1
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Ren X, Amarajeewa AWP, Jayasinghe MDT, Garstka MA. Differences in F pocket impact on HLA I genetic associations with autoimmune diabetes. Front Immunol 2024; 15:1342335. [PMID: 38596688 PMCID: PMC11003304 DOI: 10.3389/fimmu.2024.1342335] [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: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 04/11/2024] Open
Abstract
Introduction Human leukocyte antigen (HLA) I molecules present antigenic peptides to activate CD8+ T cells. Type 1 Diabetes (T1D) is an auto-immune disease caused by aberrant activation of the CD8+ T cells that destroy insulin-producing pancreatic β cells. Some HLA I alleles were shown to increase the risk of T1D (T1D-predisposing alleles), while some reduce this risk (T1D-protective alleles). Methods Here, we compared the T1D-predisposing and T1D-protective allotypes concerning peptide binding, maturation, localization and surface expression and correlated it with their sequences and energetic profiles using experimental and computational methods. Results T1D-predisposing allotypes had more peptide-bound forms and higher plasma membrane levels than T1D-protective allotypes. This was related to the fact that position 116 within the F pocket was more conserved and made more optimal contacts with the neighboring residues in T1D-predisposing allotypes than in protective allotypes. Conclusion Our work uncovers that specific polymorphisms in HLA I molecules potentially influence their susceptibility to T1D.
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Affiliation(s)
- Xu Ren
- Department of Urology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Core Research Laboratory, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Endocrinology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - A. W. Peshala Amarajeewa
- Core Research Laboratory, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | | | - Malgorzata A. Garstka
- Department of Urology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Core Research Laboratory, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Endocrinology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Tumor and Immunology, Precision Medical Institute, Western China Science and Technology Innovation Port, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
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2
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Liu S, Wei S, Sun Y, Xu G, Zhang S, Li J. Molecular Characteristics, Functional Definitions, and Regulatory Mechanisms for Cross-Presentation Mediated by the Major Histocompatibility Complex: A Comprehensive Review. Int J Mol Sci 2023; 25:196. [PMID: 38203367 PMCID: PMC10778590 DOI: 10.3390/ijms25010196] [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: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
The major histocompatibility complexes of vertebrates play a key role in the immune response. Antigen-presenting cells are loaded on MHC I molecules, which mainly present endogenous antigens; when MHC I presents exogenous antigens, this is called cross-presentation. The discovery of cross-presentation provides an important theoretical basis for the study of exogenous antigens. Cross-presentation is a complex process in which MHC I molecules present antigens to the cell surface to activate CD8+ T lymphocytes. The process of cross-representation includes many components, and this article briefly outlines the origins and development of MHC molecules, gene structures, functions, and their classical presentation pathways. The cross-presentation pathways of MHC I molecules, the cell lines that support cross-presentation, and the mechanisms of MHC I molecular transporting are all reviewed. After more than 40 years of research, the specific mechanism of cross-presentation is still unclear. In this paper, we summarize cross-presentation and anticipate the research and development prospects for cross-presentation.
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Affiliation(s)
| | | | | | | | - Shidong Zhang
- Engineering Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Animal Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.L.); (S.W.); (Y.S.); (G.X.)
| | - Jianxi Li
- Engineering Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Animal Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.L.); (S.W.); (Y.S.); (G.X.)
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3
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McShan AC, Flores-Solis D, Sun Y, Garfinkle SE, Toor JS, Young MC, Sgourakis NG. Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition. Nat Commun 2023; 14:8204. [PMID: 38081856 PMCID: PMC10713829 DOI: 10.1038/s41467-023-43654-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
The conformational landscapes of peptide/human leucocyte antigen (pHLA) protein complexes encompassing tumor neoantigens provide a rationale for target selection towards autologous T cell, vaccine, and antibody-based therapeutic modalities. Here, using complementary biophysical and computational methods, we characterize recurrent RAS55-64 Q61 neoepitopes presented by the common HLA-A*01:01 allotype. We integrate sparse NMR restraints with Rosetta docking to determine the solution structure of NRASQ61K/HLA-A*01:01, which enables modeling of other common RAS55-64 neoepitopes. Hydrogen/deuterium exchange mass spectrometry experiments alongside molecular dynamics simulations reveal differences in solvent accessibility and conformational plasticity across a panel of common Q61 neoepitopes that are relevant for recognition by immunoreceptors. Finally, we predict binding and provide structural models of NRASQ61K antigens spanning the entire HLA allelic landscape, together with in vitro validation for HLA-A*01:191, HLA-B*15:01, and HLA-C*08:02. Our work provides a basis to delineate the solution surface features and immunogenicity of clinically relevant neoepitope/HLA targets for cancer therapy.
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Affiliation(s)
- Andrew C McShan
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr NW, Atlanta, GA, 30318, USA
| | - David Flores-Solis
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 37075, Göttingen, Germany
| | - Yi Sun
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Samuel E Garfinkle
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, 48202, USA
| | - Michael C Young
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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4
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Weber JK, Morrone JA, Kang SG, Zhang L, Lang L, Chowell D, Krishna C, Huynh T, Parthasarathy P, Luan B, Alban TJ, Cornell WD, Chan TA. Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicity. Brief Bioinform 2023; 25:bbad504. [PMID: 38233090 PMCID: PMC10793977 DOI: 10.1093/bib/bbad504] [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: 08/25/2023] [Revised: 11/03/2023] [Accepted: 12/03/2023] [Indexed: 01/19/2024] Open
Abstract
Immunologic recognition of peptide antigens bound to class I major histocompatibility complex (MHC) molecules is essential to both novel immunotherapeutic development and human health at large. Current methods for predicting antigen peptide immunogenicity rely primarily on simple sequence representations, which allow for some understanding of immunogenic features but provide inadequate consideration of the full scale of molecular mechanisms tied to peptide recognition. We here characterize contributions that unsupervised and supervised artificial intelligence (AI) methods can make toward understanding and predicting MHC(HLA-A2)-peptide complex immunogenicity when applied to large ensembles of molecular dynamics simulations. We first show that an unsupervised AI method allows us to identify subtle features that drive immunogenicity differences between a cancer neoantigen and its wild-type peptide counterpart. Next, we demonstrate that a supervised AI method for class I MHC(HLA-A2)-peptide complex classification significantly outperforms a sequence model on small datasets corrected for trivial sequence correlations. Furthermore, we show that both unsupervised and supervised approaches reveal determinants of immunogenicity based on time-dependent molecular fluctuations and anchor position dynamics outside the MHC binding groove. We discuss implications of these structural and dynamic immunogenicity correlates for the induction of T cell responses and therapeutic T cell receptor design.
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Affiliation(s)
- Jeffrey K Weber
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598USA
| | - Joseph A Morrone
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598USA
| | - Seung-gu Kang
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598USA
| | - Leili Zhang
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598USA
| | - Lijun Lang
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598USA
| | - Diego Chowell
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Chirag Krishna
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tien Huynh
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598USA
| | - Prerana Parthasarathy
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44015USA
| | - Binquan Luan
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598USA
| | - Tyler J Alban
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44015USA
| | - Wendy D Cornell
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598USA
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44015USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065USA
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44015USA
- National Center for Regenerative Medicine, Cleveland Clinic, Cleveland, OH 44015USA
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5
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Stokidis S, Baxevanis CN, Fortis SP. The Prognostic Significance of Selected HLA Alleles on Prostate Cancer Outcome. Int J Mol Sci 2023; 24:14454. [PMID: 37833904 PMCID: PMC10572221 DOI: 10.3390/ijms241914454] [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: 06/29/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Recently, we have shown that HLA-A*02:01 and HLA-A*24:02 in de novo metastatic prostate cancer (MPCa) have an important role in disease progression. Since de novo MPCa represents a small group among patients diagnosed with prostate cancer (PCa), it was obvious to try to extend the validity of our results to larger cohorts of PCa patients. Herein, we analyzed patients irrespective of their disease status at diagnosis to include, besides patients with MPCa, those with localized PCa (LPCa). Our goal was to specify the prognostic value of HLA-A*02:01 and HLA-A*24:02 for overall survival (OS) prospectively and for early biochemical recurrence (BCR) and castrate resistance (CR) as additional clinical endpoints in a prospective/retrospective manner, to improve clinical decisions for patients covering all stages of PCa. On univariate analysis, HLA-A alleles were significantly associated as prognostic biomarkers with early BCR (p = 0.028; HR = 1.822), OS (p = 0.013; HR = 1.547) and showed a trend for CR (p = 0.150; HR = 1.239). On multivariate analysis, HLA-A alleles proved to be independent prognosticators for early BCR (p = 0.017; HR = 2.008), CR (p = 0.005; HR = 1.615), and OS (p = 0.002; HR = 2.063). Kaplan-Meier analyses revealed that patients belonging to the HLA-A*02:01+HLA-A*24:02- group progressed much faster to BCR and CR and had also shorter OS compared to HLA-A*24:02+ patients. Patients being HLA-A*02:01-HLA-A*24:02- exhibited varying clinical outcomes, pointing to the presence of additional HLA-A alleles with potential prognostic value. Our data underline the HLA-A alleles as valuable prognostic biomarkers for PCa that may assist with the appropriate treatment and follow-up schedule based on the risk for disease progression to avoid over-diagnosis and over-treatment.
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Affiliation(s)
| | | | - Sotirios P. Fortis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 171 Alexandras Avenue, 11522 Athens, Greece; (S.S.); (C.N.B.)
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6
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Ferrazzo F, Leto S, Malara N. The 1926 novel, "One, no one, one hundred thousand", metaphorizes the potential danger when the immune system is exposed to a repetitive antigen stimulation. Front Immunol 2023; 14:1254853. [PMID: 37771583 PMCID: PMC10524273 DOI: 10.3389/fimmu.2023.1254853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023] Open
Abstract
In the worldwide scenario of infection prevention and control, the vaccine strategies are destined to increase rapidly. The availability of numerous vaccination options allows you to plan individually on how to boost your immune system. The immune system is a highly plastic cognitive dynamic network and performs its function by recognition of the uniqueness of the organism defined as self. The identification and attack of non-self antigens contribute to improving the strategies of self/non-self discrimination. However, repetitive antigen stimulation of the immune system may lead to several outcomes reassumed in three principal risks: (i) loss of the unique self codification (one), (ii) loss of own identifying (no one), and (iii) the increase of idiotype/anti-idiotype entities (one hundred thousand). Controlled production of idiotype/anti-idiotype antibodies protects against autoimmune diseases and immunodeficiency. The title of the famous novel by Nobel Prize for Literature winner Luigi Pirandello, "One, no one, one hundred thousand", recaps the three risks and the protagonist's journey exploring the complexities of personal identity, and warns to preserve the uniqueness of the organism. Taking inspiration from this metaphor, the authors propose to monitor antibody idiotype response for personalizing vaccine plans with the aim of preserving the uniqueness of the immune system and assuring safe protection.
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Affiliation(s)
| | | | - Natalia Malara
- Department of Health Sciences, University Magna Graecia, Catanzaro, Italy
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7
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Gutierrez-Merino C. Brain Hydrophobic Peptides Antagonists of Neurotoxic Amyloid β Peptide Monomers/Oligomers-Protein Interactions. Int J Mol Sci 2023; 24:13846. [PMID: 37762148 PMCID: PMC10531495 DOI: 10.3390/ijms241813846] [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: 08/04/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Amyloid β (Aβ) oligomers have been linked to Alzheimer's disease (AD) pathogenesis and are the main neurotoxic forms of Aβ. This review focuses on the following: (i) the Aβ(1-42):calmodulin interface as a model for the design of antagonist Aβ peptides and its limitations; (ii) proteolytic degradation as the major source of highly hydrophobic peptides in brain cells; and (iii) brain peptides that have been experimentally demonstrated to bind to Aβ monomers or oligomers, Aβ fibrils, or Aβ plaques. It is highlighted that the hydrophobic amino acid residues of the COOH-terminal segment of Aβ(1-42) play a key role in its interaction with intracellular protein partners linked to its neurotoxicity. The major source of highly hydrophobic endogenous peptides of 8-10 amino acids in neurons is the proteasome activity. Many canonical antigen peptides bound to the major histocompatibility complex class 1 are of this type. These highly hydrophobic peptides bind to Aβ and are likely to be efficient antagonists of the binding of Aβ monomers/oligomers concentrations in the nanomolar range with intracellular proteins. Also, their complexation with Aβ will protect them against endopeptidases, suggesting a putative chaperon-like physiological function for Aβ that has been overlooked until now. Remarkably, the hydrophobic amino acid residues of Aβ responsible for the binding of several neuropeptides partially overlap with those playing a key role in its interaction with intracellular protein partners that mediates its neurotoxicity. Therefore, these latter neuropeptides are also potential candidates to antagonize Aβ peptides binding to target proteins. In conclusion, the analysis performed in this review points out that hydrophobic endogenous brain neuropeptides could be valuable biomarkers to evaluate the risk of the onset of sporadic AD, as well as for the prognosis of AD.
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Affiliation(s)
- Carlos Gutierrez-Merino
- Instituto de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, 06006 Badajoz, Spain
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8
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Papadaki GF, Ani O, Florio TJ, Young MC, Danon JN, Sun Y, Dersh D, Sgourakis NG. Decoupling peptide binding from T cell receptor recognition with engineered chimeric MHC-I molecules. Front Immunol 2023; 14:1116906. [PMID: 36761745 PMCID: PMC9905809 DOI: 10.3389/fimmu.2023.1116906] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
Major Histocompatibility Complex class I (MHC-I) molecules display self, viral or aberrant epitopic peptides to T cell receptors (TCRs), which employ interactions between complementarity-determining regions with both peptide and MHC-I heavy chain 'framework' residues to recognize specific Human Leucocyte Antigens (HLAs). The highly polymorphic nature of the HLA peptide-binding groove suggests a malleability of interactions within a common structural scaffold. Here, using structural data from peptide:MHC-I and pMHC:TCR structures, we first identify residues important for peptide and/or TCR binding. We then outline a fixed-backbone computational design approach for engineering synthetic molecules that combine peptide binding and TCR recognition surfaces from existing HLA allotypes. X-ray crystallography demonstrates that chimeric molecules bridging divergent HLA alleles can bind selected peptide antigens in a specified backbone conformation. Finally, in vitro tetramer staining and biophysical binding experiments using chimeric pMHC-I molecules presenting established antigens further demonstrate the requirement of TCR recognition on interactions with HLA framework residues, as opposed to interactions with peptide-centric Chimeric Antigen Receptors (CARs). Our results underscore a novel, structure-guided platform for developing synthetic HLA molecules with desired properties as screening probes for peptide-centric interactions with TCRs and other therapeutic modalities.
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Affiliation(s)
- Georgia F. Papadaki
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Omar Ani
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Tyler J. Florio
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michael C. Young
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Julia N. Danon
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yi Sun
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Devin Dersh
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nikolaos G. Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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9
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Singh A, Padariya M, Faktor J, Kote S, Mikac S, Dziadosz A, Lam TW, Brydon J, Wear MA, Ball KL, Hupp T, Sznarkowska A, Vojtesek B, Kalathiya U. Identification of novel interferon responsive protein partners of human leukocyte antigen A (HLA-A) using cross-linking mass spectrometry (CLMS) approach. Sci Rep 2022; 12:19422. [PMID: 36371414 PMCID: PMC9653400 DOI: 10.1038/s41598-022-21393-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022] Open
Abstract
The interferon signalling system elicits a robust cytokine response against a wide range of environmental pathogenic and internal pathological signals, leading to induction of a subset of interferon-induced proteins. We applied DSS (disuccinimidyl suberate) mediated cross-linking mass spectrometry (CLMS) to capture novel protein-protein interactions within the realm of interferon induced proteins. In addition to the expected interferon-induced proteins, we identified novel inter- and intra-molecular cross-linked adducts for the canonical interferon induced proteins, such as MX1, USP18, OAS3, and STAT1. We focused on orthogonal validation of a cohort of novel interferon-induced protein networks formed by the HLA-A protein (H2BFS-HLA-A-HMGA1) using co-immunoprecipitation assay, and further investigated them by molecular dynamics simulation. Conformational dynamics of the simulated protein complexes revealed several interaction sites that mirrored the interactions identified in the CLMS findings. Together, we showcase a proof-of-principle CLMS study to identify novel interferon-induced signaling complexes and anticipate broader use of CLMS to identify novel protein interaction dynamics within the tumour microenvironment.
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Affiliation(s)
- Ashita Singh
- grid.4305.20000 0004 1936 7988Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR Scotland, UK ,grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Monikaben Padariya
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Jakub Faktor
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Sachin Kote
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Sara Mikac
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Alicja Dziadosz
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Tak W. Lam
- grid.4305.20000 0004 1936 7988Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR Scotland, UK
| | - Jack Brydon
- grid.4305.20000 0004 1936 7988Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR Scotland, UK
| | - Martin A. Wear
- grid.4305.20000 0004 1936 7988School of Biological Sciences, Institute of Structural and Molecular Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
| | - Kathryn L. Ball
- grid.4305.20000 0004 1936 7988Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR Scotland, UK
| | - Ted Hupp
- grid.4305.20000 0004 1936 7988Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR Scotland, UK ,grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Alicja Sznarkowska
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Borek Vojtesek
- grid.419466.8RECAMO, Masaryk Memorial Cancer Institute, Zlutykopec 7, 65653 Brno, Czech Republic
| | - Umesh Kalathiya
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
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10
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Liu Z, Zhang R, Zhang W, Xu Y. Structure-based rational design of hydroxysteroid dehydrogenases for improving and diversifying steroid synthesis. Crit Rev Biotechnol 2022:1-17. [PMID: 35834355 DOI: 10.1080/07388551.2022.2054770] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A group of steroidogenic enzymes, hydroxysteroid dehydrogenases are involved in steroid metabolism which is very important in the cell: signaling, growth, reproduction, and energy homeostasis. The enzymes show an inherent function in the interconversion of ketosteroids and hydroxysteroids in a position- and stereospecific manner on the steroid nucleus and side-chains. However, the biocatalysis of steroids reaction is a vital and demanding, yet challenging, task to produce the desired enantiopure products with non-natural substrates or non-natural cofactors, and/or in non-physiological conditions. This has driven the use of protein design strategies to improve their inherent biosynthetic efficiency or activate their silent catalytic ability. In this review, the innate features and catalytic characteristics of enzymes based on sequence-structure-function relationships of steroidogenic enzymes are reviewed. Combining structure information and catalytic mechanisms, progress in protein redesign to stimulate potential function, for example, substrate specificity, cofactor dependence, and catalytic stability are discussed.
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Affiliation(s)
- Zhiyong Liu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Rongzhen Zhang
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Wenchi Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
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11
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Asa M, Morita D, Kuroha J, Mizutani T, Mori N, Mikami B, Sugita M. Crystal structures of N-myristoylated lipopeptide-bound HLA class I complexes indicate reorganization of B-pocket architecture upon ligand binding. J Biol Chem 2022; 298:102100. [PMID: 35667438 PMCID: PMC9243169 DOI: 10.1016/j.jbc.2022.102100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/29/2022] Open
Abstract
Rhesus monkeys have evolved major histocompatibility complex (MHC)-encoded class I allomorphs such as Mamu-B*098 that are capable of binding N-myristoylated short lipopeptides rather than conventional long peptides; however, it remains unknown whether such antigen-binding molecules exist in other species, including humans. We herein demonstrate that human leukocyte antigen (HLA)-A*24:02 and HLA-C*14:02 proteins, which are known to bind conventional long peptides, also have the potential to bind N-myristoylated short lipopeptides. These HLA class I molecules shared a serine at position 9 (Ser9) with Mamu-B*098, in contrast to most MHC class I molecules that harbor a larger amino acid residue, such as tyrosine, at this position. High resolution X-ray crystallographic analyses of lipopeptide-bound HLA-A*24:02 and HLA-C*14:02 complexes indicated that Ser9 was at the bottom of the B pocket with its small hydroxymethyl side chain directed away from the B-pocket cavity, thereby contributing to the formation of a deep hydrophobic cavity suitable for accommodating the long-chain fatty acid moiety of lipopeptide ligands. Upon peptide binding, however, we found the hydrogen-bond network involving Ser9 was reorganized, and the remodeled B pocket was able to capture the second amino acid residue (P2) of peptide ligands. Apart from the B pocket, virtually no marked alterations were observed for the A and F pockets upon peptide and lipopeptide binding. Thus, we concluded that the structural flexibility of the large B pocket of HLA-A*2402 and HLA-C*1402 primarily accounted for their previously unrecognized capacity to bind such chemically distinct ligands as conventional peptides and N-myristoylated lipopeptides.
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Affiliation(s)
- Minori Asa
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Daisuke Morita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jin Kuroha
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tatsuaki Mizutani
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naoki Mori
- Laboratory of Chemical Ecology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Bunzo Mikami
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Masahiko Sugita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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12
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Marzella DF, Parizi FM, van Tilborg D, Renaud N, Sybrandi D, Buzatu R, Rademaker DT, ‘t Hoen PAC, Xue LC. PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes. Front Immunol 2022; 13:878762. [PMID: 35619705 PMCID: PMC9127323 DOI: 10.3389/fimmu.2022.878762] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Deeper understanding of T-cell-mediated adaptive immune responses is important for the design of cancer immunotherapies and antiviral vaccines against pandemic outbreaks. T-cells are activated when they recognize foreign peptides that are presented on the cell surface by Major Histocompatibility Complexes (MHC), forming peptide:MHC (pMHC) complexes. 3D structures of pMHC complexes provide fundamental insight into T-cell recognition mechanism and aids immunotherapy design. High MHC and peptide diversities necessitate efficient computational modelling to enable whole proteome structural analysis. We developed PANDORA, a generic modelling pipeline for pMHC class I and II (pMHC-I and pMHC-II), and present its performance on pMHC-I here. Given a query, PANDORA searches for structural templates in its extensive database and then applies anchor restraints to the modelling process. This restrained energy minimization ensures one of the fastest pMHC modelling pipelines so far. On a set of 835 pMHC-I complexes over 78 MHC types, PANDORA generated models with a median RMSD of 0.70 Å and achieved a 93% success rate in top 10 models. PANDORA performs competitively with three pMHC-I modelling state-of-the-art approaches and outperforms AlphaFold2 in terms of accuracy while being superior to it in speed. PANDORA is a modularized and user-configurable python package with easy installation. We envision PANDORA to fuel deep learning algorithms with large-scale high-quality 3D models to tackle long-standing immunology challenges.
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Affiliation(s)
- Dario F. Marzella
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Farzaneh M. Parizi
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Derek van Tilborg
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Nicolas Renaud
- Natural Sciences and Engineering section, Netherlands eScience Center, Amsterdam, Netherlands
| | - Daan Sybrandi
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, Netherlands
| | - Rafaella Buzatu
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Daniel T. Rademaker
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Peter A. C. ‘t Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Li C. Xue
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
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13
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The pockets guide to HLA class I molecules. Biochem Soc Trans 2021; 49:2319-2331. [PMID: 34581761 PMCID: PMC8589423 DOI: 10.1042/bst20210410] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 01/11/2023]
Abstract
Human leukocyte antigens (HLA) are cell-surface proteins that present peptides to T cells. These peptides are bound within the peptide binding cleft of HLA, and together as a complex, are recognised by T cells using their specialised T cell receptors. Within the cleft, the peptide residue side chains bind into distinct pockets. These pockets ultimately determine the specificity of peptide binding. As HLAs are the most polymorphic molecules in humans, amino acid variants in each binding pocket influences the peptide repertoire that can be presented on the cell surface. Here, we review each of the 6 HLA binding pockets of HLA class I (HLA-I) molecules. The binding specificity of pockets B and F are strong determinants of peptide binding and have been used to classify HLA into supertypes, a useful tool to predict peptide binding to a given HLA. Over the years, peptide binding prediction has also become more reliable by using binding affinity and mass spectrometry data. Crystal structures of peptide-bound HLA molecules provide a means to interrogate the interactions between binding pockets and peptide residue side chains. We find that most of the bound peptides from these structures conform to binding motifs determined from prediction software and examine outliers to learn how these HLAs are stabilised from a structural perspective.
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14
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Rausch AO, Freiberger MI, Leonetti CO, Luna DM, Radusky LG, Wolynes PG, Ferreiro DU, Parra RG. FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations. Bioinformatics 2021; 37:3038-3040. [PMID: 33720293 DOI: 10.1093/bioinformatics/btab176] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/19/2021] [Accepted: 03/11/2021] [Indexed: 02/02/2023] Open
Abstract
SUMMARY Once folded, natural protein molecules have few energetic conflicts within their polypeptide chains. Many protein structures do however contain regions where energetic conflicts remain after folding, i.e. they are highly frustrated. These regions, kept in place over evolutionary and physiological timescales, are related to several functional aspects of natural proteins such as protein-protein interactions, small ligand recognition, catalytic sites and allostery. Here, we present FrustratometeR, an R package that easily computes local energetic frustration on a personal computer or a cluster. This package facilitates large scale analysis of local frustration, point mutants and molecular dynamics (MD) trajectories, allowing straightforward integration of local frustration analysis into pipelines for protein structural analysis. AVAILABILITY AND IMPLEMENTATION https://github.com/proteinphysiologylab/frustratometeR. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Atilio O Rausch
- Facultad de Ingeniería, Universidad Nacional de Entre Ríos, Entre Ríos E3100XAD, Argentina
| | - Maria I Freiberger
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Cesar O Leonetti
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Diego M Luna
- Facultad de Ingeniería, Universidad Nacional de Entre Ríos, Entre Ríos E3100XAD, Argentina
| | - Leandro G Radusky
- Center for Genomic Regulation, Barcelona Institute for Science and Technology, Barcelona 08003, Spain
| | - Peter G Wolynes
- Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Diego U Ferreiro
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - R Gonzalo Parra
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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15
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Sarri CA, Giannoulis T, Moutou KA, Mamuris Z. HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action. Immunol Lett 2021; 238:75-95. [PMID: 34329645 DOI: 10.1016/j.imlet.2021.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 01/24/2023]
Abstract
BACKGROUND HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR). METHODS For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used. RESULTS All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found. CONCLUSIONS Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.
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Affiliation(s)
- Constantina A Sarri
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Themistoklis Giannoulis
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece; Department of Animal Science, University of Thessaly, Trikallon 224, 43100 Karditsa, Greece
| | - Katerina A Moutou
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Zissis Mamuris
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece.
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16
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Truong HV, Sgourakis NG. Dynamics of MHC-I molecules in the antigen processing and presentation pathway. Curr Opin Immunol 2021; 70:122-128. [PMID: 34153556 PMCID: PMC8622473 DOI: 10.1016/j.coi.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 01/07/2023]
Abstract
The endogenous antigen processing and presentation (APP) is a fundamental pathway found in jawed vertebrates, which allows for a set of epitope peptides sampled from the intracellular proteome to be assembled and displayed on class I proteins of the major histocompatibility complex (MHC-I). Peptide/MHC-I antigens enable different aspects of adaptive immunity to emerge, by providing a basis for recognition of self vs. non-self by T cells and Natural Killer (NK) cells. Pioneering studies of pMHC-I molecules and their higher-order protein complexes with molecular chaperones and membrane receptors have gleaned important insights into the peptide loading and antigen recognition mechanisms. While X-ray and cryoEM structures have provided us with static snapshots of different MHC-I assembly stages, complementary biophysical techniques have revealed that MHC-I molecules are highly mobile on a range of biologically relevant timescales, which bears importance for their assembly, peptide repertoire selection, membrane display and turnover. This review summarizes insights gained from experimental and simulation studies aimed at investigating MHC-I dynamics, and their functional implications.
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Affiliation(s)
- Hau V Truong
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA.
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17
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Jantz-Naeem N, Springer S. Venus flytrap or pas de trois? The dynamics of MHC class I molecules. Curr Opin Immunol 2021; 70:82-89. [PMID: 33993034 DOI: 10.1016/j.coi.2021.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 11/25/2022]
Abstract
The peptide binding site of major histocompatibility complex (MHC) class I molecules is natively unfolded when devoid of peptides. Peptide binding stabilizes the structure and slows the dynamics, but peptide-specific and subtype-specific motions influence, and are influenced by, interaction with assembly chaperones, the T cell receptor, and other class I-binding proteins. The molecular mechanisms of cooperation between peptide, class I heavy chain, and beta-2 microglobulin are insufficiently known but are being elucidated by nuclear magnetic resonance and other modern methods. It appears that micropolymorphic clusters of charged amino acids, often hidden in the molecule interior, determine the dynamics and thus chaperone dependence, cellular fate, and disease association of class I.
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Affiliation(s)
- Nouria Jantz-Naeem
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany.
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18
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Bingöl EN, Serçinoğlu O, Ozbek P. Unraveling the Allosteric Communication Mechanisms in T-Cell Receptor-Peptide-Loaded Major Histocompatibility Complex Dynamics Using Molecular Dynamics Simulations: An Approach Based on Dynamic Cross Correlation Maps and Residue Interaction Energy Calculations. J Chem Inf Model 2021; 61:2444-2453. [PMID: 33930270 DOI: 10.1021/acs.jcim.1c00338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antigen presentation by major histocompatibility complex (MHC) proteins to T-cell receptors (TCRs) plays a crucial role in triggering the adaptive immune response. Most of our knowledge on TCR-peptide-loaded major histocompatibility complex (pMHC) interaction stemmed from experiments yielding static structures, yet the dynamic aspects of this molecular interaction are equally important to understand the underlying molecular mechanisms and to develop treatment strategies against diseases such as cancer and autoimmune diseases. To this end, computational biophysics studies including all-atom molecular dynamics simulations have provided useful insights; however, we still lack a basic understanding of an overall allosteric mechanism that results in conformational changes in the TCR and subsequent T-cell activation. Previous hydrogen-deuterium exchange and nuclear magnetic resonance studies provided clues regarding these molecular mechanisms, including global rigidification and allosteric effects on the constant domain of TCRs away from the pMHC interaction site. Here, we show that molecular dynamics simulations can be used to identify how this overall rigidification may be related to the allosteric communication within TCRs upon pMHC interaction via essential dynamics and nonbonded residue-residue interaction energy analyses. The residues taking part in the rigidification effect are highlighted with an intricate analysis on residue interaction changes, which lead to a detailed outline of the complex formation event. Our results indicate that residues of the Cβ domain of TCRs show significant differences in their nonbonded interactions upon complex formation. Moreover, the dynamic cross correlations between these residues are also increased, in line with their nonbonded interaction energy changes. Altogether, our approach may be valuable for elucidating intramolecular allosteric changes in the TCR structure upon pMHC interaction in molecular dynamics simulations.
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Affiliation(s)
- Elif Naz Bingöl
- Department of Bioengineering, Institute of Pure and Applied Sciences, Marmara University, 34722 Istanbul, Turkey
| | - Onur Serçinoğlu
- Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Kocaeli 41400, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul 34722, Turkey
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19
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Kuiper JJW, Venema WJ. HLA-A29 and Birdshot Uveitis: Further Down the Rabbit Hole. Front Immunol 2020; 11:599558. [PMID: 33262772 PMCID: PMC7687429 DOI: 10.3389/fimmu.2020.599558] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/16/2020] [Indexed: 12/26/2022] Open
Abstract
HLA class I alleles constitute established risk factors for non-infectious uveitis and preemptive genotyping of HLA class I alleles is standard practice in the diagnostic work-up. The HLA-A29 serotype is indispensable to Birdshot Uveitis (BU) and renders this enigmatic eye condition a unique model to better understand how the antigen processing and presentation machinery contributes to non-infectious uveitis or chronic inflammatory conditions in general. This review will discuss salient points regarding the protein structure of HLA-A29 and how key amino acid positions impact the peptide binding preference and interaction with T cells. We discuss to what extent the risk genes ERAP1 and ERAP2 uniquely affect HLA-A29 and how the discovery of a HLA-A29-specific submotif may impact autoantigen discovery. We further provide a compelling argument to solve the long-standing question why BU only affects HLA-A29-positive individuals from Western-European ancestry by exploiting data from the 1000 Genomes Project. We combine novel insights from structural and immunopeptidomic studies and discuss the functional implications of genetic associations across the HLA class I antigen presentation pathway to refine the etiological basis of Birdshot Uveitis.
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Affiliation(s)
- Jonas J. W. Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Wouter J. Venema
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
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