregulates FoxOs to activate its antioxidant properties and delay cell senescence. Sirt1 reverses osteogenic phenotypic transdifferentiation by influencing RUNX2 expression in VSMCs. Low Sirt1 hardly prevents acetylation by p300 and phosphorylation of β-catenin that, following the facilitation of β-catenin translocation, drives osteogenic phenotypic transdifferentiation. Hyperphosphatemia induces VC by osteogenic conversion, apoptosis, and senescence of VSMCs through the Pit-1 cotransporter, which can be retarded by the sirt1 activator resveratrol. Proinflammatory adipocytokines released from dysfunctional perivascular adipose tissue (PVAT) mediate medial calcification and arterial stiffness. Sirt1 ameliorates release of PVAT adipokines and increases adiponectin secretion, which interact with FoxO 1 against oxidative stress and inflammatory arterial insult. Conclusively, Sirt1 decelerates VC by means of influencing endothelial NO bioavailability, senescence of ECs and VSMCs, osteogenic phenotypic transdifferentiation, apoptosis of VSMCs, ECM deposition, and the inflammatory response of PVAT. Factors that aggravate VC include vitamin D deficiency-related macrophage recruitment and further inflammation responses. Supplementation with vitamin D to adequate levels is beneficial in improving PVAT macrophage infiltration and local inflammation, which further prevents VC.
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Gallart-Palau X, Tan LM, Serra A, Gao Y, Ho HH, Richards AM, Kandiah N, Chen CP, Kalaria RN, Sze SK. Degenerative protein modifications in the aging vasculature and central nervous system: A problem shared is not always halved. Ageing Res Rev 2019; 53:100909. [PMID: 31116994 DOI: 10.1016/j.arr.2019.100909] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/16/2019] [Accepted: 05/16/2019] [Indexed: 02/08/2023]
Abstract
Aging influences the pathogenesis and progression of several major diseases affecting both the cardiovascular system (CVS) and central nervous system (CNS). Defining the common molecular features that underpin these disorders in these crucial body systems will likely lead to increased quality of life and improved 'health-span' in the global aging population. Degenerative protein modifications (DPMs) have been strongly implicated in the molecular pathogenesis of several age-related diseases affecting the CVS and CNS, including atherosclerosis, heart disease, dementia syndromes, and stroke. However, these isolated findings have yet to be integrated into a wider framework, which considers the possibility that, despite their distinct features, CVS and CNS disorders may in fact be closely related phenomena. In this work, we review the current literature describing molecular roles of the major age-associated DPMs thought to significantly impact on human health, including carbamylation, citrullination and deamidation. In particular, we focus on data indicating that specific DPMs are shared between multiple age-related diseases in both CVS and CNS settings. By contextualizing these data, we aim to assist future studies in defining the universal mechanisms that underpin both vascular and neurological manifestations of age-related protein degeneration.
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Artificially intelligent proteomics improves cardiovascular risk assessment. EBioMedicine 2019; 40:23-24. [PMID: 30651217 PMCID: PMC6413680 DOI: 10.1016/j.ebiom.2019.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 01/07/2019] [Indexed: 11/22/2022] Open
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17
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Chang WC, Yu YM, Cheng AC. Curcumin suppresses pro-inflammatory adhesion response in Human Umbilical Vein Endothelial Cells. J Food Biochem 2018. [DOI: 10.1111/jfbc.12623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Weng-Cheng Chang
- Department of Otolaryngology; Taichung Tzu Chi Hospital; Buddhist Tzu Chi Medical Foundation; Taiwan
| | - Ya-Mei Yu
- Department of Senior Citizen Service Management; National Taichung University of Science and Technology; Taichung Taiwan
| | - An-Chin Cheng
- Department of Nutrition and Health Sciences; Chang Jung Christian University; Tainan Taiwan
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Kirikoshi R, Manabe N, Takahashi O. Phosphate-Catalyzed Succinimide Formation from an NGR-Containing Cyclic Peptide: A Novel Mechanism for Deammoniation of the Tetrahedral Intermediate. Molecules 2018; 23:E2217. [PMID: 30200364 PMCID: PMC6225186 DOI: 10.3390/molecules23092217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/15/2018] [Accepted: 08/30/2018] [Indexed: 01/23/2023] Open
Abstract
Spontaneous deamidation in the Asn-Gly-Arg (NGR) motif that yields an isoAsp-Gly-Arg (isoDGR) sequence has recently attracted considerable attention because of the possibility of application to dual tumor targeting. It is well known that Asn deamidation reactions in peptide chains occur via the five-membered ring succinimide intermediate. Recently, we computationally showed by the B3LYP density functional theory method, that inorganic phosphate and the Arg side chain can catalyze the NGR deamidation using a cyclic peptide, c[CH₂CO⁻NGRC]⁻NH₂. In this previous study, the tetrahedral intermediate of the succinimide formation was assumed to be readily protonated at the nitrogen originating from the Asn side chain by the solvent water before the release of an NH₃ molecule. In the present study, we found a new mechanism for the decomposition of the tetrahedral intermediate that does not require the protonation by an external proton source. The computational method is the same as in the previous study. In the new mechanism, the release of an NH₃ molecule occurs after a proton exchange between the peptide and the phosphate and conformational changes. The rate-determining step of the overall reaction course is the previously reported first step, i.e., the cyclization to form the tetrahedral intermediate.
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Affiliation(s)
- Ryota Kirikoshi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Noriyoshi Manabe
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
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