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For: Dalchau N, Phillips A, Goldstein LD, Howarth M, Cardelli L, Emmott S, Elliott T, Werner JM. A peptide filtering relation quantifies MHC class I peptide optimization. PLoS Comput Biol 2011;7:e1002144. [PMID: 22022238 DOI: 10.1371/journal.pcbi.1002144] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 06/18/2011] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Darley R, Illing PT, Duriez P, Bailey A, Purcell AW, van Hateren A, Elliott T. Evidence of focusing the MHC class I immunopeptidome by tapasin. Front Immunol 2025;16:1563789. [PMID: 40406141 PMCID: PMC12094946 DOI: 10.3389/fimmu.2025.1563789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Accepted: 04/14/2025] [Indexed: 05/26/2025]  Open
2
Xiao W, Gao M, Mo B, Huang X, Du Z, Wang S, Chen J, Luo S, Xing H. Endoplasmic Reticulum-Targeted Phototherapy Remodels the Tumor Immunopeptidome to Enhance Immunogenic Cell Death and Adaptive Anti-Tumor Immunity. Pharmaceuticals (Basel) 2025;18:491. [PMID: 40283929 PMCID: PMC12030737 DOI: 10.3390/ph18040491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Revised: 03/22/2025] [Accepted: 03/24/2025] [Indexed: 04/29/2025]  Open
3
Günther M, Sticht J, Freund C, Höfer T. Antigen presentation by MHC-II is shaped by competitive and cooperative allosteric mechanisms of peptide exchange. Structure 2025;33:389-400.e13. [PMID: 39708815 DOI: 10.1016/j.str.2024.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/12/2024] [Accepted: 11/20/2024] [Indexed: 12/23/2024]
4
van de Weijer ML, Samanta K, Sergejevs N, Jiang L, Dueñas ME, Heunis T, Huang TY, Kaufman RJ, Trost M, Sanyal S, Cowley SA, Carvalho P. Tapasin assembly surveillance by the RNF185/Membralin ubiquitin ligase complex regulates MHC-I surface expression. Nat Commun 2024;15:8508. [PMID: 39353943 PMCID: PMC11445256 DOI: 10.1038/s41467-024-52772-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 09/19/2024] [Indexed: 10/03/2024]  Open
5
Advancing our knowledge of antigen processing with computational modelling, structural biology, and immunology. Biochem Soc Trans 2023;51:275-285. [PMID: 36645000 DOI: 10.1042/bst20220782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/17/2023]
6
Boulanger DSM, Douglas LR, Duriez PJ, Kang Y, Dalchau N, James E, Elliott T. Tapasin-mediated editing of the MHC I immunopeptidome is epitope specific and dependent on peptide off-rate, abundance, and level of tapasin expression. Front Immunol 2022;13:956603. [PMID: 36389776 PMCID: PMC9659924 DOI: 10.3389/fimmu.2022.956603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022]  Open
7
Croft NP. Peptide Presentation to T Cells: Solving the Immunogenic Puzzle: Systems Immunology Profiling of Antigen Presentation for Prediction of CD8+ T Cell Immunogenicity. Bioessays 2020;42:e1900200. [PMID: 31958157 DOI: 10.1002/bies.201900200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/18/2019] [Indexed: 02/02/2023]
8
Boulanger DSM, Eccleston RC, Phillips A, Coveney PV, Elliott T, Dalchau N. A Mechanistic Model for Predicting Cell Surface Presentation of Competing Peptides by MHC Class I Molecules. Front Immunol 2018;9:1538. [PMID: 30026743 PMCID: PMC6041393 DOI: 10.3389/fimmu.2018.01538] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/21/2018] [Indexed: 12/15/2022]  Open
9
van Hateren A, Anderson M, Bailey A, Werner JM, Skipp P, Elliott T. Direct evidence for conformational dynamics in major histocompatibility complex class I molecules. J Biol Chem 2017;292:20255-20269. [PMID: 29021251 PMCID: PMC5724011 DOI: 10.1074/jbc.m117.809624] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/25/2017] [Indexed: 12/19/2022]  Open
10
Sahlgren C, Meinander A, Zhang H, Cheng F, Preis M, Xu C, Salminen TA, Toivola D, Abankwa D, Rosling A, Karaman DŞ, Salo-Ahen OMH, Österbacka R, Eriksson JE, Willför S, Petre I, Peltonen J, Leino R, Johnson M, Rosenholm J, Sandler N. Tailored Approaches in Drug Development and Diagnostics: From Molecular Design to Biological Model Systems. Adv Healthc Mater 2017;6. [PMID: 28892296 DOI: 10.1002/adhm.201700258] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/04/2017] [Indexed: 12/13/2022]
11
Sahlgren C, Meinander A, Zhang H, Cheng F, Preis M, Xu C, Salminen TA, Toivola D, Abankwa D, Rosling A, Karaman DŞ, Salo-Ahen OMH, Österbacka R, Eriksson JE, Willför S, Petre I, Peltonen J, Leino R, Johnson M, Rosenholm J, Sandler N. Tailored Approaches in Drug Development and Diagnostics: From Molecular Design to Biological Model Systems. Adv Healthc Mater 2017. [DOI: 10.1002/adhm.201700258 10.1002/adhm.201700258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
12
Eccleston RC, Coveney PV, Dalchau N. Host genotype and time dependent antigen presentation of viral peptides: predictions from theory. Sci Rep 2017;7:14367. [PMID: 29084996 PMCID: PMC5662608 DOI: 10.1038/s41598-017-14415-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 10/11/2017] [Indexed: 01/20/2023]  Open
13
Parameter estimation for gene regulatory networks: a two-stage MCMC Bayesian approach. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2017;2016:1476-1479. [PMID: 28268605 DOI: 10.1109/embc.2016.7590988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
14
Eccleston RC, Wan S, Dalchau N, Coveney PV. The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition. Front Immunol 2017;8:797. [PMID: 28740497 PMCID: PMC5502259 DOI: 10.3389/fimmu.2017.00797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 06/22/2017] [Indexed: 12/15/2022]  Open
15
Fisette O, Wingbermühle S, Schäfer LV. Partial Dissociation of Truncated Peptides Influences the Structural Dynamics of the MHCI Binding Groove. Front Immunol 2017;8:408. [PMID: 28458665 PMCID: PMC5394104 DOI: 10.3389/fimmu.2017.00408] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/22/2017] [Indexed: 12/29/2022]  Open
16
Wieczorek M, Abualrous ET, Sticht J, Álvaro-Benito M, Stolzenberg S, Noé F, Freund C. Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation. Front Immunol 2017. [PMID: 28367149 DOI: 10.3389/fimmu.2017.00292.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
17
Wieczorek M, Abualrous ET, Sticht J, Álvaro-Benito M, Stolzenberg S, Noé F, Freund C. Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation. Front Immunol 2017;8:292. [PMID: 28367149 PMCID: PMC5355494 DOI: 10.3389/fimmu.2017.00292] [Citation(s) in RCA: 645] [Impact Index Per Article: 80.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/28/2017] [Indexed: 11/21/2022]  Open
18
van Hateren A, Bailey A, Elliott T. Recent advances in Major Histocompatibility Complex (MHC) class I antigen presentation: Plastic MHC molecules and TAPBPR-mediated quality control. F1000Res 2017;6:158. [PMID: 28299193 PMCID: PMC5321123 DOI: 10.12688/f1000research.10474.1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/13/2017] [Indexed: 01/25/2023]  Open
19
Expressing Redundancy among Linear-Epitope Sequence Data Based on Residue-Level Physicochemical Similarity in the Context of Antigenic Cross-Reaction. Adv Bioinformatics 2016;2016:1276594. [PMID: 27274725 PMCID: PMC4870339 DOI: 10.1155/2016/1276594] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 03/29/2016] [Accepted: 04/10/2016] [Indexed: 01/15/2023]  Open
20
Fisette O, Wingbermühle S, Tampé R, Schäfer LV. Molecular mechanism of peptide editing in the tapasin-MHC I complex. Sci Rep 2016;6:19085. [PMID: 26754481 PMCID: PMC4709564 DOI: 10.1038/srep19085] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/30/2015] [Indexed: 11/30/2022]  Open
21
Bartocci E, Lió P. Computational Modeling, Formal Analysis, and Tools for Systems Biology. PLoS Comput Biol 2016;12:e1004591. [PMID: 26795950 PMCID: PMC4721667 DOI: 10.1371/journal.pcbi.1004591] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
22
Hermann C, Trowsdale J, Boyle LH. TAPBPR: a new player in the MHC class I presentation pathway. ACTA ACUST UNITED AC 2015;85:155-66. [PMID: 25720504 DOI: 10.1111/tan.12538] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
23
Bailey A, Dalchau N, Carter R, Emmott S, Phillips A, Werner JM, Elliott T. Selector function of MHC I molecules is determined by protein plasticity. Sci Rep 2015;5:14928. [PMID: 26482009 PMCID: PMC5224517 DOI: 10.1038/srep14928] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/09/2015] [Indexed: 12/27/2022]  Open
24
Transport and quality control of MHC class I molecules in the early secretory pathway. Curr Opin Immunol 2015;34:83-90. [PMID: 25771183 DOI: 10.1016/j.coi.2015.02.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 02/21/2015] [Accepted: 02/24/2015] [Indexed: 12/26/2022]
25
Osborne JM, Bernabeu MO, Bruna M, Calderhead B, Cooper J, Dalchau N, Dunn SJ, Fletcher AG, Freeman R, Groen D, Knapp B, McInerny GJ, Mirams GR, Pitt-Francis J, Sengupta B, Wright DW, Yates CA, Gavaghan DJ, Emmott S, Deane C. Ten simple rules for effective computational research. PLoS Comput Biol 2014;10:e1003506. [PMID: 24675742 PMCID: PMC3967918 DOI: 10.1371/journal.pcbi.1003506] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
26
Saposins modulate human invariant Natural Killer T cells self-reactivity and facilitate lipid exchange with CD1d molecules during antigen presentation. Proc Natl Acad Sci U S A 2013;110:E4753-61. [PMID: 24248359 DOI: 10.1073/pnas.1310050110] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
27
Ashraf S, Nitschke K, Warshow UM, Brooks CR, Kim AY, Lauer GM, Hydes TJ, Cramp ME, Alexander G, Little AM, Thimme R, Neumann-Haefelin C, Khakoo SI. Synergism of tapasin and human leukocyte antigens in resolving hepatitis C virus infection. Hepatology 2013;58:881-9. [PMID: 23532923 PMCID: PMC3759612 DOI: 10.1002/hep.26415] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 03/21/2013] [Indexed: 01/15/2023]
28
Kahramanoğullari O, Fantaccini G, Lecca P, Morpurgo D, Priami C. Algorithmic modeling quantifies the complementary contribution of metabolic inhibitions to gemcitabine efficacy. PLoS One 2012;7:e50176. [PMID: 23239976 PMCID: PMC3519828 DOI: 10.1371/journal.pone.0050176] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 10/22/2012] [Indexed: 01/19/2023]  Open
29
Immunodominance: a pivotal principle in host response to viral infections. Clin Immunol 2012;143:99-115. [PMID: 22391152 DOI: 10.1016/j.clim.2012.01.015] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/25/2012] [Accepted: 01/28/2012] [Indexed: 11/24/2022]
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