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Cloyd AK, Boone K, Ye Q, Snead ML, Spencer P, Tamerler C. Engineered Peptides Enable Biomimetic Route for Collagen Intrafibrillar Mineralization. Int J Mol Sci 2023; 24:ijms24076355. [PMID: 37047325 PMCID: PMC10093982 DOI: 10.3390/ijms24076355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/07/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Overcoming the short lifespan of current dental adhesives remains a significant clinical need. Adhesives rely on formation of the hybrid layer to adhere to dentin and penetrate within collagen fibrils. However, the ability of adhesives to achieve complete enclosure of demineralized collagen fibrils is recognized as currently unattainable. We developed a peptide-based approach enabling collagen intrafibrillar mineralization and tested our hypothesis on a type-I collagen-based platform. Peptide design incorporated collagen-binding and remineralization-mediating properties using the domain structure conservation approach. The structural changes from representative members of different peptide clusters were generated for each functional domain. Common signatures associated with secondary structure features and the related changes in the functional domain were investigated by attenuated total reflectance Fourier-transform infrared (ATR-FTIR) and circular dichroism (CD) spectroscopy, respectively. Assembly and remineralization properties of the peptides on the collagen platforms were studied using atomic force microscopy (AFM). Mechanical properties of the collagen fibrils remineralized by the peptide assemblies was studied using PeakForce-Quantitative Nanomechanics (PF-QNM)-AFM. The engineered peptide was demonstrated to offer a promising route for collagen intrafibrillar remineralization. This approach offers a collagen platform to develop multifunctional strategies that combine different bioactive peptides, polymerizable peptide monomers, and adhesive formulations as steps towards improving the long-term prospects of composite resins.
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Affiliation(s)
- Aya K. Cloyd
- Bioengineering Program, University of Kansas, Lawrence, KS 66045, USA
- Institute for Bioengineering Research, University of Kansas, Lawrence, KS 66045, USA
| | - Kyle Boone
- Institute for Bioengineering Research, University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66045, USA
| | - Qiang Ye
- Institute for Bioengineering Research, University of Kansas, Lawrence, KS 66045, USA
| | - Malcolm L. Snead
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA 90007, USA
| | - Paulette Spencer
- Bioengineering Program, University of Kansas, Lawrence, KS 66045, USA
- Institute for Bioengineering Research, University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66045, USA
| | - Candan Tamerler
- Bioengineering Program, University of Kansas, Lawrence, KS 66045, USA
- Institute for Bioengineering Research, University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66045, USA
- Correspondence:
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Sarfraz MH, Shahid A, Asghar S, Aslam B, Ashfaq UA, Raza H, Prieto MA, Simal-Gandara J, Barba FJ, Rajoka MSR, Khurshid M, Nashwan AJ. Personalized nutrition, microbiota, and metabolism: A triad for eudaimonia. Front Mol Biosci 2022; 9:1038830. [PMID: 36330221 PMCID: PMC9623024 DOI: 10.3389/fmolb.2022.1038830] [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] [Received: 09/07/2022] [Accepted: 10/06/2022] [Indexed: 11/28/2022] Open
Abstract
During the previous few years, the relationship between the gut microbiota, metabolic disorders, and diet has come to light, especially due to the understanding of the mechanisms that particularly link the gut microbiota with obesity in animal models and clinical trials. Research has led to the understanding that the responses of individuals to dietary inputs vary remarkably therefore no single diet can be suggested to every individual. The variations are attributed to differences in the microbiome and host characteristics. In general, it is believed that the immanent nature of host-derived factors makes them difficult to modulate. However, diet can more easily shape the microbiome, potentially influencing human physiology through modulation of digestion, absorption, mucosal immune response, and the availability of bioactive compounds. Thus, diet could be useful to influence the physiology of the host, as well as to ameliorate various disorders. In the present study, we have described recent developments in understanding the disparities of gut microbiota populations between individuals and the primary role of diet-microbiota interactions in modulating human physiology. A deeper understanding of these relationships can be useful for proposing personalized nutrition strategies and nutrition-based therapeutic interventions to improve human health.
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Affiliation(s)
| | - Aqsa Shahid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Faisalabad, Pakistan
| | - Samra Asghar
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Faisalabad, Pakistan
| | - Bilal Aslam
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Hammad Raza
- Department of Biochemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Miguel A. Prieto
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
| | - Francisco J. Barba
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
- Nutrition and Food Science Area, Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine Department, Faculty of Pharmacy, Universitat de València, Burjassot, València, Spain
| | - Muhammad Shahid Riaz Rajoka
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
- *Correspondence: Mohsin Khurshid, ; Abdulqadir J. Nashwan,
| | - Abdulqadir J. Nashwan
- Nursing Department, Hazm Mebaireek General Hospital (HMGH), Hamad Medical Corporation (HMC), Doha, Qatar
- *Correspondence: Mohsin Khurshid, ; Abdulqadir J. Nashwan,
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Gut Microbiota Disruption in COVID-19 or Post-COVID Illness Association with severity biomarkers: A Possible Role of Pre / Pro-biotics in manipulating microflora. Chem Biol Interact 2022; 358:109898. [PMID: 35331679 PMCID: PMC8934739 DOI: 10.1016/j.cbi.2022.109898] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/28/2022] [Accepted: 03/14/2022] [Indexed: 01/08/2023]
Abstract
Coronavirus disease (COVID-19), a coronavirus-induced illness attributed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, is thought to have first emerged on November 17, 2019. According to World Health Organization (WHO). COVID-19 has been linked to 379,223,560 documented occurrences and 5,693,245 fatalities globally as of 1st Feb 2022. Influenza A virus that has also been discovered diarrhea and gastrointestinal discomfort was found in the infected person, highlighting the need of monitoring them for gastro intestinal tract (GIT) symptoms regardless of whether the sickness is respiration related. The majority of the microbiome in the intestines is Firmicutes and Bacteroidetes, while Bacteroidetes, Proteobacteria, and Firmicutes are found in the lungs. Although most people overcome SARS-CoV-2 infections, many people continue to have symptoms months after the original sickness, called Long-COVID or Post COVID. The term "post-COVID-19 symptoms" refers to those that occur with or after COVID-19 and last for more than 12 weeks (long-COVID-19). The possible understanding of biological components such as inflammatory, immunological, metabolic activity biomarkers in peripheral blood is needed to evaluate the study. Therefore, this article aims to review the informative data that supports the idea underlying the disruption mechanisms of the microbiome of the gastrointestinal tract in the acute COVID-19 or post-COVID-mediated elevation of severity biomarkers.
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Zou J, Shen Y, Chen M, Zhang Z, Xiao S, Liu C, Wan Y, Yang L, Jiang S, Shang E, Qian D, Duan J. Lizhong decoction ameliorates ulcerative colitis in mice via modulating gut microbiota and its metabolites. Appl Microbiol Biotechnol 2020; 104:5999-6012. [PMID: 32418127 DOI: 10.1007/s00253-020-10665-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/23/2020] [Accepted: 05/02/2020] [Indexed: 12/11/2022]
Abstract
Ulcerative colitis (UC), a kind of inflammatory bowel disease, is generally characterized by chronic, persistent, relapsing, and nonspecific ulceration of the bowel, which is widespread in the world. Although the pathogenesis of UC is multifactorial, growing evidence has demonstrated that gut microbiota and its metabolites are closely related to the development of UC. Lizhong decoction (LZD), a well-known classical Chinese herbal prescription, has been used to clinically treat UC for long time, but its mechanism is not clear. In this study, 16S rRNA gene sequencing combining with untargeted metabolomics profiling was used to investigate how LZD worked. Results indicated that LZD could shape the gut microbiota structure and modify metabolic profiles. The abundance of opportunistic pathogens such as Clostridium sensu stricto 1, Enterobacter, and Escherichia-Shigella correlated with intestinal inflammation markedly decreased, while the levels of beneficial bacteria including Blautia, Muribaculaceae_norank, Prevotellaceae UCG-001, and Ruminiclostridium 9 elevated in various degrees. Additionally, fecal metabolite profiles reflecting microbial activities showed that adenosine, lysoPC(18:0), glycocholic acid, and deoxycholic acid notably decreased, while cholic acid, α-linolenic acid, stearidonic acid, and L-tryptophan significantly increased after LZD treatment. Hence, based on the systematic analysis of 16S rRNA gene sequencing and metabolomics of gut flora, the results provided a novel insight that microbiota and its metabolites might be potential targets for revealing the mechanism of LZD on amelioration of UC.Key Points • The potential mechanism of LZD on the amelioration of UC was firstly investigated.• LZD could significantly shape the structure of gut microbiota.• LZD could notably modulate the fecal metabolic profiling of UC mice. Graphical abstract.
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Affiliation(s)
- Junfeng Zou
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China
| | - Yumeng Shen
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China
| | - Mengjun Chen
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China
| | - Zhimiao Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China
| | - Suwei Xiao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China
| | - Chen Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China
| | - Yue Wan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China
| | - Lei Yang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China
| | - Shu Jiang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China.
| | - Erxin Shang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China
| | - Dawei Qian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China
| | - Jinao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, People's Republic of China.
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5
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Genetic coding algorithm for sense and antisense peptide interactions. Biosystems 2018; 164:199-216. [DOI: 10.1016/j.biosystems.2017.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/13/2017] [Accepted: 10/16/2017] [Indexed: 12/31/2022]
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Van Regenmortel MHV. Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition. J Mol Recognit 2015; 27:627-39. [PMID: 25277087 DOI: 10.1002/jmr.2394] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 11/09/2022]
Abstract
The concept of antibody specificity is analyzed and shown to reside in the ability of an antibody to discriminate between two antigens. Initially, antibody specificity was attributed to sequence differences in complementarity determining regions (CDRs), but as increasing numbers of crystallographic antibody-antigen complexes were elucidated, specificity was analyzed in terms of six antigen-binding regions (ABRs) that only roughly correspond to CDRs. It was found that each ABR differs significantly in its amino acid composition and tends to bind different types of amino acids at the surface of proteins. In spite of these differences, the combined preference of the six ABRs does not allow epitopes to be distinguished from the rest of the protein surface. These findings explain the poor success of past and newly proposed methods for predicting protein epitopes. Antibody polyspecificity refers to the ability of one antibody to bind a large variety of epitopes in different antigens, and this property explains how the immune system develops an antibody repertoire that is able to recognize every antigen the system is likely to encounter. Antibody heterospecificity arises when an antibody reacts better with another antigen than with the one used to raise the antibody. As a result, an antibody may sometimes appear to have been elicited by an antigen with which it is unable to react. The implications of antibody polyspecificity and heterospecificity in vaccine development are pointed out.
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Affiliation(s)
- Marc H V Van Regenmortel
- Wallenberg Research Center, Stellenbosch Institute for Advanced Study, Stellenbosch University, Stellenbosch, South Africa
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7
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Stemmer N, Strekalova E, Djogo N, Plöger F, Loers G, Lutz D, Buck F, Michalak M, Schachner M, Kleene R. Generation of amyloid-β is reduced by the interaction of calreticulin with amyloid precursor protein, presenilin and nicastrin. PLoS One 2013; 8:e61299. [PMID: 23585889 PMCID: PMC3621835 DOI: 10.1371/journal.pone.0061299] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 03/11/2013] [Indexed: 12/28/2022] Open
Abstract
Dysregulation of the proteolytic processing of amyloid precursor protein by γ-secretase and the ensuing generation of amyloid-β is associated with the pathogenesis of Alzheimer's disease. Thus, the identification of amyloid precursor protein binding proteins involved in regulating processing of amyloid precursor protein by the γ-secretase complex is essential for understanding the mechanisms underlying the molecular pathology of the disease. We identified calreticulin as novel amyloid precursor protein interaction partner that binds to the γ-secretase cleavage site within amyloid precursor protein and showed that this Ca2+- and N-glycan-independent interaction is mediated by amino acids 330–344 in the C-terminal C-domain of calreticulin. Co-immunoprecipitation confirmed that calreticulin is not only associated with amyloid precursor protein but also with the γ-secretase complex members presenilin and nicastrin. Calreticulin was detected at the cell surface by surface biotinylation of cells overexpressing amyloid precursor protein and was co-localized by immunostaining with amyloid precursor protein and presenilin at the cell surface of hippocampal neurons. The P-domain of calreticulin located between the N-terminal N-domain and the C-domain interacts with presenilin, the catalytic subunit of the γ-secretase complex. The P- and C-domains also interact with nicastrin, another functionally important subunit of this complex. Transfection of amyloid precursor protein overexpressing cells with full-length calreticulin leads to a decrease in amyloid-β42 levels in culture supernatants, while transfection with the P-domain increases amyloid-β40 levels. Similarly, application of the recombinant P- or C-domains and of a synthetic calreticulin peptide comprising amino acid 330–344 to amyloid precursor protein overexpressing cells result in elevated amyloid-β40 and amyloid-β42 levels, respectively. These findings indicate that the interaction of calreticulin with amyloid precursor protein and the γ-secretase complex regulates the proteolytic processing of amyloid precursor protein by the γ-secretase complex, pointing to calreticulin as a potential target for therapy in Alzheimer's disease.
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Affiliation(s)
- Nina Stemmer
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Elena Strekalova
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Nevena Djogo
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Frank Plöger
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele Loers
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - David Lutz
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Buck
- Institut für Klinische Chemie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Melitta Schachner
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
- Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
- Center for Neuroscience, Shantou University Medical College, Shantou, China
- * E-mail:
| | - Ralf Kleene
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
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Linden R, Martins VR, Prado MAM, Cammarota M, Izquierdo I, Brentani RR. Physiology of the prion protein. Physiol Rev 2008; 88:673-728. [PMID: 18391177 DOI: 10.1152/physrev.00007.2007] [Citation(s) in RCA: 435] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Prion diseases are transmissible spongiform encephalopathies (TSEs), attributed to conformational conversion of the cellular prion protein (PrP(C)) into an abnormal conformer that accumulates in the brain. Understanding the pathogenesis of TSEs requires the identification of functional properties of PrP(C). Here we examine the physiological functions of PrP(C) at the systemic, cellular, and molecular level. Current data show that both the expression and the engagement of PrP(C) with a variety of ligands modulate the following: 1) functions of the nervous and immune systems, including memory and inflammatory reactions; 2) cell proliferation, differentiation, and sensitivity to programmed cell death both in the nervous and immune systems, as well as in various cell lines; 3) the activity of numerous signal transduction pathways, including cAMP/protein kinase A, mitogen-activated protein kinase, phosphatidylinositol 3-kinase/Akt pathways, as well as soluble non-receptor tyrosine kinases; and 4) trafficking of PrP(C) both laterally among distinct plasma membrane domains, and along endocytic pathways, on top of continuous, rapid recycling. A unified view of these functional properties indicates that the prion protein is a dynamic cell surface platform for the assembly of signaling modules, based on which selective interactions with many ligands and transmembrane signaling pathways translate into wide-range consequences upon both physiology and behavior.
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Affiliation(s)
- Rafael Linden
- Instituto de Biofísica da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Hajj GNM, Lopes MH, Mercadante AF, Veiga SS, da Silveira RB, Santos TG, Ribeiro KCB, Juliano MA, Jacchieri SG, Zanata SM, Martins VR. Cellular prion protein interaction with vitronectin supports axonal growth and is compensated by integrins. J Cell Sci 2007; 120:1915-26. [PMID: 17504807 DOI: 10.1242/jcs.03459] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The physiological functions of the cellular prion protein, PrP(C), as a cell surface pleiotropic receptor are under debate. We report that PrP(C) interacts with vitronectin but not with fibronectin or collagen. The binding sites mediating this PrP(C)-vitronectin interaction were mapped to residues 105-119 of PrP(C) and the residues 307-320 of vitronectin. The two proteins were co-localized in embryonic dorsal root ganglia from wild-type mice. Vitronectin addition to cultured dorsal root ganglia induced axonal growth, which could be mimicked by vitronectin peptide 307-320 and abrogated by anti-PrP(C) antibodies. Full-length vitronectin, but not the vitronectin peptide 307-320, induced axonal growth of dorsal root neurons from two strains of PrP(C)-null mice. Functional assays demonstrated that relative to wild-type cells, PrP(C)-null dorsal root neurons were more responsive to the Arg-Gly-Asp peptide (an integrin-binding site), and exhibited greater alphavbeta3 activity. Our findings indicate that PrP(C) plays an important role in axonal growth, and this function may be rescued in PrP(C)-knockout animals by integrin compensatory mechanisms.
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Affiliation(s)
- Glaucia N M Hajj
- Ludwig Institute for Cancer Research, Hospital Alemão Oswaldo Cruz, São Paulo, Brazil
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10
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Erlich RB, Kahn SA, Lima FRS, Muras AG, Martins RAP, Linden R, Chiarini LB, Martins VR, Moura Neto V. STI1 promotes glioma proliferation through MAPK and PI3K pathways. Glia 2007; 55:1690-8. [PMID: 17886292 DOI: 10.1002/glia.20579] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gliomas are tumors derived from glia or their precursors within the central nervous system. Clinically, gliomas are divided into four grades and the glioblastoma multiforme (GBM), also referred as grade IV astrocytoma, is the most aggressive and the most common glioma in humans. The prognosis for patients with GBM remains dismal, with a median survival of 9-12 months. Despite their striking heterogeneity, common alterations in specific cellular signal transduction pathways occur within most GBMs. Previous work from our group identified the co-chaperone stress-inducible protein 1 (STI1) as a cell surface ligand for cellular prion (PrP(C)), which leads to the activation of several signal transduction pathways, some of which modulate cell survival. In the present work, we used thymidine incorporation assays to investigate the effect of STI1 upon proliferation of the human glioblastoma-derived cell line A172. Here we report that STI1 is secreted by and induces proliferation in tumor cells, an effect that is modulated by the Erk and PI3K pathways, and that, in contrast to glioma cells, STI1 does not induce proliferation of normal glia. In addition, our data suggest the involvement of PrP(C) in STI1-induced proliferation of A172 cells. These results provide initial evidence of a new functional role for STI1 on the physiology of human gliomas, and may lead to the identification of new therapeutic targets in these tumors.
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Affiliation(s)
- Rafael B Erlich
- Departamento de Anatomia, Universidade Federal do Rio de Janeiro, Brazil
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11
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Kwak JW, Kim HK, Chae CB. Potential Lead for an Alzheimer Drug: A Peptide That Blocks Intermolecular Interaction and Amyloid β Protein-Induced Cytotoxicity. J Med Chem 2006; 49:4813-7. [PMID: 16884292 DOI: 10.1021/jm050718v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A peptide chAbeta30-16 (15-mer; CTFVRTHIFCKEHQF) was designed to bind to a region encompassing the entire polymerization-related (16KLVFF20) and part of the polymerization and toxicity-related (25GSNKGAIIGLM35) regions of amyloid beta-protein, Abeta1-42 by a hydropathic complementary approach. This peptide efficiently binds to Abeta and blocks intermolecular interaction and the formation of Abeta aggregates. In addition, the peptide neutralizes the cell toxicity of Abeta fibrils. The chAbeta30-16 peptide or its derivatives may be a starting point for the future development of drugs that prevent the neurotoxicity and deposition of Abeta in the brain of Alzheimer's disease.
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Affiliation(s)
- Ju-Won Kwak
- Division of Molecular and Life Sciences, Postech Biotech Center, Pohang University of Science and Technology, San31 Hyoja-dong, Pohang, Kyungbuk 790-784, Republic of Korea
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12
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Jacchieri SG, Torquato R, Brentani RR. Structural study of binding of flagellin by Toll-like receptor 5. J Bacteriol 2003; 185:4243-7. [PMID: 12837800 PMCID: PMC164893 DOI: 10.1128/jb.185.14.4243-4247.2003] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In order to predict the binding regions within the complex formed by Toll-like receptor 5 (TLR-5) and flagellin, a complementary hydropathy between the two proteins was sought. A region common to the flagellins of Salmonella enterica serovar Typhimurium, Pseudomonas aeruginosa, and Listeria monocytogenes was shown to be hydropathically complementary to the 552-to-561 fragment of TLR-5, whose sequence is EILDISRNQL. The hydrophobicity profile of this region is shared with flagellins of 377 bacterial species out of a total of 723 publicly available sequences. A conformational analysis of the predicted binding site of TLR-5, whose structure is still unknown, was carried out with a methodology already applied to similar problems. To sample the conformations available to the peptide chain, a plot of the number of conformations per unit energy interval (density of states) versus energy was built. Following a theoretical argument, conformations belonging to maxima in this plot were selected. The most stable structure obtained in this search, an alpha-helical conformation, was shown to form the electrostatic interactions Glu552-Gln89, Asp555-Arg92, and Arg558-Glu93 with the predicted binding site of the flagellin of S. enterica serovar Typhimurium, formed by the 88-to-97 chain fragment (LQRVRELAVQ), which is likewise alpha helical.
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Affiliation(s)
- Saul G Jacchieri
- Centro de Pesquisas, Fundação Antônio Prudente. Sao Paulo Branch, Ludwig Institute for Cancer Research, São Paulo, SP 01509-090, Brazil.
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13
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Andrew CD, Bhattacharjee S, Kokkoni N, Hirst JD, Jones GR, Doig AJ. Stabilizing interactions between aromatic and basic side chains in alpha-helical peptides and proteins. Tyrosine effects on helix circular dichroism. J Am Chem Soc 2002; 124:12706-14. [PMID: 12392418 DOI: 10.1021/ja027629h] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we investigate the structures and energetics of interactions between aromatic (Phe or Tyr) and basic (Lys or Arg) amino acids in alpha-helices. Side chain interaction energies are measured using helical peptides, by quantifying their helicities with circular dichroism at 222 nm and interpreting the results with Lifson-Roig-based helix/coil theory. A difficulty in working with Tyr is that the aromatic ring perturbs the CD spectrum, giving an incorrect helicity. We calculated the effect of Tyr on the CD at 222 nm by deriving the intensities of the bands directly from the electronic and magnetic transition dipole moments through the rotational strengths corresponding to each excited state of the polypeptide. This gives an improved value of the helix preference of Tyr (from 0.48 to 0.35) and a correction to the helicity for the peptides containing Tyr. We find that Phe-Lys, Lys-Phe, Phe-Arg, Arg-Phe, and Tyr-Lys are all stabilizing by -0.10 to -0.18 kcal.mol-1 when placed i, i + 4 on the surface of a helix in aqueous solution, despite the great difference in polarity between these residues. Interactions between these side chains have previously been attributed to cation-pi bonds. A survey of protein structures shows that they are in fact predominantly hydrophobic interactions between the CH2 groups of Lys or Arg and the aromatic rings.
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Affiliation(s)
- Charles D Andrew
- Department of Biomolecular Sciences, UMIST, P.O. Box 88, Manchester M60 1QD, UK
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14
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Zanata SM, Lopes MH, Mercadante AF, Hajj GN, Chiarini LB, Nomizo R, Freitas AR, Cabral AL, Lee KS, Juliano MA, de Oliveira E, Jachieri SG, Burlingame A, Huang L, Linden R, Brentani RR, Martins VR. Stress-inducible protein 1 is a cell surface ligand for cellular prion that triggers neuroprotection. EMBO J 2002; 21:3307-16. [PMID: 12093732 PMCID: PMC125391 DOI: 10.1093/emboj/cdf325] [Citation(s) in RCA: 324] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Prions are composed of an isoform of a normal sialoglycoprotein called PrP(c), whose physiological role has been under investigation, with focus on the screening for ligands. Our group described a membrane 66 kDa PrP(c)-binding protein with the aid of antibodies against a peptide deduced by complementary hydropathy. Using these antibodies in western blots from two-dimensional protein gels followed by sequencing the specific spot, we have now identified the molecule as stress-inducible protein 1 (STI1). We show that this protein is also found at the cell membrane besides the cytoplasm. Both proteins interact in a specific and high affinity manner with a K(d) of 10(-7) M. The interaction sites were mapped to amino acids 113-128 from PrP(c) and 230-245 from STI1. Cell surface binding and pull-down experiments showed that recombinant PrP(c) binds to cellular STI1, and co-immunoprecipitation assays strongly suggest that both proteins are associated in vivo. Moreover, PrP(c) interaction with either STI1 or with the peptide we found that represents the binding domain in STI1 induce neuroprotective signals that rescue cells from apoptosis.
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Affiliation(s)
- Silvio M. Zanata
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Marilene H. Lopes
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Adriana F. Mercadante
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Glaucia N.M. Hajj
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Luciana B. Chiarini
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Regina Nomizo
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Adriana R.O. Freitas
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Ana L.B. Cabral
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Kil S. Lee
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Maria A. Juliano
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Elizabeth de Oliveira
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Saul G. Jachieri
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Alma Burlingame
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Lan Huang
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Rafael Linden
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Ricardo R. Brentani
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
| | - Vilma R. Martins
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua Prof. Antônio Prudente 109 4A, São Paulo 01509010, Departamento de Bioquímica and Departamento de Química Fundamental, Instituto de Química da USP, Centro de Tratamento e Pesquisa Hospital do Câncer, INFAR, Universidade Federal de São Paulo, São Paulo, Laboratório de Neurogênese, Instituto de Biofísica da UFRJ, Rio de Janeiro, Brasil and Department of Pharmaceutical Chemistry, USCF, CA, USA Corresponding author e-mail: S.M.Zanata, M.H.Lopes, A.F.Mercadante and G.N.M.Hajj contributed equally to this work
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15
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Chiarini LB, Freitas AR, Zanata SM, Brentani RR, Martins VR, Linden R. Cellular prion protein transduces neuroprotective signals. EMBO J 2002; 21:3317-26. [PMID: 12093733 PMCID: PMC125390 DOI: 10.1093/emboj/cdf324] [Citation(s) in RCA: 290] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2001] [Revised: 05/02/2002] [Accepted: 05/02/2002] [Indexed: 02/02/2023] Open
Abstract
To test for a role for the cellular prion protein (PrP(c)) in cell death, we used a PrP(c)-binding peptide. Retinal explants from neonatal rats or mice were kept in vitro for 24 h, and anisomycin (ANI) was used to induce apoptosis. The peptide activated both cAMP/protein kinase A (PKA) and Erk pathways, and partially prevented cell death induced by ANI in explants from wild-type rodents, but not from PrP(c)-null mice. Neuroprotection was abolished by treatment with phosphatidylinositol-specific phospholipase C, with human peptide 106-126, with certain antibodies to PrP(c) or with a PKA inhibitor, but not with a MEK/Erk inhibitor. In contrast, antibodies to PrP(c) that increased cAMP also induced neuroprotection. Thus, engagement of PrP(c) transduces neuroprotective signals through a cAMP/PKA-dependent pathway. PrP(c) may function as a trophic receptor, the activation of which leads to a neuroprotective state.
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Affiliation(s)
| | - Adriana R.O. Freitas
- Instituto de Biofísica da UFRJ, CCS, bloco G, Cidade Universitária, 21949-900, Rio de Janeiro,
Instituto Ludwig de Pesquisa sobre o Câncer, Centro de Tratamento e Pesquisa do Hospital do Câncer and Departamento de Bioquímica, Instituto de Química da USP, São Paulo, Brasil Corresponding author e-mail: L.B.Chiarini and A.R.O.Freitas contributed equally to this work
| | - Silvio M. Zanata
- Instituto de Biofísica da UFRJ, CCS, bloco G, Cidade Universitária, 21949-900, Rio de Janeiro,
Instituto Ludwig de Pesquisa sobre o Câncer, Centro de Tratamento e Pesquisa do Hospital do Câncer and Departamento de Bioquímica, Instituto de Química da USP, São Paulo, Brasil Corresponding author e-mail: L.B.Chiarini and A.R.O.Freitas contributed equally to this work
| | - Ricardo R. Brentani
- Instituto de Biofísica da UFRJ, CCS, bloco G, Cidade Universitária, 21949-900, Rio de Janeiro,
Instituto Ludwig de Pesquisa sobre o Câncer, Centro de Tratamento e Pesquisa do Hospital do Câncer and Departamento de Bioquímica, Instituto de Química da USP, São Paulo, Brasil Corresponding author e-mail: L.B.Chiarini and A.R.O.Freitas contributed equally to this work
| | - Vilma R. Martins
- Instituto de Biofísica da UFRJ, CCS, bloco G, Cidade Universitária, 21949-900, Rio de Janeiro,
Instituto Ludwig de Pesquisa sobre o Câncer, Centro de Tratamento e Pesquisa do Hospital do Câncer and Departamento de Bioquímica, Instituto de Química da USP, São Paulo, Brasil Corresponding author e-mail: L.B.Chiarini and A.R.O.Freitas contributed equally to this work
| | - Rafael Linden
- Instituto de Biofísica da UFRJ, CCS, bloco G, Cidade Universitária, 21949-900, Rio de Janeiro,
Instituto Ludwig de Pesquisa sobre o Câncer, Centro de Tratamento e Pesquisa do Hospital do Câncer and Departamento de Bioquímica, Instituto de Química da USP, São Paulo, Brasil Corresponding author e-mail: L.B.Chiarini and A.R.O.Freitas contributed equally to this work
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16
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Abstract
According to the molecular recognition theory, the complementarity of the sense and nonsense DNA strands is reflected in a complementarity of polypeptides and the corresponding nonsense polypeptides. A comparison of the sense and nonsense code matrices, and of the antisense and antinonsense code matrices, either by visual inspection or by comparing the corresponding hydrophobicity matrices (e.g. by simply adding them together), revealed no complementarity of these pairs of matrices in terms of possible attractive physical forces. Instead, it was evident that the codes divide the amino acids into two major groups: hydrophilic and hydrophobic, a division which is directly correlated with the folding property of proteins. A simple primordial genetic code distinguishing between these two types of amino acids would have been capable of generating three-dimensionally folded peptides, which could stabilize coding RNAs by forming ribonucleoprotein complexes. This evolutionary scheme is reflected in the present organisation of information processing and storage in essentially all organisms. RNAs are processed and translated into proteins by ribonucleoproteins, while other steps in information retrieval and processing, such as DNA replication, transcription, protein folding and posttranslational processing, are catalyzed by proteins. This shows that the evolution of DNA as an information storage medium was a secondary event, unrelated to the evolution of the genetic code. From the primordial hydrophilic/hydrophobic (f.ex. Leu/Arg) code, evolution proceeded by introduction of a catalytic amino acid (Ser). The further evolution of the code has mainly served to increase the number of functional hydrophilic amino acids, since there has not been a great advantage in increasing the number of structural, hydrophobic amino acids. At some stage during the evolution of the genetic code, double-stranded DNA was introduced as a maximally safe genetic copy of RNA. This required the action of highly specific enzymes, and was therefore preceded by the refinement of the genetic code. As a conclusion of this evolutionary scheme, it can be inferred that, in general only the sense strand encodes proteins.
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Affiliation(s)
- G Houen
- Department of Protein Chemistry, Statens Serum Institut, Copenhagen S, Denmark.
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17
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Abstract
Prions are an unconventional form of infectious agents composed only of protein and involved in transmissible spongiform encephalopathies in humans and animals. The infectious particle is composed by PrPsc which is an isoform of a normal cellular glycosyl-phosphatidylinositol (GPI) anchored protein, PrPc, of unknown function. The two proteins differ only in conformation, PrPc is composed of 40% alpha helix while PrPsc has 60% beta-sheet and 20% alpha helix structure. The infection mechanism is trigged by interaction of PrPsc with cellular prion protein causing conversion of the latter's conformation. Therefore, the infection spreads because new PrPsc molecules are generated exponentially from the normal PrPc. The accumulation of insoluble PrPsc is probably one of the events that lead to neuronal death. Conflicting data in the literature showed that PrPc internalization is mediated either by clathrin-coated pits or by caveolae-like membranous domains. However, both pathways seem to require a third protein (a receptor or a prion-binding protein) either to make the connection between the GPI-anchored molecule to clathrin or to convert PrPc into PrPsc. We have recently characterized a 66-kDa membrane receptor which binds PrPc in vitro and in vivo and mediates the neurotoxicity of a human prion peptide. Therefore, the receptor should have a role in the pathogenesis of prion-related diseases and in the normal cellular process. Further work is necessary to clarify the events triggered by the association of PrPc/PrPsc with the receptor.
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Affiliation(s)
- V R Martins
- Fundação Antônio Prudente, São Paulo, Brasil
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18
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Martins VR, Graner E, Garcia-Abreu J, de Souza SJ, Mercadante AF, Veiga SS, Zanata SM, Neto VM, Brentani RR. Complementary hydropathy identifies a cellular prion protein receptor. Nat Med 1997; 3:1376-82. [PMID: 9396608 DOI: 10.1038/nm1297-1376] [Citation(s) in RCA: 142] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Prions, the etiological agents for infectious degenerative encephalopathies, act by entering the cell and inducing conformational changes in PrPC (a normal cell membrane sialoglycoprotein), which result in cell death. A specific cell-surface receptor to mediate PrPC and prion endocytosis has been predicted. Complementary hydropathy let us generate a hypothetical peptide mimicking the receptor binding site. Antibodies raised against this peptide stain the surface of mouse neurons and recognize a 66-kDa membrane protein that binds PrPC both in vitro and in vivo. Furthermore, both the complementary prion peptide and antiserum against it inhibit the toxicity of a prion-derived peptide toward neuronal cells in culture. Such reagents might therefore have therapeutic applications.
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Affiliation(s)
- V R Martins
- Fundação Antônio Prudente, São Paulo, Brazil
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19
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Davids JW, El-Bakri A, Heal J, Christie G, Roberts GW, Raynes JG, Miller AD. Selektive Inhibierung von Interleukin-1 durch Antisense-Peptide. Angew Chem Int Ed Engl 1997. [DOI: 10.1002/ange.19971090911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Rodin SN, Ohno S. Two types of aminoacyl-tRNA synthetases could be originally encoded by complementary strands of the same nucleic acid. ORIGINS LIFE EVOL B 1995; 25:565-89. [PMID: 7494636 DOI: 10.1007/bf01582025] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The lack of even a marginal similarity between the two aminoacyl-tRNA synthetase (aaRS) classes suggests their independent origins (Eriani et al., 1990; Nagel and Doolittle, 1991). Yet, this independence is a puzzle inconsistent with the common origin of transfer RNAs, the coevolutionary theory of the genetic code (Wong, 1975, 1981) and other associated data and ideas. We present here the results of antiparallel 'class I versus class II' comparisons of aaRSs within their signature sequences. The two main HIGH- and KMSKS-containing motifs of class I appeared to be complementary to the class II motifs 2 and 1, respectively. The above sequence complementarity along with the mirror-image between crystal structures of complexes formed by the opposite aaRSs and their cognate tRNAs (Ruff et al., 1991), and the generally mirror ('head-to-tail') mapping of the basic functional sites in the sequences of aaRSs from the opposite two classes led us to conclude that these two synthetases emerged synchronously as complementary strands of the same primordial nucleic acid. This conclusion, combined with the hypothesis of tRNA concerted origin (Rodin et al., 1993a,b), may explain many intriguing features of aaRSs and favor the elucidation of the origin of the genetic code.
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Affiliation(s)
- S N Rodin
- Beckman Research Institute of the City of Hope, Duarte, California 91010-3000, USA
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21
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Seetharaman J, Srinivasan R. The Use of Observed Amino Acid Composition in the Proteins to the Analysis of the Sense and Antisense Strands Of DNA. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 1995. [DOI: 10.1080/10601329508020345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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LéJohn H, Cameron L, Yang B, Rennie S. Molecular characterization of an NAD-specific glutamate dehydrogenase gene inducible by L-glutamine. Antisense gene pair arrangement with L-glutamine-inducible heat shock 70-like protein gene. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)41809-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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23
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Fasina G, Verdoliva A, Cassani G, Melli M. Binding of type I IL-1 beta receptor fragment 151-162 to interleukin-1 beta. Growth Factors 1994; 10:99-106. [PMID: 8068354 DOI: 10.3109/08977199409010983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The relevance of hydropathically complementary sequences in ligand receptor interactions has been evaluated in the interleukin-1 beta/receptor type I case. Computer assisted comparison of the hydropathic profiles of IL-1 beta and its receptor (type I) identified residues 88-99 in IL-1 beta and 151-162 in the receptor as the sequences pair characterized by the highest level of hydropathic complementarity. These fragments, once produced by chemical synthesis and derivatized with biotin, displayed specific recognition properties for each other, as detected by solid phase binding assays. Binding between the two fragments occurred independently from the assay format, was saturable and specifically inhibited by unlabeled peptides. Receptor fragment (151-162) derivatized with biotin recognized also full length recombinant IL-1 beta, and binding was inhibited to 50% in the presence of 3 microM IL-1 beta (88-99) peptide. Interaction specificity was further confirmed by the non competitive effect on the interaction of a sequence scrambled IL-1 beta (88-99) peptide. In a similar way, full length biotinylated IL-1 beta recognized immobilized IL-1 beta receptor fragment (151-162), and this interaction was diminished in the presence of unlabeled receptor fragment or IL-1 beta Results indicate that IL-1 beta receptor fragment (151-162) binds IL-1 beta recognizing the IL-1 beta (88-99) sequence, thus suggesting a possible role of these fragments in the protein/receptor recognition surface.
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Affiliation(s)
- G Fasina
- Protein Engineering Unit, TECNOGEN S.C.p.A., Milano, Italy
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24
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Konecny J, Eckert M, Schöniger M, Hofacker GL. Neutral adaptation of the genetic code to double-strand coding. J Mol Evol 1993; 36:407-16. [PMID: 8510176 DOI: 10.1007/bf02406718] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We lay new foundations to the hypothesis that the genetic code is adapted to evolutionary retention of information in the antisense strands of natural DNA/RNA sequences. In particular, we show that the genetic code exhibits, beyond the neutral replacement patterns of amino acid substitutions, optimal properties by favoring simultaneous evolution of proteins encoded in DNA/RNA sense-antisense strands. This is borne out in the sense-antisense transformations of the codons of every amino acid which target amino acids physicochemically similar to each other. Moreover, silent mutations in the sense strand generate conservative ones in its antisense counterpart and vice versa. Coevolution of proteins coded by complementary strands is shown to be a definite possibility, a result which does not depend on any physical interaction between the coevolving proteins. Likewise, the degree to which the present genetic code is dedicated to evolutionary sense-antisense tolerance is demonstrated by comparison with many randomized codes. Double-strand coding is quantified from an information-theoretical point of view.
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Affiliation(s)
- J Konecny
- Tech University Munich, Garching, Federal Republic of Germany
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Collagen binding site in collagenase can be determined using the concept of sense-antisense peptide interactions. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42279-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Tropsha A, Kizer JS, Chaiken IM. Making sense from antisense: a review of experimental data and developing ideas on sense--antisense peptide recognition. J Mol Recognit 1992; 5:43-54. [PMID: 1472380 DOI: 10.1002/jmr.300050202] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Peptides encoded in the antisense strand of DNA have been predicted and found experimentally to bind to sense peptides and proteins with significant selectivity and affinity. Such sense--antisense peptide recognition has been observed in many systems, most often by detecting binding between immobilized and soluble interaction partners. Data obtained so far on sequence and solvent dependence of interaction support a hydrophobic-hydrophilic (amphipathic) model of peptide recognition. Nonetheless, the mechanistic understanding of this type of molecular recognition remains incomplete. Improving this understanding likely will require expanding the types of characteristics measured for sense--antisense peptide complexes and hence the types of analytical methods applied to such interactions. Understanding the mechanism of sense--antisense peptide recognition also may provide insights into mechanisms of native (sense) peptide and protein interactions and protein folding. Such insight may be helpful to learn how to design macromolecular recognition agents in technology for separation, diagnostics and therapeutics.
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Affiliation(s)
- A Tropsha
- Brain and Development Research Center, University of North Carolina, Chapel Hill 27599-7250
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Abstract
Antisense peptides, amino acid sequences encoded in the antisense strand of DNA, can interact with significant affinity and selectivity with their corresponding sensepeptides. Experimentally, sense-antisense peptide recognition has been observed repeatedly. However, skepticism about the biological relevance of this phenomenon has persisted. This is due in part to the unexpected and somewhat couterintutive nature of the interaction as well as to its non-universality as an empirical observation. Nonetheless, antisense peptides in several cases investigated so far have been used as immobilized ligands for the successful affinity chromatographic separation of native (sense) peptides and proteins. For example, immobilized antisense peptides corresponding to Arg8-vasopressin (AVP) have been used to separate vasopressin from oxytocin chromatographically as well as to affinity capture AVP-receptor complex. These results, together with improved understanding of the general features of amino acid sequence which drive antisense-sense peptide interactions as well as new ideas for making antisense peptides chimeras, are beginning to suggest improved ways to make antisense-related peptides as affinity agents for separation as well as for other biotechnology applications.
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Affiliation(s)
- I Chaiken
- Biopharmaceuticals R&D, SmithKline Beecham, King of Prussia, PA 19406
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Abstract
We have calculated the average effect of changing a codon by a single base for all possible single-base changes in the genetic code and for changes in the first, second, and third codon positions separately. Such values were calculated for an amino acid's polar requirement, hydropathy, molecular volume, and isoelectric point. For each attribute the average effect of single-base changes was also calculated for a large number of randomly generated codes that retained the same level of redundancy as the natural code. Amino acids whose codons differed by a single base in the first and third codon positions were very similar with respect to polar requirement and hydropathy. The major differences between amino acids were specified by the second codon position. Codons with U in the second position are hydrophobic, whereas most codons with A in the second position are hydrophilic. This accounts for the observation of complementary hydropathy. Single-base changes in the natural code had a smaller average effect on polar requirement than all but 0.02% of random codes. This result is most easily explained by selection to minimize deleterious effects of translation errors during the early evolution of the code.
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Affiliation(s)
- D Haig
- Department of Plant Sciences, University of Oxford, United Kingdom
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Lu FX, Aiyar N, Chaiken I. Affinity capture of [Arg8]vasopressin-receptor complex using immobilized antisense peptide. Proc Natl Acad Sci U S A 1991; 88:3642-6. [PMID: 2023913 PMCID: PMC51508 DOI: 10.1073/pnas.88.9.3642] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Solubilized noncovalent complexes of [Arg8]-vasopressin (AVP) with receptor proteins from rat liver membranes were isolated by selective binding to silica-immobilized antisense (AS) peptide. The affinity chromatographic support was prepared with a chemically synthesized AS peptide whose sequence is encoded by the AS DNA corresponding to the 20 amino-terminal residues of the AVP bovine neurophysin II biosynthetic precursor [pro-AVP/BNPII-(20-1)], a region that includes the AVP sequence at residues 1-9. The AVP-related AS peptide previously was shown to bind selectively to AVP. The AS peptide-AVP interaction mechanism hypothesized, contact by hydropathic complementarily at multiple sites along the peptide chains, led to the prediction that AVP bound to its receptor would still have enough free surface to interact with immobilized AS peptide. To test this prediction of a three-way interaction, [3H]AVP-receptor was obtained as a solubilized, partially purified fraction from rat liver membrane. When this fraction was eluted through AS pro-AVP/BNPII-(20-1) silica, a complex containing [3H]AVP was bound and separated from the major, unretarded membrane protein fraction as well as from free AVP. Chemical crosslinking of [3H]AVP complex, SDS/PAGE of the products, and analysis of gel slices by scintillation counting led to detection of two major radiolabeled bands of 31 and 38 kDa. Covalent labeling was blocked when unlabeled AVP was added as a competitor before crosslinking. A third radiolabeled protein band of 15 kDa was found when the receptor complex was solubilized from rat liver membranes in the absence of the protease inhibitor phenylmethylsulfonyl fluoride. Covalently crosslinked [3H]AVP complex also was bound to the AS peptide column; binding was blocked by competition with unlabeled AVP in the elution buffer. Since the AVP-linked 31- and 38-kDa proteins have the same apparent molecular mass on SDS/PAGE as found previously by photo-affinity labeling, we conclude that the AS peptide column has affinity-captured AVP-receptor complexes. The 15-kDa protein appears to be an active AVP-receptor fragment of one or both of the larger proteins. It is generally concluded that immobilized AS peptides may be useful to isolate peptide and protein-receptor complexes in other systems as well.
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Affiliation(s)
- F X Lu
- Department of Macromolecular Sciences, SmithKline Beecham, King of Prussia, PA 19406
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Pasqualini R, Chamone DF, Brentani RR. Determination of the Putative Binding site for Fibronectin on Platelet Glycoprotein IIb-IIIa Complex through a Hydropathic Complementarity Approach. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)71716-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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