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Antonelli AC, Almeida VP, da Fonseca SG. Immunoinformatics Vaccine Design for Zika Virus. Methods Mol Biol 2023; 2673:411-429. [PMID: 37258930 DOI: 10.1007/978-1-0716-3239-0_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Zika virus (ZIKV) is an emerging virus from the Flaviviridae family and Flavivirus genus that has caused important outbreaks around the world. ZIKV infection is associated with severe neuropathology in newborns and adults. Until now, there is no licensed vaccine available for ZIKV infection. Therefore, the development of a safe and effective vaccine against ZIKV is an urgent need. Recently, we designed an in silico multi-epitope vaccine for ZIKV based on immunoinformatics tools. To construct this in silico ZIKV vaccine, we used a consensus sequence generated from ZIKV sequences available in databank. Then, we selected CD4+ and CD8+ T cell epitopes from all ZIKV proteins based on the binding prediction to class II and class I human leukocyte antigen (HLA) molecules, promiscuity, and immunogenicity. ZIKV Envelope protein domain III (EDIII) was added to the construct and B cell epitopes were identified. Adjuvants were associated to increase immunogenicity. Distinct linkers were used for connecting the CD4+ and CD8+ T cell epitopes, EDIII, and adjuvants. Several analyses, such as antigenicity, population coverage, allergenicity, autoimmunity, and secondary and tertiary structures of the vaccine, were evaluated using various immunoinformatics tools and online web servers. In this chapter, we present the protocols with the rationale and detailed steps needed for this in silico multi-epitope ZIKV vaccine design.
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Affiliation(s)
- Ana Clara Antonelli
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Vinnycius Pereira Almeida
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Simone Gonçalves da Fonseca
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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Shah SZ, Jabbar B, Mirza MU, Waqas M, Aziz S, Halim SA, Ali A, Rafique S, Idrees M, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. An Immunoinformatics Approach to Design a Potent Multi-Epitope Vaccine against Asia-1 Genotype of Crimean-Congo Haemorrhagic Fever Virus Using the Structural Glycoproteins as a Target. Vaccines (Basel) 2022; 11:61. [PMID: 36679906 PMCID: PMC9867508 DOI: 10.3390/vaccines11010061] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Crimean-Congo haemorrhagic fever (CCHF), caused by Crimean-Congo haemorrhagic fever virus (CCHFV), is a disease of worldwide importance (endemic yet not limited to Asia, Middle East, and Africa) and has triggered several outbreaks amounting to a case fatality rate of 10-40% as per the World Health Organization. Genetic diversity and phylogenetic data revealed that the Asia-1 genotype of CCHFV remained dominant in Pakistan, where 688 confirmed cases were reported between the 2012-2022 period. Currently, no approved vaccine is available to tackle the viral infection. Epitope-based vaccine design has gained significant attention in recent years due to its safety, timeliness, and cost efficiency compared to conventional vaccines. In the present study, we employed a robust immunoinformatics-based approach targeting the structural glycoproteins G1 and G2 of CCHFV (Asia-1 genotype) to design a multi-epitope vaccine construct. Five B-cells and six cytotoxic T-lymphocytes (CTL) epitopes were mapped and finalized from G1 and G2 and were fused with suitable linkers (EAAAK, GGGS, AAY, and GPGPG), a PADRE sequence (13 aa), and an adjuvant (50S ribosomal protein L7/L12) to formulate a chimeric vaccine construct. The selected CTL epitopes showed high affinity and stable binding with the binding groove of common human HLA class I molecules (HLA-A*02:01 and HLA-B*44:02) and mouse major histocompatibility complex class I molecules. The chimeric vaccine was predicted to be an antigenic, non-allergenic, and soluble molecule with a suitable physicochemical profile. Molecular docking and molecular dynamics simulation indicated a stable and energetically favourable interaction between the constructed antigen and Toll-like receptors (TLR2, TLR3, and TLR4). Our results demonstrated that innate, adaptive, and humoral immune responses could be elicited upon administration of such a potent muti-epitope vaccine construct. These results could be helpful for an experimental vaccinologist to develop an effective vaccine against the Asia-1 genotype of CCHFV.
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Affiliation(s)
- Syed Zawar Shah
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Basit Jabbar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
| | - Shazia Rafique
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Idrees
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P.O. Box 2404, Khartoum 11111, Sudan
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
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Melo ARDS, de Macêdo LS, Invenção MDCV, de Moura IA, da Gama MATM, de Melo CML, Silva AJD, Batista MVDA, de Freitas AC. Third-Generation Vaccines: Features of Nucleic Acid Vaccines and Strategies to Improve Their Efficiency. Genes (Basel) 2022; 13:genes13122287. [PMID: 36553554 PMCID: PMC9777941 DOI: 10.3390/genes13122287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Gene immunization comprises mRNA and DNA vaccines, which stand out due to their simple design, maintenance, and high efficacy. Several studies indicate promising results in preclinical and clinical trials regarding immunization against ebola, human immunodeficiency virus (HIV), influenza, and human papillomavirus (HPV). The efficiency of nucleic acid vaccines has been highlighted in the fight against COVID-19 with unprecedented approval of their use in humans. However, their low intrinsic immunogenicity points to the need to use strategies capable of overcoming this characteristic and increasing the efficiency of vaccine campaigns. These strategies include the improvement of the epitopes' presentation to the system via MHC, the evaluation of immunodominant epitopes with high coverage against emerging viral subtypes, the use of adjuvants that enhance immunogenicity, and the increase in the efficiency of vaccine transfection. In this review, we provide updates regarding some characteristics, construction, and improvement of such vaccines, especially about the production of synthetic multi-epitope genes, widely employed in the current gene-based vaccines.
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Affiliation(s)
- Alanne Rayssa da Silva Melo
- Laboratory of Molecular Studies and Experimental Therapy—LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Larissa Silva de Macêdo
- Laboratory of Molecular Studies and Experimental Therapy—LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Maria da Conceição Viana Invenção
- Laboratory of Molecular Studies and Experimental Therapy—LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Ingrid Andrêssa de Moura
- Laboratory of Molecular Studies and Experimental Therapy—LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Marco Antonio Turiah Machado da Gama
- Laboratory of Molecular Studies and Experimental Therapy—LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Cristiane Moutinho Lagos de Melo
- Laboratory of Immunological and Antitumor Analysis, Department of Antibiotics, Bioscience Center, and Keizo Asami Imunophatology Laboratory, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Anna Jéssica Duarte Silva
- Laboratory of Molecular Studies and Experimental Therapy—LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Marcus Vinicius de Aragão Batista
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão 49100-000, Brazil
| | - Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy—LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
- Correspondence: ; Tel.: +55-8199-6067-671
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Antonelli ACB, Almeida VP, de Castro FOF, Silva JM, Pfrimer IAH, Cunha-Neto E, Maranhão AQ, Brígido MM, Resende RO, Bocca AL, Fonseca SG. In silico construction of a multiepitope Zika virus vaccine using immunoinformatics tools. Sci Rep 2022; 12:53. [PMID: 34997041 PMCID: PMC8741764 DOI: 10.1038/s41598-021-03990-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 12/01/2021] [Indexed: 01/02/2023] Open
Abstract
Zika virus (ZIKV) is an arbovirus from the Flaviviridae family and Flavivirus genus. Neurological events have been associated with ZIKV-infected individuals, such as Guillain-Barré syndrome, an autoimmune acute neuropathy that causes nerve demyelination and can induce paralysis. With the increase of ZIKV infection incidence in 2015, malformation and microcephaly cases in newborns have grown considerably, which suggested congenital transmission. Therefore, the development of an effective vaccine against ZIKV became an urgent need. Live attenuated vaccines present some theoretical risks for administration in pregnant women. Thus, we developed an in silico multiepitope vaccine against ZIKV. All structural and non-structural proteins were investigated using immunoinformatics tools designed for the prediction of CD4 + and CD8 + T cell epitopes. We selected 13 CD8 + and 12 CD4 + T cell epitopes considering parameters such as binding affinity to HLA class I and II molecules, promiscuity based on the number of different HLA alleles that bind to the epitopes, and immunogenicity. ZIKV Envelope protein domain III (EDIII) was added to the vaccine construct, creating a hybrid protein domain-multiepitope vaccine. Three high scoring continuous and two discontinuous B cell epitopes were found in EDIII. Aiming to increase the candidate vaccine antigenicity even further, we tested secondary and tertiary structures and physicochemical parameters of the vaccine conjugated to four different protein adjuvants: flagellin, 50S ribosomal protein L7/L12, heparin-binding hemagglutinin, or RS09 synthetic peptide. The addition of the flagellin adjuvant increased the vaccine's predicted antigenicity. In silico predictions revealed that the protein is a probable antigen, non-allergenic and predicted to be stable. The vaccine’s average population coverage is estimated to be 87.86%, which indicates it can be administered worldwide. Peripheral Blood Mononuclear Cells (PBMC) of individuals with previous ZIKV infection were tested for cytokine production in response to the pool of CD4 and CD8 ZIKV peptide selected. CD4 + and CD8 + T cells showed significant production of IFN-γ upon stimulation and IL-2 production was also detected by CD8 + T cells, which indicated the potential of our peptides to be recognized by specific T cells and induce immune response. In conclusion, we developed an in silico universal vaccine predicted to induce broad and high-coverage cellular and humoral immune responses against ZIKV, which can be a good candidate for posterior in vivo validation.
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Affiliation(s)
- Ana Clara Barbosa Antonelli
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil
| | - Vinnycius Pereira Almeida
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil
| | - Fernanda Oliveira Feitosa de Castro
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil.,Departament of Master in Environmental Sciences and Health, School of Medical, Pharmaceutical and Biomedical Sciences, Pontifical Catholic University of Goiás, Goiânia, Brazil
| | | | - Irmtraut Araci Hoffmann Pfrimer
- Departament of Master in Environmental Sciences and Health, School of Medical, Pharmaceutical and Biomedical Sciences, Pontifical Catholic University of Goiás, Goiânia, Brazil
| | - Edecio Cunha-Neto
- Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil.,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil
| | - Andréa Queiroz Maranhão
- Department of Cell Biology, University of Brasília, Brasília, Brazil.,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil
| | - Marcelo Macedo Brígido
- Department of Cell Biology, University of Brasília, Brasília, Brazil.,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil
| | | | | | - Simone Gonçalves Fonseca
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil. .,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil.
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5
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Frayssinhes JYA, Cerruti F, Laulin J, Cattaneo A, Bachi A, Apcher S, Coux O, Cascio P. PA28γ-20S proteasome is a proteolytic complex committed to degrade unfolded proteins. Cell Mol Life Sci 2021; 79:45. [PMID: 34913092 PMCID: PMC11071804 DOI: 10.1007/s00018-021-04045-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023]
Abstract
PA28γ is a nuclear activator of the 20S proteasome that, unlike the 19S regulatory particle, stimulates hydrolysis of several substrates in an ATP- and ubiquitin-independent manner and whose exact biological functions and molecular mechanism of action still remain elusive. In an effort to shed light on these important issues, we investigated the stimulatory effect of PA28γ on the hydrolysis of different fluorogenic peptides and folded or denatured full-length proteins by the 20S proteasome. Importantly, PA28γ was found to dramatically enhance breakdown rates by 20S proteasomes of several naturally or artificially unstructured proteins, but not of their native, folded counterparts. Furthermore, these data were corroborated by experiments in cell lines with a nucleus-tagged myelin basic protein. Finally, mass spectrometry analysis of the products generated during proteasomal degradation of two proteins demonstrated that PA28γ does not increase, but rather decreases, the variability of peptides that are potentially suitable for MHC class I antigen presentation. These unexpected findings indicate that global stimulation of the degradation of unfolded proteins may represent a more general feature of PA28γ and suggests that this proteasomal activator might play a broader role in the pathway of protein degradation than previously believed.
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Affiliation(s)
| | - Fulvia Cerruti
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Justine Laulin
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Immunologie Des Tumeurs et Immunothérapie, Villejuif, France
| | | | - Angela Bachi
- The FIRC Institute of Molecular Oncology (IFOM), 20139, Milan, Italy
| | - Sebastien Apcher
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Immunologie Des Tumeurs et Immunothérapie, Villejuif, France
| | - Olivier Coux
- Centre de Recherche de Biologie Cellulaire de Montpellier (CRBM), CNRS UMR 5237, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy.
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6
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Sami SA, Marma KKS, Mahmud S, Khan MAN, Albogami S, El-Shehawi AM, Rakib A, Chakraborty A, Mohiuddin M, Dhama K, Uddin MMN, Hossain MK, Tallei TE, Emran TB. Designing of a Multi-epitope Vaccine against the Structural Proteins of Marburg Virus Exploiting the Immunoinformatics Approach. ACS OMEGA 2021; 6:32043-32071. [PMID: 34870027 PMCID: PMC8638006 DOI: 10.1021/acsomega.1c04817] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 05/08/2023]
Abstract
Marburg virus disease (MVD) caused by the Marburg virus (MARV) generally appears with flu-like symptoms and leads to severe hemorrhagic fever. It spreads via direct contact with infected individuals or animals. Despite being considered to be less threatening in terms of appearances and the number of infected patients, the high fatality rate of this pathogenic virus is a major concern. Until now, no vaccine has been developed to combat this deadly virus. Therefore, vaccination for this virus is necessary to reduce its mortality. Our current investigation focuses on the design and formulation of a multi-epitope vaccine based on the structural proteins of MARV employing immunoinformatics approaches. The screening of potential T-cell and B-cell epitopes from the seven structural proteins of MARV was carried out through specific selection parameters. Afterward, we compiled the shortlisted epitopes by attaching them to an appropriate adjuvant and linkers. Population coverage analysis, conservancy analysis, and MHC cluster analysis of the shortlisted epitopes were satisfactory. Importantly, physicochemical characteristics, human homology assessment, and structure validation of the vaccine construct delineated convenient outcomes. We implemented disulfide bond engineering to stabilize the tertiary or quaternary interactions. Furthermore, stability and physical movements of the vaccine protein were explored using normal-mode analysis. The immune simulation study of the vaccine complexes also exhibited significant results. Additionally, the protein-protein docking and molecular dynamics simulation of the final construct exhibited a higher affinity toward toll-like receptor-4 (TLR4). From simulation trajectories, multiple descriptors, namely, root mean square deviations (rmsd), radius of gyration (Rg), root mean square fluctuations (RMSF), solvent-accessible surface area (SASA), and hydrogen bonds, have been taken into account to demonstrate the inflexible and rigid nature of receptor molecules and the constructed vaccine. Inclusively, our findings suggested the vaccine constructs' ability to regulate promising immune responses against MARV pathogenesis.
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Affiliation(s)
- Saad Ahmed Sami
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Kay Kay Shain Marma
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Shafi Mahmud
- Microbiology
Laboratory, Bioinformatics Division, Department of Genetic Engineering
and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Asif Nadim Khan
- Department of Biochemistry and Molecular
Biology, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh
| | - Sarah Albogami
- Department
of Biotechnology, College of Science, Taif
University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed M. El-Shehawi
- Department
of Biotechnology, College of Science, Taif
University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed Rakib
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Agnila Chakraborty
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Mostafah Mohiuddin
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary
Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Mir Muhammad Nasir Uddin
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Mohammed Kamrul Hossain
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Trina Ekawati Tallei
- Department of Biology,
Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, North Sulawesi 95115, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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Sanches RCO, Tiwari S, Ferreira LCG, Oliveira FM, Lopes MD, Passos MJF, Maia EHB, Taranto AG, Kato R, Azevedo VAC, Lopes DO. Immunoinformatics Design of Multi-Epitope Peptide-Based Vaccine Against Schistosoma mansoni Using Transmembrane Proteins as a Target. Front Immunol 2021; 12:621706. [PMID: 33737928 PMCID: PMC7961083 DOI: 10.3389/fimmu.2021.621706] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/08/2021] [Indexed: 12/17/2022] Open
Abstract
Schistosomiasis remains a serious health issue nowadays for an estimated one billion people in 79 countries around the world. Great efforts have been made to identify good vaccine candidates during the last decades, but only three molecules reached clinical trials so far. The reverse vaccinology approach has become an attractive option for vaccine design, especially regarding parasites like Schistosoma spp. that present limitations for culture maintenance. This strategy also has prompted the construction of multi-epitope based vaccines, with great immunological foreseen properties as well as being less prone to contamination, autoimmunity, and allergenic responses. Therefore, in this study we applied a robust immunoinformatics approach, targeting S. mansoni transmembrane proteins, in order to construct a chimeric antigen. Initially, the search for all hypothetical transmembrane proteins in GeneDB provided a total of 584 sequences. Using the PSORT II and CCTOP servers we reduced this to 37 plasma membrane proteins, from which extracellular domains were used for epitope prediction. Nineteen common MHC-I and MHC-II binding epitopes, from eight proteins, comprised the final multi-epitope construct, along with suitable adjuvants. The final chimeric multi-epitope vaccine was predicted as prone to induce B-cell and IFN-γ based immunity, as well as presented itself as stable and non-allergenic molecule. Finally, molecular docking and molecular dynamics foresee stable interactions between the putative antigen and the immune receptor TLR 4. Our results indicate that the multi-epitope vaccine might stimulate humoral and cellular immune responses and could be a potential vaccine candidate against schistosomiasis.
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Affiliation(s)
- Rodrigo C. O. Sanches
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Sandeep Tiwari
- Programa de Pós-Graduação em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Laís C. G. Ferreira
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Flávio M. Oliveira
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Marcelo D. Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Maria J. F. Passos
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Eduardo H. B. Maia
- Laboratório de Química Farmacêutica Medicinal, Universidade Federal de São João del-Rei, Divinópolis, Brazil
- Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Divinópolis, Brazil
| | - Alex G. Taranto
- Laboratório de Química Farmacêutica Medicinal, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Rodrigo Kato
- Programa de Pós-Graduação em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Vasco A. C. Azevedo
- Programa de Pós-Graduação em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Debora O. Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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9
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Safavi A, Kefayat A, Abiri A, Mahdevar E, Behnia AH, Ghahremani F. In silico analysis of transmembrane protein 31 (TMEM31) antigen to design novel multiepitope peptide and DNA cancer vaccines against melanoma. Mol Immunol 2019; 112:93-102. [PMID: 31079006 DOI: 10.1016/j.molimm.2019.04.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/25/2019] [Accepted: 04/30/2019] [Indexed: 12/18/2022]
Abstract
Multiepitope cancer vaccines are announcing themselves as the future of melanoma treatment. Herein, high immunogenic regions of transmembrane protein 31 (TMEM31) antigen were selected according to cytotoxic T lymphocytes' (CTL) epitopes and major histocompatibility complex (MHC) binding affinity through in silico analyses. The 32-62, 77-105, and 125-165 residues of the TMEM31 were selected as the immunodominant fragments. They were linked together by RVRR and HEYGAEALERAG motifs to improve epitopes separation and presentation. In addition, to activate helper T lymphocytes (HTL), Pan HLA DR-binding epitope (PADRE) peptide sequence and tetanus toxin fragment C (TTFrC) were incorporated into the final construct. Also, the Beta-defensin conserved domain was utilized in the final construct as a novel adjuvant for Toll-like receptor 4/myeloid differentiation factor (TLR4-MD) activation. The CTL epitopes, cleavage sites, post-translational modifications, TAP transport efficiency, and B cells epitopes were predicted for the peptide vaccine. The final construct contained multiple CTL and B cell epitopes. In addition, it showed 93.55% and 99.13% population coverage in the world for HLA I and HLA II, respectively. According to these preliminary results, the multiepitope cancer vaccine can be an appropriate choice for further experimental investigations.
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Affiliation(s)
- Ashkan Safavi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Amirhosein Kefayat
- Department of Oncology, Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Elham Mahdevar
- Department of Biology, Faculty of Science and Engineering, Science and Arts University, Yazd, Iran
| | - Amir Hossein Behnia
- Department of Biology, Faculty of the Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Fatemeh Ghahremani
- Department of Medical Physics and Radiotherapy, Arak University of Medical Sciences, Arak, Iran
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10
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Kasahara M, Flajnik MF. Origin and evolution of the specialized forms of proteasomes involved in antigen presentation. Immunogenetics 2019; 71:251-261. [PMID: 30675634 DOI: 10.1007/s00251-019-01105-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 01/10/2023]
Abstract
Proteasomes are a multi-subunit protease complex that produces peptides bound by major histocompatibility complex (MHC) class I molecules. Phylogenetic studies indicate that two specialized forms of proteasomes, immunoproteasomes and thymoproteasomes, and the proteasome activator PA28αβ emerged in a common ancestor of jawed vertebrates which acquired adaptive immunity based on the MHC, T cell receptors, and B cell receptors ~ 500 million years ago. Comparative genomics studies now provide strong evidence that the genes coding for the immunoproteasome subunits emerged by genome-wide duplication. On the other hand, the gene encoding the thymoproteasome subunit β5t emerged by tandem duplication from the gene coding for the β5 subunit. Strikingly, birds lack immunoproteasomes, thymoproteasomes, and the proteasome activator PA28αβ, raising an interesting question of whether they have evolved any compensatory mechanisms.
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Affiliation(s)
- Masanori Kasahara
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638, Japan.
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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11
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Cordeiro MN, De Lima RDCP, Paolini F, Melo ARDS, Campos APF, Venuti A, De Freitas AC. Current research into novel therapeutic vaccines against cervical cancer. Expert Rev Anticancer Ther 2018; 18:365-376. [DOI: 10.1080/14737140.2018.1445527] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Marcelo Nazário Cordeiro
- Laboratório de Estudos Moleculares e Terapia Experimental – LEMTE, Brazil Universidade Federal de Pernambuco – UFPE, Brazil
| | - Rita de Cássia Pereira De Lima
- Laboratório de Estudos Moleculares e Terapia Experimental – LEMTE, Brazil Universidade Federal de Pernambuco – UFPE, Brazil
| | - Francesca Paolini
- HPV-Unit UOSD Immunology and Tumor Immunotherapy, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Alanne Rayssa da Silva Melo
- Laboratório de Estudos Moleculares e Terapia Experimental – LEMTE, Brazil Universidade Federal de Pernambuco – UFPE, Brazil
| | - Ana Paula Ferreira Campos
- Laboratório de Estudos Moleculares e Terapia Experimental – LEMTE, Brazil Universidade Federal de Pernambuco – UFPE, Brazil
| | - Aldo Venuti
- HPV-Unit UOSD Immunology and Tumor Immunotherapy, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Antonio Carlos De Freitas
- Laboratório de Estudos Moleculares e Terapia Experimental – LEMTE, Brazil Universidade Federal de Pernambuco – UFPE, Brazil
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12
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Rut W, Drag M. Human 20S proteasome activity towards fluorogenic peptides of various chain lengths. Biol Chem 2017; 397:921-6. [PMID: 27176742 DOI: 10.1515/hsz-2016-0176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/03/2016] [Indexed: 11/15/2022]
Abstract
The proteasome is a multicatalytic protease responsible for the degradation of misfolded proteins. We have synthesized fluorogenic substrates in which the peptide chain was systematically elongated from two to six amino acids and evaluated the effect of peptide length on all three catalytic activities of human 20S proteasome. In the cases of five- and six-membered peptides, we have also synthesized libraries of fluorogenic substrates. Kinetic analysis revealed that six-amino-acid substrates are significantly better for chymotrypsin-like and caspase-like activity than shorter peptidic substrates. In the case of trypsin-like activity, a five-amino-acid substrate was optimal.
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13
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Athanasiou E, Agallou M, Tastsoglou S, Kammona O, Hatzigeorgiou A, Kiparissides C, Karagouni E. A Poly(Lactic- co-Glycolic) Acid Nanovaccine Based on Chimeric Peptides from Different Leishmania infantum Proteins Induces Dendritic Cells Maturation and Promotes Peptide-Specific IFNγ-Producing CD8 + T Cells Essential for the Protection against Experimental Visceral Leishmaniasis. Front Immunol 2017; 8:684. [PMID: 28659922 PMCID: PMC5468442 DOI: 10.3389/fimmu.2017.00684] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/26/2017] [Indexed: 01/19/2023] Open
Abstract
Visceral leishmaniasis, caused by Leishmania (L.) donovani and L. infantum protozoan parasites, can provoke overwhelming and protracted epidemics, with high case-fatality rates. An effective vaccine against the disease must rely on the generation of a strong and long-lasting T cell immunity, mediated by CD4+ TH1 and CD8+ T cells. Multi-epitope peptide-based vaccine development is manifesting as the new era of vaccination strategies against Leishmania infection. In this study, we designed chimeric peptides containing HLA-restricted epitopes from three immunogenic L. infantum proteins (cysteine peptidase A, histone H1, and kinetoplastid membrane protein 11), in order to be encapsulated in poly(lactic-co-glycolic) acid nanoparticles with or without the adjuvant monophosphoryl lipid A (MPLA) or surface modification with an octapeptide targeting the tumor necrosis factor receptor II. We aimed to construct differentially functionalized peptide-based nanovaccine candidates and investigate their capacity to stimulate the immunomodulatory properties of dendritic cells (DCs), which are critical regulators of adaptive immunity generated upon vaccination. According to our results, DCs stimulation with the peptide-based nanovaccine candidates with MPLA incorporation or surface modification induced an enhanced maturation profile with prominent IL-12 production, promoting allogeneic T cell proliferation and intracellular production of IFNγ by CD4+ and CD8+ T cell subsets. In addition, DCs stimulated with the peptide-based nanovaccine candidate with MPLA incorporation exhibited a robust transcriptional activation, characterized by upregulated genes indicative of vaccine-driven DCs differentiation toward type 1 phenotype. Immunization of HLA A2.1 transgenic mice with this peptide-based nanovaccine candidate induced peptide-specific IFNγ-producing CD8+ T cells and conferred significant protection against L. infantum infection. Concluding, our findings supported that encapsulation of more than one chimeric multi-epitope peptides from different immunogenic L. infantum proteins in a proper biocompatible delivery system with the right adjuvant is considered as an improved promising approach for the development of a vaccine against VL.
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Affiliation(s)
- Evita Athanasiou
- Laboratory of Cellular Immunology, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Maria Agallou
- Laboratory of Cellular Immunology, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | | | - Olga Kammona
- Laboratory of Polymer Reaction Engineering, Chemical Process and Energy Resources Institute, Centre for Research and Technology-Hellas, Thessaloniki, Greece
| | | | - Costas Kiparissides
- Laboratory of Polymer Reaction Engineering, Chemical Process and Energy Resources Institute, Centre for Research and Technology-Hellas, Thessaloniki, Greece.,Laboratory of Chemical Engineering B, Department of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evdokia Karagouni
- Laboratory of Cellular Immunology, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
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14
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In situ structural studies of tripeptidyl peptidase II (TPPII) reveal spatial association with proteasomes. Proc Natl Acad Sci U S A 2017; 114:4412-4417. [PMID: 28396430 DOI: 10.1073/pnas.1701367114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Tripeptidyl peptidase II (TPPII) is a eukaryotic protease acting downstream of the 26S proteasome; it removes tripeptides from the degradation products released by the proteasome. Structural studies in vitro have revealed the basic architecture of TPPII, a two-stranded linear polymer that assembles to form a spindle-shaped complex of ∼6 MDa. Dependent on protein concentration, TPPII has a distinct tendency for polymorphism. Therefore, its structure in vivo has remained unclear. To resolve this issue, we have scrutinized cryo-electron tomograms of rat hippocampal neurons for the occurrence and spatial distribution of TPPII by template matching. The quality of the tomograms recorded with the Volta phase plate enabled a detailed structural analysis of TPPII despite its low abundance. Two different assembly states (36-mers and 32-mers) coexist as well as occasional extended forms with longer strands. A distance analysis of the relative locations of TPPII and 26S proteasomes confirmed the visual impression that these two complexes spatially associate in agreement with TPPII's role in postproteasomal degradation.
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15
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Alizadeh AA, Hamzeh-Mivehroud M, Farajzadeh M, Dastmalchi S. Identification of novel peptides against TNF-α using phage display technique and in silico modeling of their modes of binding. Eur J Pharm Sci 2017; 96:490-498. [DOI: 10.1016/j.ejps.2016.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 01/15/2023]
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16
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Farhadi T, Ranjbar MM. Designing and modeling of complex DNA vaccine based on MOMP of Chlamydia trachomatis: an in silico approach. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s13721-016-0142-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Nezafat N, Sadraeian M, Rahbar MR, Khoshnoud MJ, Mohkam M, Gholami A, Banihashemi M, Ghasemi Y. Production of a novel multi-epitope peptide vaccine for cancer immunotherapy in TC-1 tumor-bearing mice. Biologicals 2014; 43:11-7. [PMID: 25467837 DOI: 10.1016/j.biologicals.2014.11.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/17/2014] [Accepted: 11/03/2014] [Indexed: 10/24/2022] Open
Abstract
In our previous research, several bioinformatic strategies were utilized to design an efficient multi-epitope peptide vaccine (MEV) against cancer. The designed vaccine consists of Wilms tumor-1 (WT-1) and human papillomavirus (HPV) E7 cytotoxic T lymphocyte (CTL) epitopes, tetanus toxin fragment C (TTFrC) and HLA-DR epitope (PADRE) helper T lymphocyte (HTL) epitopes and heparin-binding hemagglutinin (HBHA) as an immunostimulatory adjuvant. All segments were fused together by suitable linkers. In the current study, we cloned and expressed the designed MEV in E. coli. We subsequently performed in vivo preventative and therapeutic assays to evaluate antitumor efficacy of the vaccine against the HPV-16 E7-expressing murine tumor cell line TC-1 as a model for cancer immunotherapy. The results showed that in preventive experiments, vaccination with MEV significantly augmented the IgG antibody titer and the percentage of tumor-free mice compared to control groups (PBS and E7). Moreover, in therapeutic experiments, vaccination with MEV led to a reduction in the number of metastatic nodules, lung weights and the ratio of lung weights to body weights compared to other groups. In sum, our epitope vaccine could efficiently induce preventive and therapeutic antitumor immunity in TC-1 tumor bearing mice.
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Affiliation(s)
- Navid Nezafat
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Sadraeian
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Rahbar
- Department of Molecular Diagnosis, Saadati Pathobiology Laboratory, Shiraz, Iran
| | - Mohammad Javad Khoshnoud
- Department of Toxicology and Pharmacology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Milad Mohkam
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Pharmaceutical Biotechnology and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Shiraz University of Medical Science, Shiraz, Iran
| | - Ahmad Gholami
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Pharmaceutical Biotechnology and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Shiraz University of Medical Science, Shiraz, Iran
| | - Mehrzad Banihashemi
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Pharmaceutical Biotechnology and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Shiraz University of Medical Science, Shiraz, Iran.
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18
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Cascio P. PA28αβ: the enigmatic magic ring of the proteasome? Biomolecules 2014; 4:566-84. [PMID: 24970231 PMCID: PMC4101498 DOI: 10.3390/biom4020566] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/15/2014] [Accepted: 06/08/2014] [Indexed: 11/16/2022] Open
Abstract
PA28αβ is a γ-interferon-induced 11S complex that associates with the ends of the 20S proteasome and stimulates in vitro breakdown of small peptide substrates, but not proteins or ubiquitin-conjugated proteins. In cells, PA28 also exists in larger complexes along with the 19S particle, which allows ATP-dependent degradation of proteins; although in vivo a large fraction of PA28 is present as PA28αβ-20S particles whose exact biological functions are largely unknown. Although several lines of evidence strongly indicate that PA28αβ plays a role in MHC class I antigen presentation, the exact molecular mechanisms of this activity are still poorly understood. Herein, we review current knowledge about the biochemical and biological properties of PA28αβ and discuss recent findings concerning its role in modifying the spectrum of proteasome's peptide products, which are important to better understand the molecular mechanisms and biological consequences of PA28αβ activity.
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Affiliation(s)
- Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Grugliasco 10095, Italy.
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19
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Raule M, Cerruti F, Benaroudj N, Migotti R, Kikuchi J, Bachi A, Navon A, Dittmar G, Cascio P. PA28αβ reduces size and increases hydrophilicity of 20S immunoproteasome peptide products. ACTA ACUST UNITED AC 2014; 21:470-480. [PMID: 24631123 DOI: 10.1016/j.chembiol.2014.02.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 12/20/2013] [Accepted: 02/03/2014] [Indexed: 11/25/2022]
Abstract
The specific roles that immunoproteasome variants play in MHC class I antigen presentation are unknown at present. To investigate the biochemical properties of different immunoproteasome forms and unveil the molecular mechanisms of PA28 activity, we performed in vitro degradation of full-length proteins by 20S, 26S, and PA28αβ-20S immunoproteasomes and analyzed the spectrum of peptides released. Notably, PA28αβ-20S immunoproteasomes hydrolyze proteins at the same low rates as 20S alone, which is in line with PA28, neither stimulating nor preventing entry of unfolded polypeptides into the core particle. Most importantly, binding of PA28αβ to 20S greatly reduces the size of proteasomal products and favors the release of specific, more hydrophilic, longer peptides. Hence, PA28αβ may either allosterically modify proteasome active sites or act as a selective "smart" sieve that controls the efflux of products from the 20S proteolytic chamber.
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Affiliation(s)
- Mary Raule
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Italy
| | - Fulvia Cerruti
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Italy
| | - Nadia Benaroudj
- Unité Biologie des Spirochètes, Institut Pasteur, 75015 Paris, France
| | - Rebekka Migotti
- Mass Spectrometry Core Unit, Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Julia Kikuchi
- Mass Spectrometry Core Unit, Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Angela Bachi
- IFOM, FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Ami Navon
- Department of Biological Regulation, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Gunnar Dittmar
- Mass Spectrometry Core Unit, Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Paolo Cascio
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Italy.
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20
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Nezafat N, Ghasemi Y, Javadi G, Khoshnoud MJ, Omidinia E. A novel multi-epitope peptide vaccine against cancer: an in silico approach. J Theor Biol 2014; 349:121-34. [PMID: 24512916 DOI: 10.1016/j.jtbi.2014.01.018] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/30/2013] [Accepted: 01/14/2014] [Indexed: 11/25/2022]
Abstract
Cancer immunotherapy has an outstanding position in cancer prevention and treatment. In this kind of therapy, the immune system is activated to eliminate cancerous cells. Multi-epitope peptide cancer vaccines are manifesting as the next generation of cancer immunotherapy. In the present study, we have implemented various strategies to design an efficient multi-epitope vaccine. CD8+ cytolytic T lymphocytes (CTLs) epitopes, which have a pivotal role in cellular immune responses, helper epitopes and adjuvant, are three crucial components of peptide vaccine. CTL epitopes were determined from two high immunogenic protein Wilms tumor-1 (WT1) and human papillomavirus (HPV) E7 by various servers, which apply different algorithms. CTL epitopes were linked together by AAY and HEYGAEALERAG motifs to enhance epitope presentation. Pan HLA DR-binding epitope (PADRE) peptide sequence and helper epitopes, which have defined from Tetanus toxin fragment C (TTFrC) by various servers, were used to induce CD4+ helper T lymphocytes (HTLs) responses. Additionally, helper epitopes were conjugated together via GPGPG motifs that stimulate HTL immunity. Heparin-Binding Hemagglutinin (HBHA), a novel TLR4 agonist was employed as an adjuvant to polarize CD4+ T cells toward T-helper 1 to induce strong CTL responses. Moreover, the EAAAK linker was introduced to N and C terminals of HBHA for efficient separation. 3D model of protein was generated and predicted B cell epitopes were determined from the surface of built structure. Our protein contains several linear and conformational B cell epitopes, which suggests the antibody triggering property of this novel vaccine. Hence, our final protein can be used for prophylactic or therapeutic usages, because it can potentially stimulate both cellular and humoral immune responses.
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Affiliation(s)
- Navid Nezafat
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Javadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Javad Khoshnoud
- Department of Toxicology and Pharmacology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Eskandar Omidinia
- Enzyme Technology Lab., Genetics & Metabolism Research Group, Pasteur Institute of Iran, Tehran, Iran
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21
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Rockel B, Kopec KO, Lupas AN, Baumeister W. Structure and function of tripeptidyl peptidase II, a giant cytosolic protease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:237-45. [PMID: 21771670 DOI: 10.1016/j.bbapap.2011.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/29/2011] [Accepted: 07/01/2011] [Indexed: 01/25/2023]
Abstract
Tripeptidyl peptidase II is the largest known eukaryotic peptidase. It has been described as a multi-purpose peptidase, which, in addition to its house-keeping function in intracellular protein degradation, plays a role in several vital cellular processes such as antigen processing, apoptosis, or cell division, and is involved in diseases like muscle wasting, obesity, and in cancer. Biochemical studies and bioinformatics have identified TPPII as a subtilase, but its structure is very unusual: it forms a large homooligomeric complex (6 MDa) with a spindle-like shape. Recently, the high-resolution structure of TPPII homodimers (300 kDa) was solved and a hybrid structure of the holocomplex built of 20 dimers was obtained by docking it into the EM-density. Here, we summarize our current knowledge about TPPII with a focus on structural aspects. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
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Affiliation(s)
- Beate Rockel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.
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22
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In silico identification of novel protective VSG antigens expressed by Trypanosoma brucei and an effort for designing a highly immunogenic DNA vaccine using IL-12 as adjuvant. Microb Pathog 2011; 51:77-87. [PMID: 21349321 DOI: 10.1016/j.micpath.2011.01.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 01/24/2011] [Accepted: 01/24/2011] [Indexed: 11/22/2022]
Abstract
African trypanosomiasis continues to be a major health problem, with more adults dying from this disease world-wide. As the sequence diversity of Trypanosoma brucei is extreme, with VSGs having 15-25% identity with most other VSGs, hence it displays a huge diversity of adaptations and host specificities. Therefore the need for an improved vaccine has become an international priority. The highly conserved and specific epitopes acting as both CD8+ and CD4+ T-cell epitopes (FLINKKPAL and FTALCTLAA) were predicted from large bunch of VSGs of T. brucei. Besides, some other potential epitopes with very high affinity for MHC I and II molecules were also determined while taking consideration on the most common HLA in the general population which accounts for major ethnicities. The vaccine candidates were found to be effective even for non-african populations as predicted by population coverage analysis. Hence the migrating travelers acting as a spread means of the infection can probably also be treated successfully after injection of such a multiepitopic vaccine. Exploiting the immunoinformatics approaches, we designed a potential vaccine by using the consensus epitopic sequence of 388 VSG proteins of T. brucei and performed in silico cloning of multiepitopic antigenic DNA sequence in pBI-CMV1 vector. Moreover, various techniques like codon adaptation, CpG optimization, removal of self recognized epitopes, use of adjuvant and co-injection with plasmids expressing immune-stimulatory molecules were implemented to enhance the immunogenicity of the proposed in silico vaccine.
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23
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Classen M, Breuer S, Baumeister W, Guckenberger R, Witt S. Force spectroscopy of substrate molecules en route to the proteasome's active sites. Biophys J 2011; 100:489-97. [PMID: 21244845 DOI: 10.1016/j.bpj.2010.12.3689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 11/23/2010] [Accepted: 12/02/2010] [Indexed: 10/18/2022] Open
Abstract
We used an atomic force microscope to study the mechanism underlying the translocation of substrate molecules inside the proteasome. Our specific experimental setup allowed us to measure interaction forces between the 20S proteasome and its substrates. The substrate (β-casein) was covalently bound either via a thiol-Au bond or by a PEG-based binding procedure to the atomic force microscope cantilever tip and offered as bait to proteasomes from Methanosarcina mazei. The proteasomes were immobilized densely in an upright orientation on mica, which made their upper pores accessible for substrates to enter. Besides performing conventional single-molecule force spectroscopy experiments, we developed a three-step procedure that allows the detection of specific proteasome-substrate single-molecule events without tip-sample contact. Using the active 20S wild type and an inactive active-site mutant, as well as two casein mutants bound with opposite termini to the microscope tip, we detected no directional preference of the proteasome-substrate interactions. By comparing the distribution of the measured forces for the proteasome-substrate interactions, were observed that a significant proportion of interaction events occurred at higher forces for the active versus the inactive proteasome. These forces can be attributed to the translocation of substrate en route to the active sites that are harbored deep inside the proteasome.
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Affiliation(s)
- Mirjam Classen
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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24
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Urru SAM, Veglianese P, De Luigi A, Fumagalli E, Erba E, Gonella Diaza R, Carrà A, Davoli E, Borsello T, Forloni G, Pengo N, Monzani E, Cascio P, Cenci S, Sitia R, Salmona M. A new fluorogenic peptide determines proteasome activity in single cells. J Med Chem 2010; 53:7452-60. [PMID: 20883027 DOI: 10.1021/jm100362x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ubiquitin-proteasome system plays a critical role in many diseases, making it an attractive biomarker and therapeutic target. However, the impact of results obtained in vitro using purified proteasome particles or whole cell extracts is limited by the lack of efficient methods to assess proteasome activity in living cells. We have engineered an internally quenched fluorogenic peptide with a proteasome-specific cleavage motif fused to TAT and linked to the fluorophores DABCYL and EDANS. This peptide penetrates cell membranes and is rapidly cleaved by the proteasomal chymotrypsin-like activity, generating a quantitative fluorescent reporter of in vivo proteasome activity as assessed by time-lapse or flow cytometry fluorescence analysis. This reporter is an innovative tool for monitoring proteasomal proteolytic activities in physiological and pathological conditions.
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Affiliation(s)
- Silvana A M Urru
- Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, Milan 20156, Italy
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25
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Castro LM, Berti DA, Russo LC, Coelho V, Gozzo FC, Oliveira V, Ferro ES. Similar intracellular peptide profile of TAP1/β2 microglobulin double-knockout mice and C57BL/6 wild-type mice as revealed by peptidomic analysis. AAPS JOURNAL 2010; 12:608-16. [PMID: 20665142 DOI: 10.1208/s12248-010-9224-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Accepted: 07/13/2010] [Indexed: 12/14/2022]
Abstract
Cells produce and use peptides in distinctive ways. In the present report, using isotope labeling plus semi-quantitative mass spectrometry, we evaluated the intracellular peptide profile of TAP1/β2m⁻(/)⁻ (transporter associated with antigen-processing 1/ß2 microglobulin) double-knockout mice and compared it with that of C57BL/6 wild-type animals. Overall, 92 distinctive peptides were identified, and most were shown to have a similar concentration in both mouse strains. However, some peptides showed a modest increase or decrease (~2-fold), whereas a glycine-rich peptide derived from the C-terminal of neurogranin (KGPGPGGPGGAGGARGGAGGGPSGD) showed a substantial increase (6-fold) in TAP1/β2m⁻(/)⁻ mice. Thus, TAP1 and β2microglobulin have a small influence on the peptide profile of neuronal tissue, suggesting that the presence of peptides derived from intracellular proteins in neuronal tissue is not associated with antigens of the class I major histocompatibility complex. Therefore, it is possible that these intracellular peptides play a physiological role.
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Affiliation(s)
- Leandro M Castro
- Department of Cell Biology and Development, Biomedical Science Institute, São Paulo, SP, Brazil
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26
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In silico DNA vaccine designing against human papillomavirus (HPV) causing cervical cancer. Vaccine 2009; 28:120-31. [DOI: 10.1016/j.vaccine.2009.09.095] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 09/17/2009] [Accepted: 09/22/2009] [Indexed: 12/15/2022]
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27
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Felderer K, Groves M, Diez J, Pohl E, Witt S. Crystallization and preliminary X-ray analysis of the Thermoplasma acidophilum 20S proteasome in complex with protein substrates. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:899-902. [PMID: 18931431 DOI: 10.1107/s1744309108026791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 08/20/2008] [Indexed: 11/10/2022]
Abstract
The 20S proteasome is a 700 kDa barrel-shaped proteolytic complex that is traversed by an internal channel which widens into three cavities: two antechambers and one central chamber. Entrance to the complex is restricted by the narrow opening of the channel, which only allows unfolded substrates to reach the active sites located within the central cavity. The X-ray structures of 20S proteasomes from different organisms with and without inhibitors bound have led to a detailed knowledge of their structure and proteolytic function. Nevertheless, the mechanisms that underlie substrate translocation into the 20S proteasome and the role of the antechambers remain elusive. To investigate putative changes within the proteasome that occur during substrate translocation, ;host-guest' complexes between the Thermoplasma acidophilum 20S proteasomes and either cytochrome c (cyt c) or green fluorescent protein (GFP) were produced and crystallized. Orthorhombic crystals belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 116, b = 207, c = 310 A (cyt c) and a = 116, b = 206, c = 310 A (GFP), were formed and X-ray diffraction data were collected to 3.4 A (cyt c) and 3.8 A (GFP) resolution.
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Affiliation(s)
- Karin Felderer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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28
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Cunha FM, Berti DA, Ferreira ZS, Klitzke CF, Markus RP, Ferro ES. Intracellular peptides as natural regulators of cell signaling. J Biol Chem 2008; 283:24448-59. [PMID: 18617518 PMCID: PMC3259820 DOI: 10.1074/jbc.m801252200] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Revised: 06/20/2008] [Indexed: 12/25/2022] Open
Abstract
Protein degradation by the ubiquitin proteasome system releases large amounts of oligopeptides within cells. To investigate possible functions for these intracellularly generated oligopeptides, we fused them to a cationic transactivator peptide sequence using reversible disulfide bonds, introduced them into cells, and analyzed their effect on G protein-coupled receptor (GPCR) signal transduction. A mixture containing four of these peptides (20-80 microm) significantly inhibited the increase in the extracellular acidification response triggered by angiotensin II (ang II) in CHO-S cells transfected with the ang II type 1 receptor (AT1R-CHO-S). Subsequently, either alone or in a mixture, these peptides increased luciferase gene transcription in AT1R CHO-S cells stimulated with ang II and in HEK293 cells treated with isoproterenol. These peptides without transactivator failed to affect GPCR cellular responses. All four functional peptides were shown in vitro to competitively inhibit the degradation of a synthetic substrate by thimet oligopeptidase. Overexpression of thimet oligopeptidase in both CHO-S and HEK293 cells was sufficient to reduce luciferase activation triggered by a specific GPCR agonist. Moreover, using individual peptides as baits in affinity columns, several proteins involved in GPCR signaling were identified, including alpha-adaptin A and dynamin 1. These results suggest that before their complete degradation, intracellular peptides similar to those generated by proteasomes can actively affect cell signaling, probably representing additional bioactive molecules within cells.
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Affiliation(s)
- Fernanda M. Cunha
- Departments of Cell Biology and
Development and Physiology, Biomedical Science
Institute, University of São Paulo, São Paulo, SP 05508-900, the
Department of Biochemistry, Federal University
of São Paulo, São Paulo, SP 04044-020, and the
Center for Applied Toxinology, CAT/CEPID,
Butantan Institute, São Paulo, SP 05503-900, Brazil
| | - Denise A. Berti
- Departments of Cell Biology and
Development and Physiology, Biomedical Science
Institute, University of São Paulo, São Paulo, SP 05508-900, the
Department of Biochemistry, Federal University
of São Paulo, São Paulo, SP 04044-020, and the
Center for Applied Toxinology, CAT/CEPID,
Butantan Institute, São Paulo, SP 05503-900, Brazil
| | - Zulma S. Ferreira
- Departments of Cell Biology and
Development and Physiology, Biomedical Science
Institute, University of São Paulo, São Paulo, SP 05508-900, the
Department of Biochemistry, Federal University
of São Paulo, São Paulo, SP 04044-020, and the
Center for Applied Toxinology, CAT/CEPID,
Butantan Institute, São Paulo, SP 05503-900, Brazil
| | - Clécio F. Klitzke
- Departments of Cell Biology and
Development and Physiology, Biomedical Science
Institute, University of São Paulo, São Paulo, SP 05508-900, the
Department of Biochemistry, Federal University
of São Paulo, São Paulo, SP 04044-020, and the
Center for Applied Toxinology, CAT/CEPID,
Butantan Institute, São Paulo, SP 05503-900, Brazil
| | - Regina P. Markus
- Departments of Cell Biology and
Development and Physiology, Biomedical Science
Institute, University of São Paulo, São Paulo, SP 05508-900, the
Department of Biochemistry, Federal University
of São Paulo, São Paulo, SP 04044-020, and the
Center for Applied Toxinology, CAT/CEPID,
Butantan Institute, São Paulo, SP 05503-900, Brazil
| | - Emer S. Ferro
- Departments of Cell Biology and
Development and Physiology, Biomedical Science
Institute, University of São Paulo, São Paulo, SP 05508-900, the
Department of Biochemistry, Federal University
of São Paulo, São Paulo, SP 04044-020, and the
Center for Applied Toxinology, CAT/CEPID,
Butantan Institute, São Paulo, SP 05503-900, Brazil
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29
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Modeling the in Vitro 20S Proteasome Activity: The Effect of PA28–αβ and of the Sequence and Length of Polypeptides on the Degradation Kinetics. J Mol Biol 2008; 377:1607-17. [DOI: 10.1016/j.jmb.2008.01.086] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 01/25/2008] [Accepted: 01/29/2008] [Indexed: 11/20/2022]
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30
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Zaikin A, Kurths J. Optimal length transportation hypothesis to model proteasome product size distribution. J Biol Phys 2006; 32:231-43. [PMID: 19669465 DOI: 10.1007/s10867-006-9014-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2006] [Accepted: 02/10/2006] [Indexed: 11/30/2022] Open
Abstract
This paper discusses translocation features of the 20S proteasome in order to explain typical proteasome length distributions. We assume that the protein transport depends significantly on the fragment length with some optimal length which is transported most efficiently. By means of a simple one-channel model, we show that this hypothesis can explain both the one- and the three-peak length distributions found in experiments. A possible mechanism of such translocation is provided by so-called fluctuation-driven transport.
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Affiliation(s)
- Alexey Zaikin
- Institute of Physics, University of Potsdam, D-14415 Potsdam, Germany.
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31
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Sharon M, Witt S, Felderer K, Rockel B, Baumeister W, Robinson CV. 20S Proteasomes Have the Potential to Keep Substrates in Store for Continual Degradation. J Biol Chem 2006; 281:9569-75. [PMID: 16446364 DOI: 10.1074/jbc.m511951200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 20S core of the proteasome, which together with the regulatory particle plays a major role in the degradation of proteins in eukaryotic cells, is traversed by an internal system of cavities, namely two antechambers and one central proteolytic chamber. Little is known about the mechanisms underlying substrate binding and translocation of polypeptide chains into the interior of 20S proteasomes. Specifically, the role of the antechambers is not fully understood, and the number of substrate molecules sequestered within the internal cavities at any one time is unknown. Here we have shown that by applying both electron microscopy and tandem mass spectrometry (MS) approaches to this multisubunit complex we obtain precise information regarding the stoichiometry and location of substrates within the three chambers. The dissociation pattern in tandem MS allows us to conclude that a maximum of three green fluorescent protein and four cytochrome c substrate molecules are bound within the cavities. Our results also show that >95% of the population of proteasome molecules contain the maximum number of partially folded substrates. Moreover, we deduce that one green fluorescent protein or two cytochrome c molecules must reside within the central proteolytic chamber while the remaining substrate molecules occupy, singly, both antechambers. The results imply therefore an additional role for 20S proteasomes in the storage of substrates prior to their degradation, specifically in cases where translocation rates are slower than proteolysis. More generally, the ability to locate relatively small protein ligands sequestered within the 28-subunit core particle highlights the tremendous potential of tandem MS for deciphering substrate binding within large macromolecular assemblies.
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Affiliation(s)
- Michal Sharon
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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32
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Luciani F, Keşmir C, Mishto M, Or-Guil M, de Boer RJ. A mathematical model of protein degradation by the proteasome. Biophys J 2005; 88:2422-32. [PMID: 15665121 PMCID: PMC1305341 DOI: 10.1529/biophysj.104.049221] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The proteasome is the major protease for intracellular protein degradation. The influx rate of protein substrates and the exit rate of the fragments/products are regulated by the size of the axial channels. Opening the channels is known to increase the overall degradation rate and to change the length distribution of fragments. We develop a mathematical model with a flux that depends on the gate size and a phenomenological cleavage mechanism. The model has Michaelis-Menten kinetics with a V(max) that is inversely related to the length of the substrate, as observed in the in vitro experiments. We study the distribution of fragment lengths assuming that proteasomal cleavage takes place at a preferred distance from the ends of a protein fragment, and find multipeaked fragment length distributions similar to those found experimentally. Opening the gates in the model increases the degradation rate, increases the average length of the fragments, and increases the peak in the distribution around a length of 8-10 amino acids. This behavior is also observed in immunoproteasomes equipped with PA28. Finally, we study the effect of re-entry of processed fragments in the degradation kinetics and conclude that re-entry is only expected to affect the cleavage dynamics when short fragments enter the proteasome much faster than the original substrate. In summary, the model proposed in this study captures the known characteristics of proteasomal degradation, and can therefore help to quantify MHC class I antigen processing and presentation.
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Affiliation(s)
- Fabio Luciani
- Institute for Theoretical Biology, Humboldt University-Berlin, Berlin, Germany
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33
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Huffman HA, Sadeghi M, Seemuller E, Baumeister W, Dunn MF. Proteasome-cytochrome c interactions: a model system for investigation of proteasome host-guest interactions. Biochemistry 2003; 42:8679-86. [PMID: 12873127 DOI: 10.1021/bi027310+] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Owing to its high thermal stability and structural simplicity, the archaebacterium Thermoplasma Acidophilum 20S proteasome was selected for mechanistic studies in this work. This oligomeric enzyme complex consists of a barrel-shaped 20S core (approximately 700kDa) comprised of four stacked seven-membered rings with a alpha(7)beta(7)beta(7)alpha(7) subunit structure situated around a 7-fold symmetry axis. The hollow interior of the proteasome has three large interconnected chambers with narrow (13 A diameter) entrances from solution located at either end of the barrel. The 14 beta-subunit proteolytic sites are located on the inner surface of the central chamber. Herein, we demonstrate that unfolded horse heart ferricytochrome c (Cyt c) is a novel chromophoric probe for investigation of the mechanism of proteasome action. Under conditions of temperature and denaturant which unfold Cyt c but do not alter the thermophilic proteasome, Cyt c is extensively cleaved by the proteasome. Ten peptides were isolated and sequenced from the proteasome digest. Analysis of the cleavage products established that unfolded Cyt c and its covalently attached heme prosthetic group are translocated to the central chamber where proteolysis occurs. In the presence of site-specific inhibitors of the proteasome, we demonstrate that unfolded cytochrome c can be sequestered inside the proteasome complex. Upon cooling, a quasistable host-guest complex is formed. Analysis of the complex via UV/visible spectroscopy and mass spectrometry gave evidence that the sequestered Cyt c is essentially intact within the inhibited proteasome. High-performance liquid chromatography data show that (1) complexes with an apparent stoichiometry of approximately one Cyt c per proteasome can be formed and (2) when inhibition is removed from the complex, a rapid turnover of the sequestered Cyt c occurs.
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Affiliation(s)
- Holly A Huffman
- Department of Biochemistry, University of California, Riverside, California 92521, USA
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34
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Grommé M, Neefjes J. Antigen degradation or presentation by MHC class I molecules via classical and non-classical pathways. Mol Immunol 2002; 39:181-202. [PMID: 12200050 DOI: 10.1016/s0161-5890(02)00101-3] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Major histocompatibility complex (MHC) class I molecules usually present endogenous peptides at the cell surface. This is the result of a cascade of events involving various dedicated proteins like the peptide transporter associated with antigen processing (TAP) and the ER chaperone tapasin. However, alternative ways for class I peptide loading exist which may be highly relevant in a process called cross-priming. Both pathways are described here in detail. One major difference between these pathways is that the proteases involved in the generation of peptides are different. How proteases and peptidases influence peptide generation and degradation will be discussed. These processes determine the amount of peptides available for TAP translocation and class I binding and ultimately the immune response.
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Affiliation(s)
- Monique Grommé
- Division of Tumor Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
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35
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Zwickl P, Seemüller E, Kapelari B, Baumeister W. The proteasome: a supramolecular assembly designed for controlled proteolysis. ADVANCES IN PROTEIN CHEMISTRY 2002; 59:187-222. [PMID: 11868272 DOI: 10.1016/s0065-3233(01)59006-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- P Zwickl
- Department of Molecular Structural Biology, Max-Planck Institute for Biochemistry, Am Klopferspitz 18a, 82152 Martinsried, Germany
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36
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Abstract
In contrast to our detailed knowledge of prokaryotic proteasomes, we have only a limited understanding of the prokaryotic regulators and their functional interaction with the proteasome. Most probably, we will soon learn more about the molecular structure and the mechanism of action of the prokaryotic regulators. Nevertheless, it still remains to be unravelled which signals or/and modifications transform an endogenous prokaryotic protein into a substrate of the proteasomal degradation machinery.
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Affiliation(s)
- P Zwickl
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Am Klopferspitz 18a, 82152 Martinsried, Germany
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37
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Abstract
Although substantial progress has been made in understanding the biochemical properties of 11S regulators since their discovery in 1992, we still only have a rudimentary understanding of their biological role. As discussed above, we have proposed a model in which the alpha/beta complex promotes the production of antigenic peptides by opening the exit port of the 20S proteasome (Whitby et al. 2000). There are other possibilities, however, that are not exclusive of the exit port hypothesis. For example the alpha/beta complex may promote assembly of immunoproteasome as suggested by Preckel et al. 1999, or it may function as a docking module and conduit for the delivery of peptides to the ER lumen (Realini et al. 1994b). There are also unanswered structural and mechanistic questions. Higher resolution data are needed to discern important structural details of the PA26/20S proteasome complex. The models for binding and activation that are suggested from the structural data have to be tested by mutagenesis and biochemical analysis. What is the role of homolog-specific inserts? Will cognate regulator/proteasome complexes show conformational changes that are not apparent in the currently available crystal structures, including perhaps signs of allosteric communication between the regulator and the proteasome active sites?
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Affiliation(s)
- C P Hill
- Biochemistry Department, University of Utah Medical School, 50 N Medical Drive, Salt Lake City, UT 84132, USA
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38
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Abstract
Proteasomes are highly abundant cytosolic and nuclear protease complexes that degrade most intracellular proteins in higher eukaryotes and appear to play a major role in the cytosolic steps of MHC class I antigen processing. This review summarizes the knowledge of the role of proteasomes in antigen processing and the impact of proteasomal proteolysis on T cell-mediated immunity.
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Affiliation(s)
- G Niedermann
- Max Planck Institute of Immunobiology, Stübeweg 51, 79108 Freiburg, Germany
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39
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Peters B, Janek K, Kuckelkorn U, Holzhütter HG. Assessment of proteasomal cleavage probabilities from kinetic analysis of time-dependent product formation. J Mol Biol 2002; 318:847-62. [PMID: 12054828 DOI: 10.1016/s0022-2836(02)00167-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteasomes are multicatalytic cellular protease complexes that degrade intracellular proteins into smaller peptides. Proteasomal in vitro digests have revealed that the various peptide bonds of a given substrate are cleaved in a highly selective manner. Regarding the key role of proteasomes as the main supplier of antigenic peptides for MHC class I-mediated antigen presentation, it is important to know to what extent these preferences for specific peptide bonds may vary among proteasomes of different cellular origin and of different subunit composition. Here, we quantify such cleavage rates by means of a kinetic proteasome model that relates the time-dependent changes of the amount of any generated peptide to the rates with which this peptide can be either generated from longer precursor peptides or degraded into smaller successor peptides. Numerical values for these rates are estimated by minimizing the distance between simulated and measured time-courses. The proposed method is applied to kinetic data obtained by combining HPLC fractionation and mass spectrometry (MS) to trace the degradation of two model peptides (pp89-25mer and LLO-27mer) by either the constitutive (T2) or immunoproteasome (T2.27). To convert the intensity of the MS signals into the respective peptide amounts, we use two methods leading to similar results: experimental calibration curves and theoretically determined linear scaling functions based on a novel approach using mass conservation rules. Comparison of the cleavage probabilities and procession rates obtained for the two types of proteasomes reveals that the striking differences between the time-dependent peptide profiles can be accounted for mainly by a generally higher turnover rate of the immunoproteasome. For the pp89-25mer, there is no significant change of the cleavage probabilities for any of the ten observed cleavage sites. For the LLO-27mer, there appears to be a significant change in the cleavage probabilities for four of the nine observed cleavage sites when switching from the constitutive to the immunoproteasome.
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Affiliation(s)
- Björn Peters
- Medizinische Fakultät, Charité, Institut für Biochemie, Humboldt Universität Berlin, Monbijoustr. 2, D-10117 Berlin, Germany
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40
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Self-Processing of Subunits of the Proteasome. CO- AND POSTTRANSLATIONAL PROTEOLYSIS OF PROTEINS 2002. [DOI: 10.1016/s1874-6047(02)80013-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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41
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Cascio P, Hilton C, Kisselev AF, Rock KL, Goldberg AL. 26S proteasomes and immunoproteasomes produce mainly N-extended versions of an antigenic peptide. EMBO J 2001; 20:2357-66. [PMID: 11350924 PMCID: PMC125470 DOI: 10.1093/emboj/20.10.2357] [Citation(s) in RCA: 244] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Protein degradation by proteasomes is the source of most antigenic peptides presented on MHC class I molecules. To determine whether proteasomes generate these peptides directly or longer precursors, we developed new methods to measure the efficiency with which 26S and 20S particles, during degradation of a protein, generate the presented epitope or potential precursors. Breakdown of ovalbumin by the 26S and 20S proteasomes yielded the immunodominant peptide SIINFEKL, but produced primarily variants containing 1-7 additional N-terminal residues. Only 6-8% of the times that ovalbumin molecules were digested was a SIINFEKL or an N-extended version produced. Surprisingly, immunoproteasomes which contain the interferon-gamma-induced beta-subunits and are more efficient in antigen presentation, produced no more SIINFEKL than proteasomes. However, the immunoproteasomes released 2-4 times more of certain N-extended versions. These observations show that the changes in cleavage specificity of immunoproteasomes influence not only the C-terminus, but also the N-terminus of potential antigenic peptides, and suggest that most MHC-presented peptides result from N-terminal trimming of larger proteasome products by aminopeptidases (e.g. the interferon-gamma-induced enzyme leucine aminopeptidase).
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Affiliation(s)
| | - Craig Hilton
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 and
Department Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA Corresponding author e-mail:
| | | | - Kenneth L. Rock
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 and
Department Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA Corresponding author e-mail:
| | - Alfred L. Goldberg
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 and
Department Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA Corresponding author e-mail:
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42
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Li J, Gao X, Ortega J, Nazif T, Joss L, Bogyo M, Steven AC, Rechsteiner M. Lysine 188 substitutions convert the pattern of proteasome activation by REGgamma to that of REGs alpha and beta. EMBO J 2001; 20:3359-69. [PMID: 11432824 PMCID: PMC125523 DOI: 10.1093/emboj/20.13.3359] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
11S REGs (PA28s) are multimeric rings that bind proteasomes and stimulate peptide hydrolysis. Whereas REGalpha activates proteasomal hydrolysis of peptides with hydrophobic, acidic or basic residues in the P1 position, REGgamma only activates cleavage after basic residues. We have isolated REGgamma mutants capable of activating the hydrolysis of fluorogenic peptides diagnostic for all three active proteasome beta subunits. The most robust REGgamma specificity mutants involve substitution of Glu or Asp for Lys188. REGgamma(K188E/D) variants are virtually identical to REGalpha in proteasome activation but assemble into less stable heptamers/hexamers. Based on the REGalpha crystal structure, Lys188 of REGgamma faces the aqueous channel through the heptamer, raising the possibility that REG channels function as substrate-selective gates. However, covalent modification of proteasome chymotrypsin-like subunits by 125I-YL3-VS demonstrates that REGgamma(K188E)'s activation of all three proteasome active sites is not due to relaxed gating. We propose that decreased stability of REGgamma(K188E) heptamers allows them to change conformation upon proteasome binding, thus relieving inhibition of the CT and PGPH sites normally imposed by the wild-type REGgamma molecule.
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Affiliation(s)
- J Li
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132-0001, USA
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43
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Hofmann M, Nussbaum AK, Emmerich NPN, Stoltze L, Schild H. Mechanisms of MHC class I-restricted antigen presentation. Expert Opin Ther Targets 2001; 5:379-393. [PMID: 12540272 DOI: 10.1517/14728222.5.3.379] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The vertebrate immune system monitors whether an organism is invaded by pathogens. Therefore, each cell has to prove itself as healthy. This is achieved by presenting fragments of intracellular protein degradation products on the surface, i.e., each cell displays peptides on specialised proteins known as major histocompatibility complex (MHC) class I proteins. A displayed peptide has to pass certain constraints before its presentation: It has to be excised out of a protein, translocated into the endoplasmic reticulum (ER) and fit into the binding groove of a MHC molecule. In theory, alteration of the cellular protein profile by mutation or infection should force pathogen-specific T-cells to take action via recognition of foreign peptide bound to MHC class I molecules on the cell surface. Unfortunately, pathogens and tumours have evolved many ways to affect antigen presentation and to escape from immune response. Understanding the exact mechanisms of antigen presentation, i.e., protein cleavage and peptide binding by MHC molecules, would allow their manipulation by drugs and lead to the re-establishment of the correct antigen presentation pathway. This review will summarise current knowledge of the mechanisms of antigen presentation and discuss putative targets for therapeutic treatment as well as for vaccination strategies.
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Affiliation(s)
- Matthias Hofmann
- Institut für Zellbiologie, Abteilung Immunologie, Universität Tübingen, D-72076 Tübingen, Germany
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44
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Köhler A, Cascio P, Leggett DS, Woo KM, Goldberg AL, Finley D. The axial channel of the proteasome core particle is gated by the Rpt2 ATPase and controls both substrate entry and product release. Mol Cell 2001; 7:1143-52. [PMID: 11430818 DOI: 10.1016/s1097-2765(01)00274-x] [Citation(s) in RCA: 318] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Substrates enter the proteasome core particle (CP) through a channel that opens upon association with the regulatory particle (RP). Using yeast mutants, we show that channel opening is mediated by the ATPase domain of Rpt2, one of six ATPases in the RP. To test whether degradation products exit through this channel, we analyzed their size distribution. Their median length from an open-channel CP mutant was 40% greater than that from the wild-type. Thus, channel opening may enhance the yield of peptides long enough to function in antigen presentation. These experiments demonstrate that gating of the RP channel controls both substrate entry and product release, and is specifically regulated by an ATPase in the base of the RP.
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Affiliation(s)
- A Köhler
- Department of Cell Biology, Harvard Medical School, 02115, Boston, MA, USA
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Schwarz K, Eggers M, Soza A, Koszinowski UH, Kloetzel PM, Groettrup M. The proteasome regulator PA28alpha/beta can enhance antigen presentation without affecting 20S proteasome subunit composition. Eur J Immunol 2000; 30:3672-9. [PMID: 11169410 DOI: 10.1002/1521-4141(200012)30:12<3672::aid-immu3672>3.0.co;2-b] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
PA28alpha/beta is a regulatory complex of the 20S proteasome which consists of two IFN-gamma inducible subunits. Both subunits, alpha and beta, contribute equally to the formation of hexa- or heptameric rings which can associate with the 20S proteasome. Previously, we have shown that overexpression of the PA28alpha subunit enhanced the MHC class I-restricted presentation of two viral epitopes and that purified PA28alpha/beta accelerated T cell epitope generation by the 20S proteasome in vitro, indicating a role for PA28alpha/beta in antigen presentation. This conclusion was recently confirmed in PA28beta gene targeted mice which were severely deficient in MHC class I-restricted antigen presentation. These mice displayed a defect in the assembly of immunoproteasomes, suggesting that a lack of the proteasome subunits LMP2, LMP7, and MECL-1 may account for the deficiency in antigen presentation. In this study we investigated whether the effect of PA28alpha/beta on antigen presentation is dependent on a change of proteasome subunit composition. We have analyzed the assembly and subunit composition of proteasomes in fibroblast transfectants overexpressing both, alpha and beta subunits of PA28. In these transfectants we found a marked enhancement in the presentation of the immunodominant H-2Ld-restricted pp89 epitope of murine cytomegalovirus, although the 20S proteasome composition was the same as in recipient cells. We, therefore, conclude that PA28alpha/beta can enhance antigen processing independently of changes in 20S proteasome subunit composition or assembly.
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Affiliation(s)
- K Schwarz
- Research Department, Cantonal Hospital St. Gall, St. Gallen, Switzerland
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Voges D, Zwickl P, Baumeister W. The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu Rev Biochem 2000; 68:1015-68. [PMID: 10872471 DOI: 10.1146/annurev.biochem.68.1.1015] [Citation(s) in RCA: 1377] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In eukaryotic cells, most proteins in the cytosol and nucleus are degraded via the ubiquitin-proteasome pathway. The 26S proteasome is a 2.5-MDa molecular machine built from approximately 31 different subunits, which catalyzes protein degradation. It contains a barrel-shaped proteolytic core complex (the 20S proteasome), capped at one or both ends by 19S regulatory complexes, which recognize ubiquitinated proteins. The regulatory complexes are also implicated in unfolding and translocation of ubiquitinated targets into the interior of the 20S complex, where they are degraded to oligopeptides. Structure, assembly and enzymatic mechanism of the 20S complex have been elucidated, but the functional organization of the 19S complex is less well understood. Most subunits of the 19S complex have been identified, however, specific functions have been assigned to only a few. A low-resolution structure of the 26S proteasome has been obtained by electron microscopy, but the precise arrangement of subunits in the 19S complex is unclear.
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Affiliation(s)
- D Voges
- Max-Planck-Institut für Biochemie, Martinsried, Germany
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Li J, Gao X, Joss L, Rechsteiner M. The proteasome activator 11 S REG or PA28: chimeras implicate carboxyl-terminal sequences in oligomerization and proteasome binding but not in the activation of specific proteasome catalytic subunits. J Mol Biol 2000; 299:641-54. [PMID: 10835274 DOI: 10.1006/jmbi.2000.3800] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The REG homologs, alpha, beta and gamma, activate mammalian proteasomes in distinct ways. REGalpha and REGbeta activate the trypsin-like, chymotrypsin-like and peptidylglutamyl-preferring active sites, whereas REGgamma only activates the proteasome's trypsin-like subunit. The three REG homologs differ in carboxyl-terminal sequences that are located next to activation loops on their proteasome binding surface. To assess the importance of these carboxyl-terminal sequences in the activation of specific proteasome beta catalytic subunits, we characterized chimeras in which 8 or 12 residues were exchanged among the three proteins. Like the wild-type molecule, REGalpha chimeras activated all three proteasome catalytic subunits regardless of the carboxyl-terminal sequence. However, REGalpha-beta chimeras activated the proteasome at lower concentrations than wild-type REGalpha and higher levels of REGalpha-gamma chimeras were needed for maximal activation because exchanged carboxyl-terminal sequences can stabilize (REGalpha-beta) or destabilize (REGalpha-gamma) the REGalpha heptamer. REGgamma chimeras were equivalent to REGgamma in their activation properties, but they bound the proteasome less tightly than the wild-type molecule. REGbeta chimeras also bound the proteasome more weakly than wild-type REGbeta and were virtually unable to activate it. Our findings demonstrate that the carboxyl-terminal sequences of REG subunits can affect heptamer stability and proteasome affinity, but they do not determine which proteasome beta subunits become activated.
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Affiliation(s)
- J Li
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
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Kuttler C, Nussbaum AK, Dick TP, Rammensee HG, Schild H, Hadeler KP. An algorithm for the prediction of proteasomal cleavages. J Mol Biol 2000; 298:417-29. [PMID: 10772860 DOI: 10.1006/jmbi.2000.3683] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proteasomes, major proteolytic sites in eukaryotic cells, play an important part in major histocompatibility class I (MHC I) ligand generation and thus in the regulation of specific immune responses. Their cleavage specificity is of outstanding interest for this process. In order to generalize previously determined cleavage motifs of 20 S proteasomes, we developed network-based model proteasomes trained by an evolutionary algorithm with experimental cleavage data of yeast and human 20 S proteasomes. A window of ten flanking amino acid residues proved sufficient for the model proteasomes to reproduce the experimental results with 98-100 % accuracy. Actual experimental data were reproduced significantly better than randomly selected cleavage sites, suggesting that our model proteasomes were able to extract rules inherent to proteasomal cleavage data. The affinity parameters of the model, which decide for or against cleavage, correspond with the cleavage motifs determined experimentally. The predictive power of the model was verified for unknown (to the program) test conditions: the prediction of cleavage numbers in proteins and the generation of MHC I ligands from short peptides. In summary, our model proteasomes reproduce and predict proteasomal cleavages with high degree of accuracy. They present a promising approach for predicting proteasomal cleavage products in future attempts and, in combination with existing algorithms for MHC I ligand prediction, will be tested to improve cytotoxic T lymphocyte epitope prediction.
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Affiliation(s)
- C Kuttler
- Biomathematik, University of Tübingen, Auf der Morgenstelle 10, Tübingen, D-72076, Germany
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Abstract
There are two immune responses in vertebrates: humoral immunity is mediated by circulating antibodies, whereas cytotoxic T lymphocytes (CTL) confer cellular immunity. CTL lyse infected cells upon recognition of cell-surface MHC Class I molecules complexed with foreign peptides. The displayed peptides are produced in the cytosol by degradation of host proteins or proteins from intracellular pathogens that might be present. Proteasomes are cylindrical multisubunit proteases that generate many of the peptides eventually transferred to the cell surface for immune surveillance. In mammalian proteasomes, six active sites face a central chamber. As this chamber is sealed off from the enzyme's surface, there must be mechanisms to promote entry of substrates. Two protein complexes have been found to bind the ends of the proteasome and activate it. One of the activators is the 19 S regulatory complex of the 26 S proteasome; the other activator is '11 S REG' [Dubiel, Pratt, Ferrell and Rechsteiner (1992) J. Biol. Chem. 267, 22369-22377] or 'PA28' [Ma, Slaughter and DeMartino (1992) J. Biol. Chem. 267, 10515-10523]. During the past 7 years, our understanding of the structure of REG molecules has increased significantly, but much less is known about their biological functions. There are three REG subunits, namely alpha, beta and gamma. Recombinant REGalpha forms a ring-shaped heptamer of known crystal structure. 11 S REG is a heteroheptamer of alpha and beta subunits. REGgamma is also presumably a heptameric ring, and it is found in the nuclei of the nematode work Caenorhabditis elegans and higher organisms, where it may couple proteasomes to other nuclear components. REGalpha and REGbeta, which are abundant in vertebrate immune tissues, are located mostly in the cytoplasm. Synthesis of REG alpha and beta subunits is induced by interferon-gamma, and this has led to the prevalent hypothesis that REG alpha/beta hetero-oligomers play an important role in Class I antigen presentation. In the present review we focus on the structural properties of REG molecules and on the evidence that REGalpha/beta functions in the Class I immune response.
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Niedermann G, Geier E, Lucchiari-Hartz M, Hitziger N, Ramsperger A, Eichmann K. The specificity of proteasomes: impact on MHC class I processing and presentation of antigens. Immunol Rev 1999; 172:29-48. [PMID: 10631935 DOI: 10.1111/j.1600-065x.1999.tb01354.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have studied polypeptide processing by purified proteasomes, with regard to proteolytic specificity and cytotoxic T-lymphocyte (CTL) epitope generation. Owing to defined preferences with respect to cleavage sites and fragment length, proteasomes degrade polypeptide substrates into cohorts of overlapping oligopeptides. Many of the proteolytic fragments exhibit structural features in common with major histocompatibility complex (MHC) class I ligands including fragment size and frequencies of amino acids at fragment boundaries. Proteasomes frequently generate definitive MHC class I ligands and/or slightly longer peptides, while substantially larger peptides are rare. Individual CTL epitopes are produced in widely varying amounts, often consistent with immunohierarchies among CTL epitopes. We further found that polypeptide processing is remarkably conserved among proteasomes of eukaryotic origin and that invertebrate proteasomes can efficiently produce known high-copy MHC class I ligands, suggesting evolutionary adaptation of the transporter associated with antigen processing and MHC class I to ancient constraints imposed by proteasomal protein degradation.
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Affiliation(s)
- G Niedermann
- Max-Planck Institute of Immunobiology, Freiburg, Germany.
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