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Saikia A, Springer S. Peptide-MHC I complex stability measured by nanoscale differential scanning fluorimetry reveals molecular mechanism of thermal denaturation. Mol Immunol 2021; 136:73-81. [PMID: 34091103 DOI: 10.1016/j.molimm.2021.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/08/2021] [Accepted: 04/29/2021] [Indexed: 12/22/2022]
Abstract
Recombinant major histocompatibility complex class I molecules are used in diagnostic and therapeutic approaches in cancer immunotherapy, with many studies exploring their binding to antigenic peptides. Current techniques for kinetic peptide binding studies are hampered by high sample consumption, low throughput, interference with protein stability, and/or high background signal. Here, we validate nanoscale differential scanning fluorimetry (nanoDSF), a method using the tryptophan fluorescence of class I molecules, for class I/peptide binding, and we use it to determine the molecular mechanism of the thermal denaturation of HLA-A*02:01.
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Affiliation(s)
- Ankur Saikia
- Department of Life Science and Chemistry, Jacobs University Bremen, Germany
| | - Sebastian Springer
- Department of Life Science and Chemistry, Jacobs University Bremen, Germany.
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2
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Smith AR, Alonso JA, Ayres CM, Singh NK, Hellman LM, Baker BM. Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner. Proc Natl Acad Sci U S A 2021; 118:e2018125118. [PMID: 33468649 PMCID: PMC7848747 DOI: 10.1073/pnas.2018125118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Presentation of peptides by class I MHC proteins underlies T cell immune responses to pathogens and cancer. The association between peptide binding affinity and immunogenicity has led to the engineering of modified peptides with improved MHC binding, with the hope that these peptides would be useful for eliciting cross-reactive immune responses directed toward their weak binding, unmodified counterparts. Increasing evidence, however, indicates that T cell receptors (TCRs) can perceive such anchor-modified peptides differently than wild-type (WT) peptides, although the scope of discrimination is unclear. We show here that even modifications at primary anchors that have no discernible structural impact can lead to substantially stronger or weaker T cell recognition depending on the TCR. Surprisingly, the effect of peptide anchor modification can be sensed by a TCR at regions distant from the site of modification, indicating a through-protein mechanism in which the anchor residue serves as an allosteric modulator for TCR binding. Our findings emphasize caution in the use and interpretation of results from anchor-modified peptides and have implications for how anchor modifications are accounted for in other circumstances, such as predicting the immunogenicity of tumor neoantigens. Our data also highlight an important need to better understand the highly tunable dynamic nature of class I MHC proteins and the impact this has on various forms of immune recognition.
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MESH Headings
- Allosteric Regulation
- Binding Sites
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/immunology
- Humans
- Jurkat Cells
- Kinetics
- Models, Molecular
- Peptides/chemistry
- Peptides/genetics
- Peptides/immunology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Engineering
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Th2 Cells/cytology
- Th2 Cells/immunology
- Thermodynamics
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Affiliation(s)
- Angela R Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Nishant K Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Lance M Hellman
- Department of Physical and Life Sciences, Nevada State College, Henderson, NV 89002
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556;
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
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3
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Kaur N, Aditya RN, Singh A, Kuo TR. Biomedical Applications for Gold Nanoclusters: Recent Developments and Future Perspectives. NANOSCALE RESEARCH LETTERS 2018; 13:302. [PMID: 30259230 PMCID: PMC6158143 DOI: 10.1186/s11671-018-2725-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/18/2018] [Indexed: 05/30/2023]
Abstract
Gold nanoclusters (AuNCs) have been extensively applied as a fluorescent probe for biomedical applications in imaging, detection, and therapy due to their unique chemical and physical properties. Fluorescent probes of AuNCs have exhibited high compatibility, superior photostablility, and excellent water solubility which resulted in remarkable biomedical applications for long-term imaging, high-sensitivity detection, and target-specific treatment. Recently, great efforts have been made in the developments of AuNCs as the fluorescent probes for various biomedical applications. In this review, we have collected fluorescent AuNCs prepared by different ligands, including small molecules, polymers, and biomacromolecules, and highlighted current achievements of AuNCs in biomedical applications for imaging, detection, and therapy. According to these advances, we further provided conclusions of present challenges and future perspectives of AuNCs for fundamental investigations and practical biomedical applications.
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Affiliation(s)
- Navdeep Kaur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 11031 Taiwan
| | - Robby Nur Aditya
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031 Taiwan
| | - Arshdeep Singh
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 11031 Taiwan
| | - Tsung-Rong Kuo
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031 Taiwan
- Graduate Institute of Nanomedicine and Medical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031 Taiwan
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4
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Ross P, Nemec PS, Kapatos A, Miller KR, Holmes JC, Suter SE, Buntzman AS, Soderblom EJ, Collins EJ, Hess PR. The canine MHC class Ia allele DLA-88*508:01 presents diverse self- and canine distemper virus-origin peptides of varying length that have a conserved binding motif. Vet Immunol Immunopathol 2018; 197:76-86. [PMID: 29475511 DOI: 10.1016/j.vetimm.2018.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/03/2018] [Accepted: 01/12/2018] [Indexed: 01/06/2023]
Abstract
Ideally, CD8+ T-cell responses against virally infected or malignant cells are defined at the level of the specific peptide and restricting MHC class I element, a determination not yet made in the dog. To advance the discovery of canine CTL epitopes, we sought to determine whether a putative classical MHC class Ia gene, Dog Leukocyte Antigen (DLA)-88, presents peptides from a viral pathogen, canine distemper virus (CDV). To investigate this possibility, DLA-88*508:01, an allele prevalent in Golden Retrievers, was expressed as a FLAG-tagged construct in canine histiocytic cells to allow affinity purification of peptide-DLA-88 complexes and subsequent elution of bound peptides. Pattern analysis of self peptide sequences, which were determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS), permitted binding preferences to be inferred. DLA-88*508:01 binds peptides that are 9-to-12 amino acids in length, with a modest preference for 9- and 11-mers. Hydrophobic residues are favored at positions 2 and 3, as are K, R or F residues at the C-terminus. Testing motif-matched and -unmatched synthetic peptides via peptide-MHC surface stabilization assay using a DLA-88*508:01-transfected, TAP-deficient RMA-S line supported these conclusions. With CDV infection, 22 viral peptides ranging from 9-to-12 residues in length were identified in DLA-88*508:01 eluates by LC-MS/MS. Combined motif analysis and surface stabilization assay data suggested that 11 of these 22 peptides, derived from CDV hemagglutinin, large polymerase, matrix, nucleocapsid, and V proteins, were processed and presented, and thus, potential targets of anti-viral CTL in DLA-88*508:01-bearing dogs. The presentation of diverse self and viral peptides indicates that DLA-88 is a classical MHC class Ia gene.
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Affiliation(s)
- Peter Ross
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
| | - Paige S Nemec
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
| | - Alexander Kapatos
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
| | - Keith R Miller
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jennifer C Holmes
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
| | - Steven E Suter
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
| | - Adam S Buntzman
- Department of Immunobiology, University of Arizona, Tucson, AZ, 85724, USA
| | - Erik J Soderblom
- Proteomics Core Facility, Institute for Genome Science and Policy, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Edward J Collins
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA; Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Paul R Hess
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA.
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Saini SK, Abualrous ET, Tigan AS, Covella K, Wellbrock U, Springer S. Not all empty MHC class I molecules are molten globules: Tryptophan fluorescence reveals a two-step mechanism of thermal denaturation. Mol Immunol 2013; 54:386-96. [DOI: 10.1016/j.molimm.2013.01.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 12/26/2012] [Accepted: 01/04/2013] [Indexed: 11/27/2022]
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6
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Aldeek F, Muhammed MAH, Palui G, Zhan N, Mattoussi H. Growth of highly fluorescent polyethylene glycol- and zwitterion-functionalized gold nanoclusters. ACS NANO 2013; 7:2509-21. [PMID: 23394608 DOI: 10.1021/nn305856t] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We have prepared and characterized a new set of highly fluorescent gold nanoclusters (AuNCs) using one-step aqueous reduction of a gold precursor in the presence of bidentate ligands made of lipoic acid anchoring groups, appended with either a poly(ethylene glycol) short chain or a zwitterion group. The AuNCs fluoresce in the red to near-infrared region of the optical spectrum with emission centered at ∼750 nm and a quantum yield of ∼10-14%, and they exhibit long fluorescence lifetimes (up to ∼300 ns). Dispersions of these AuNCs exhibit great long-term colloidal stability, over a wide range of pHs (2-13) and in the presence of high electrolyte concentrations, and a strong resistance to reducing agents such as glutathione. The growth strategy further permitted the controlled, in situ functionalization of the NCs with reactive groups (e.g., carboxylic acid or amine), making these nanoclusters compatible with common and simple-to-implement coupling strategies, such as carbodiimide chemistry. These properties combined make these fluorescent NCs greatly promising for use in various imaging and sensing applications where NIR and long-lived excitations are desired.
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Affiliation(s)
- Fadi Aldeek
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
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7
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Borbulevych OY, Do P, Baker BM. Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A*0201: implications for WT1-based cancer therapeutics. Mol Immunol 2010; 47:2519-24. [PMID: 20619457 DOI: 10.1016/j.molimm.2010.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 06/09/2010] [Accepted: 06/12/2010] [Indexed: 01/28/2023]
Abstract
Presentation of peptides by class I or class II major histocompatibility complex (MHC) molecules is required for the initiation and propagation of a T cell-mediated immune response. Peptides from the Wilms Tumor 1 transcription factor (WT1), upregulated in many hematopoetic and solid tumors, can be recognized by T cells and numerous efforts are underway to engineer WT1-based cancer vaccines. Here we determined the structures of the class I MHC molecule HLA-A*0201 bound to the native 126-134 epitope of the WT1 peptide and a recently described variant (R1Y) with improved MHC binding. The R1Y variant, a potential vaccine candidate, alters the positions of MHC charged side chains near the peptide N-terminus and significantly reduces the peptide/MHC electrostatic surface potential. These alterations indicate that the R1Y variant is an imperfect mimic of the native WT1 peptide, and suggest caution in its use as a therapeutic vaccine. Stability measurements revealed how the R1Y substitution enhances MHC binding affinity, and together with the structures suggest a strategy for engineering WT1 variants with improved MHC binding that retain the structural features of the native peptide/MHC complex.
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Affiliation(s)
- Oleg Y Borbulevych
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, United States
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Leonhardt RM, Fiegl D, Rufer E, Karger A, Bettin B, Knittler MR. Post-endoplasmic reticulum rescue of unstable MHC class I requires proprotein convertase PC7. THE JOURNAL OF IMMUNOLOGY 2010; 184:2985-98. [PMID: 20164418 DOI: 10.4049/jimmunol.0900308] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The function of the peptide-loading complex (PLC) is to facilitate loading of MHC class I (MHC I) molecules with antigenic peptides in the endoplasmic reticulum and to drive the selection of these ligands toward a set of high-affinity binders. When the PLC fails to perform properly, as frequently observed in virus-infected or tumor cells, structurally unstable MHC I peptide complexes are generated, which are prone to disintegrate instead of presenting Ags to cytotoxic T cells. In this study we show that a second quality control checkpoint dependent on the serine protease proprotein convertase 7 (PC7) can rescue unstable MHC I, whereas the related convertase furin is completely dispensable. Cells with a malfunctioning PLC and silenced for PC7 have substantially reduced MHC I surface levels caused by high instability and significantly delayed surface accumulation of these molecules. Instead of acquiring stability along the secretory route, MHC I appears to get largely routed to lysosomes for degradation in these cells. Moreover, mass spectrometry analysis provides evidence that lack of PLC quality control and/or loss of PC7 expression alters the MHC I-presented peptide profile. Finally, using exogenously applied peptide precursors, we show that liberation of MHC I epitopes may directly require PC7. We demonstrate for the first time an important function for PC7 in MHC I-mediated Ag presentation.
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Affiliation(s)
- Ralf M Leonhardt
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
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Leonhardt RM, Keusekotten K, Bekpen C, Knittler MR. Critical role for the tapasin-docking site of TAP2 in the functional integrity of the MHC class I-peptide-loading complex. THE JOURNAL OF IMMUNOLOGY 2005; 175:5104-14. [PMID: 16210614 DOI: 10.4049/jimmunol.175.8.5104] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The transporter associated with Ag processing (TAP) translocates antigenic peptides into the endoplasmic reticulum for binding onto MHC class I (MHC I) molecules. Tapasin organizes a peptide-loading complex (PLC) by recruiting MHC I and accessory chaperones to the N-terminal regions (N domains) of the TAP subunits TAP1 and TAP2. To investigate the function of the tapasin-docking sites of TAP in MHC I processing, we expressed N-terminally truncated variants of TAP1 and TAP2 in combination with wild-type chains, as fusion proteins or as single subunits. Strikingly, TAP variants lacking the N domain in TAP2, but not in TAP1, build PLCs that fail to generate stable MHC I-peptide complexes. This correlates with a substantially reduced recruitment of accessory chaperones into the PLC demonstrating their important role in the quality control of MHC I loading. However, stable surface expression of MHC I can be rescued in post-endoplasmic reticulum compartments by a proprotein convertase-dependent mechanism.
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Miley MJ, Messaoudi I, Metzner BM, Wu Y, Nikolich-Zugich J, Fremont DH. Structural basis for the restoration of TCR recognition of an MHC allelic variant by peptide secondary anchor substitution. ACTA ACUST UNITED AC 2004; 200:1445-54. [PMID: 15557346 PMCID: PMC2211956 DOI: 10.1084/jem.20040217] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Major histocompatibility complex (MHC) class I variants H-2Kb and H-2Kbm8 differ primarily in the B pocket of the peptide-binding groove, which serves to sequester the P2 secondary anchor residue. This polymorphism determines resistance to lethal herpes simplex virus (HSV-1) infection by modulating T cell responses to the immunodominant glycoprotein B498-505 epitope, HSV8. We studied the molecular basis of these effects and confirmed that T cell receptors raised against Kb–HSV8 cannot recognize H-2Kbm8–HSV8. However, substitution of SerP2 to GluP2 (peptide H2E) reversed T cell receptor (TCR) recognition; H-2Kbm8–H2E was recognized whereas H-2Kb–H2E was not. Insight into the structural basis of this discrimination was obtained by determining the crystal structures of all four MHC class I molecules in complex with bound peptide (pMHCs). Surprisingly, we find no concerted pMHC surface differences that can explain the differential TCR recognition. However, a correlation is apparent between the recognition data and the underlying peptide-binding groove chemistry of the B pocket, revealing that secondary anchor residues can profoundly affect TCR engagement through mechanisms distinct from the alteration of the resting state conformation of the pMHC surface.
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Affiliation(s)
- Michael J Miley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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Buslepp J, Zhao R, Donnini D, Loftus D, Saad M, Appella E, Collins EJ. T cell activity correlates with oligomeric peptide-major histocompatibility complex binding on T cell surface. J Biol Chem 2001; 276:47320-8. [PMID: 11584024 DOI: 10.1074/jbc.m109231200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recognition of virally infected cells by CD8+ T cells requires differentiation between self and nonself peptide-class I major histocompatibility complexes (pMHC). Recognition of foreign pMHC by host T cells is a major factor in the rejection of transplanted organs from the same species (allotransplant) or different species (xenotransplant). AHIII12.2 is a murine T cell clone that recognizes the xenogeneic (human) class I MHC HLA-A2.1 molecule (A2) and the syngeneic murine class I MHC H-2 D(b) molecule (D(b)). Recognition of both A2 and D(b) are peptide-dependent, and the sequences of the peptides recognized have been determined. Alterations in the antigenic peptides bound to A2 cause large changes in AHIII12.2 T cell responsiveness. Crystal structures of three representative peptides (agonist, null, and antagonist) bound to A2 partially explain the changes in AHIII12.2 responsiveness. Using class I pMHC octamers, a strong correlation is seen between T cell activity and the affinity of pMHC complexes for the T cell receptor. However, contrary to previous studies, we see similar half-lives for the pMHC multimers bound to the AHIII12.2 cell surface.
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Affiliation(s)
- J Buslepp
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
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