A study of CDR3 loop dynamics reveals distinct mechanisms of peptide recognition by T‐cell receptors exhibiting different levels of cross‐reactivity

T‐cell receptors (TCRs) can productively interact with many different peptides bound within the MHC binding groove. This property varies with the level of cross‐reactivity of TCRs; some TCRs are particularly hyper cross‐reactive while others exhibit greater specificity. To elucidate the mechanism behind these differences, we studied five TCRs in complex with the same class II MHC (1Ab)‐peptide (3K), that are known to exhibit different levels of cross‐reactivity. Although these complexes have similar binding affinities, the interface areas between the TCR and the peptide–MHC (pMHC) differ significantly. We investigated static and dynamic structural features of the TCR–pMHC complexes and of TCRs in a free state, as well as the relationship between binding affinity and interface area. It was found that the TCRs known to exhibit lower levels of cross‐reactivity bound to pMHC using an induced‐fitting mechanism, forming large and tight interfaces rich in specific hydrogen bonds. In contrast, TCRs known to exhibit high levels of cross‐reactivity used a more rigid binding mechanism where non‐specific π‐interactions involving the bulky Trp residue in CDR3β dominated. As entropy loss upon binding in these highly degenerate and rigid TCRs is smaller than that in less degenerate TCRs, they can better tolerate changes in residues distal from the major contacts with MHC‐bound peptide. Hence, our dynamics study revealed that differences in the peptide recognition mechanisms by TCRs appear to correlate with the levels of T‐cell cross‐reactivity.

[1]  Clemencia Pinilla,et al.  How the T Cell Repertoire Becomes Peptide and MHC Specific , 2005, Cell.

[2]  P. Marrack,et al.  Alternate interactions define the binding of peptides to the MHC molecule IAb , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[3]  J. Drijfhout,et al.  Structural basis of human β-cell killing by CD8+ T cells in Type 1 diabetes , 2011, Nature Immunology.

[4]  Andrew K. Sewell,et al.  Hydrophobic CDR3 residues promote the development of self-reactive T cells , 2016, Nature Immunology.

[5]  L. Stern,et al.  Effect of CDR3 Sequences and Distal V Gene Residues in Regulating TCR–MHC Contacts and Ligand Specificity , 2014, The Journal of Immunology.

[6]  K. Garcia,et al.  How a Single T Cell Receptor Recognizes Both Self and Foreign MHC , 2007, Cell.

[7]  L R Pease,et al.  Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen. , 1998, Science.

[8]  Kazuo Kitaura,et al.  A new energy decomposition scheme for molecular interactions within the Hartree‐Fock approximation , 1976 .

[9]  Susana Gordo,et al.  Crossreactivity of a human autoimmune TCR is dominated by a single TCR loop , 2013, Nature Communications.

[10]  Mark M. Davis,et al.  Two-step binding mechanism for T-cell receptor recognition of peptide–MHC , 2002, Nature.

[11]  K. Wucherpfennig,et al.  A highly tilted binding mode by a self-reactive T cell receptor results in altered engagement of peptide and MHC , 2011, The Journal of experimental medicine.

[12]  Philippa Marrack,et al.  Crossreactive T Cells spotlight the germline rules for alphabeta T cell-receptor interactions with MHC molecules. , 2008, Immunity.

[13]  Kaori Fukuzawa,et al.  Fragment molecular orbital method: use of approximate electrostatic potential , 2002 .

[14]  James McCluskey,et al.  T cell receptor reversed polarity recognition of a self-antigen major histocompatibility complex , 2015, Nature Immunology.

[15]  L. K. Ely,et al.  The molecular basis of TCR germline bias for MHC is surprisingly simple , 2009, Nature Immunology.

[16]  Roland L. Dunbrack,et al.  A new clustering of antibody CDR loop conformations. , 2011, Journal of molecular biology.

[17]  M. Nishio,et al.  CH/pi interactions as demonstrated in the crystal structure of guanine-nucleotide binding proteins, Src homology-2 domains and human growth hormone in complex with their specific ligands. , 1998, Bioorganic & medicinal chemistry.

[18]  Kengo Kinoshita,et al.  Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity. , 2006, Protein engineering, design & selection : PEDS.

[19]  Mark M Davis,et al.  Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation. , 2003, Molecular cell.

[20]  A. Sewell,et al.  Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity , 2016, The Journal of clinical investigation.

[21]  David M Kranz,et al.  TCR affinity for p/MHC formed by tumor antigens that are self-proteins: impact on efficacy and toxicity. , 2015, Current opinion in immunology.

[22]  J. Gorski,et al.  Cross-reactivity of T cells and its role in the immune system. , 2012, Critical reviews in immunology.

[23]  L. Stern,et al.  A role for differential variable gene pairing in creating T cell receptors specific for unique major histocompatibility ligands. , 2011, Immunity.

[24]  J. Drijfhout,et al.  Structural basis for the killing of human beta cells by CD 8 + T cells in type 1 diabetes , 2012 .

[25]  D. Mason,et al.  A very high level of crossreactivity is an essential feature of the T-cell receptor. , 1998, Immunology today.

[26]  R. Mariuzza,et al.  The multiple mechanisms of T cell receptor cross-reactivity. , 2009, Immunity.

[27]  J. Correa-Basurto,et al.  Energetic and flexibility properties captured by long molecular dynamics simulations of a membrane-embedded pMHCII-TCR complex. , 2016, Molecular bioSystems.

[28]  A. Sewell,et al.  Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity , 2016, The Journal of clinical investigation.

[29]  J. Thornton,et al.  Satisfying hydrogen bonding potential in proteins. , 1994, Journal of molecular biology.

[30]  A. Sewell,et al.  A structural voyage toward an understanding of the MHC‐I‐restricted immune response: lessons learned and much to be learned , 2012, Immunological reviews.

[31]  K. M. Armstrong,et al.  A comprehensive calorimetric investigation of an entropically driven T cell receptor-peptide/major histocompatibility complex interaction. , 2007, Biophysical journal.

[32]  Philippa Marrack,et al.  A single T cell receptor bound to major histocompatibility complex class I and class II glycoproteins reveals switchable TCR conformers. , 2011, Immunity.

[33]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[34]  P. Marrack,et al.  Interface-disrupting amino acids establish specificity between T cell receptors and complexes of major histocompatibility complex and peptide , 2006, Nature Immunology.

[35]  Mark M. Davis,et al.  Deconstructing the Peptide-MHC Specificity of T Cell Recognition , 2014, Cell.

[36]  K. Shekhar,et al.  Hydrophobic CDR 3 residues promote the development of self-reactive T cells , 2016 .

[37]  François Ehrenmann,et al.  IMGT/3Dstructure-DB: querying the IMGT database for 3D structures in immunology and immunoinformatics (IG or antibodies, TR, MH, RPI, and FPIA). , 2011, Cold Spring Harbor protocols.

[38]  K. Wucherpfennig,et al.  Structural alterations in peptide-MHC recognition by self-reactive T cell receptors. , 2009, Current opinion in immunology.

[39]  K. M. Armstrong,et al.  Thermodynamics of T‐cell receptor–peptide/MHC interactions: progress and opportunities , 2008, Journal of molecular recognition : JMR.

[40]  Carsten Kutzner,et al.  Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS , 2015, EASC.