The Role of Molecular Flexibility in Antigen Presentation and T Cell Receptor-Mediated Signaling

Natarajan, Kannan; Jiang, Jiansheng; May, Nathan A.; Mage, Michael G.; Boyd, Lisa F.; McShan, Andrew C.; Sgourakis, Nikolaos G.; Bax, Ad; Margulies, David H.

doi:10.3389/fimmu.2018.01657

Cited by 56 publications

(51 citation statements)

References 130 publications

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“…This is expected to heavily influence the accessible space into which all four OH groups of 5‐OP‐RU can project, and therefore regulate their interactions with surrounding residues from the MR1 and TCR proteins. Although some recent studies have implicated peptide‐based antigen conformation and flexibility as factors in antigen recognition, the concept has not been explored with MAIT cells, perhaps because conformationally constrained antigens have not been available to date.…”

Section: Resultsmentioning

confidence: 99%

Computer Modelling and Synthesis of Deoxy and Monohydroxy Analogues of a Ribitylaminouracil Bacterial Metabolite that Potently Activates Human T Cells

Ler

Mak

et al. 2019

Chemistry A European J

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5-(2-Oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU) is an atural productf ormedd uring bacterial synthesis of vitamin B2. It potently activates mucosal associated invariant T( MAIT) cells and has immunomodulatory,i nflammatory,a nd anticancer properties. This highly polar and unstable compound forms ar emarkablys table Schiff base with al ysine residuei nm ajor histocompatibility complex class Irelated protein (MR1) expressed in antigen-presentingc ells. Inspiredb yt he importance of the ribityl moiety of 5-OP-RU for binding to both MR1 and the Tc ell receptor (TCR) on MAIT cells, each OH was removed in silico. DFT calculations and MD simulations revealedavery stable hydrogen bond betweent he C3'ÀOH and uracil N1H, which profoundly restrictsf lexibility and positioning of each ribityl-OH, potentially impacting their interactionsw ith MR1 and TCR. By using deoxygenation strategies and kinetically controlled imine formation,f our monodeoxyribityl and four monohydroxyalkyl analogues of 5-OP-RU were synthesised as new tools for probingTcell activation mechanisms.[a] G.Scheme4.Synthesis of 4-deoxy-d-ribitylamine (32)b yB arton-McCombied eoxygenation of d-ribose (24).Scheme5.Synthesis of 5-deoxy-d-ribitylamine (40)b yC 5-tosylate reduction of d-ribose (24).

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Section: Resultsmentioning

confidence: 99%

Computer Modelling and Synthesis of Deoxy and Monohydroxy Analogues of a Ribitylaminouracil Bacterial Metabolite that Potently Activates Human T Cells

Ler

Mak

et al. 2019

Chemistry A European J

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“…50]. Recently, 'ensemble refinement' of crystal data with MD simulations has suggested conformational diversity in the microsecond range, but the conformational changes implicated here-in would be on the millisecond to minutes scale; in this regard, NMR of membrane-bound receptors may offer promise [50][51][52][53][54] Finally, a dynamics mechanism driven by H-bonding networks is consistent with the knowledge that different T-cell dose-response curves are found at the same TCR affinity for the same pMHC [40,[55][56][57][58]. Even if we assume similar TCR-affinity for the three 4OZ structures, it appears that somatic selection directly effects H-bonds implicated in V-domain dynamics (dV), and (indirectly) germline:germline contacts between CDR2 and the MHC -helices (d) [24,44,49,[59][60][61].…”

Section: Discussionmentioning

confidence: 99%

CDR3 binding chemistry controls TCR V-domain rotational probability and germline CDR2 scanning of polymorphic MHC

Js¹

2019

Preprint

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The mechanism which 'adapts' the T-cell antigen receptor (TCR) repertoire within a given major histocompatibility complex (MHC; HLA, in humans) genotype is essential for protection against rapidly dividing pathogens. Historically attributed to relative affinity, genetically vast TCRs are surprisingly "focused" towards a micromolar affinity for their respective pHLA ligands. Thus, the somatic diversity of the TCR with respect to MHC restriction, and (ultimately) to pathogens, remains enigmatic. Here, we derive a triple integral equation (from fixed geometry) for any given V-domain in TCR bound to pMHC. We examined solved complexes involving HLA-DR and HLA-DQ, where all the available structures are still reasonably analysed. Certain V-beta domains displayed "rare" geometry within this panelspecifying a very low ("highly-restricted") rotational probability/volumetric density (dV). Remarkably, hydrogen (H)-bond charge-relays spanning CDR3-beta, the peptide, and polymorphic MHC distinguished these structures from the others; suggesting that CDR3 binding chemistry dictates CDR2 'scanning' on the respective MHC-II alpha-helix. Taken together, this analysis (n = 38 V-domains) supports a novel geometric theory for MHC restriction-one not constrained by a thymus "optimized" TCR-affinity.

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“…Conformational dynamics have been implicated in several aspects of MHC-I function, including peptide loading, T cell receptor triggering, and chaperone recognition (2,17,49). Solution NMR allows the quantitative measurement of dynamics across biologically relevant timescales ranging from psec-nsec (side-chain and loop motions), μs-ms (minor domain movements) to seconds (major domain reorientation) (50).…”

Section: Pmhc-i Molecules Exhibit Allele-specific Conformational Dynamentioning

confidence: 99%

Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection

McShan¹,

Devlin²,

Overall³

et al. 2019

Preprint

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Highlights Deep mutagenesis identifies a conformational disulfide-linked epitope as the main requirement for association of nascent MHC-I molecules with the TAPBPR chaperone  Analysis of μs-ms timescale conformational dynamics by methyl NMR reveals allelespecific profiles at the TAPBPR interaction surfaces of peptide-loaded MHC-I molecules  μs-ms dynamics dictate the specificity of TAPBPR interactions for different MHC-I alleles through the sampling of a minor, "excited state" conformation  Restriction of dynamics though an engineered disulfide bond abrogates interactions with TAPBPR, both in solution and on a cellular membrane Keywords Major Histocompatibility Complex • MHC-I • NMR spectroscopy • protein dynamics • molecular chaperone • TAPBPR • peptide editing • deep mutagenesis mapping • conformational landscape • peptide repertoire Graphical Abstract AbstractThe interplay between a highly polymorphic set of MHC-I alleles and molecular chaperones shapes the repertoire of peptide antigens displayed on the cell surface for T cell surveillance.Here, we demonstrate that the molecular chaperone TAPBPR associates with a broad range of partially folded MHC-I species inside the cell. Bimolecular fluorescence complementation and deep mutational scanning reveal that TAPBPR recognition is polarized towards one side of the peptide-binding groove, and depends on the formation of a conserved MHC-I disulfide epitope in the α 2 domain. Conversely, thermodynamic measurements of TAPBPR binding for a representative set of properly conformed, peptide-loaded molecules suggest a narrower MHC-I specificity range. Using solution NMR, we find that the extent of dynamics at "hotspot" surfaces confers TAPBPR recognition of a sparsely populated MHC-I state attained through a global conformational change. Consistently, restriction of MHC-I groove plasticity through the introduction of a disulfide bond between the α 1 /α 2 helices abrogates TAPBPR binding, both in solution and on a cellular membrane, while intracellular binding is tolerant of many destabilizing MHC-I substitutions. Our data support parallel TAPBPR functions of i) chaperoning unstable MHC-I molecules at early stages of their folding process, akin to a holdase with broad allelespecificity, and ii) editing the peptide cargo of properly conformed MHC-I molecules en route to the surface, which demonstrates a narrower specificity. Our results suggest that TAPBPR exploits localized structural adaptations, both near and distant to the peptide-binding groove, to selectively recognize discrete conformational states sampled by MHC-I alleles, towards editing Sithe repertoire of displayed antigens. Significance StatementThe human population contains thousands of MHC-I alleles, showing a range of dependencies on molecular chaperones for loading of their peptide cargo, which are then displayed on the cell surface for T cell surveillance. Using the chaperone TAPBPR as a model, we combine deep mutagenesis with functional and biophysical data, especially solution NMR, to provide a compl...

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The Role of Molecular Flexibility in Antigen Presentation and T Cell Receptor-Mediated Signaling

Cited by 56 publications

References 130 publications

Computer Modelling and Synthesis of Deoxy and Monohydroxy Analogues of a Ribitylaminouracil Bacterial Metabolite that Potently Activates Human T Cells

Computer Modelling and Synthesis of Deoxy and Monohydroxy Analogues of a Ribitylaminouracil Bacterial Metabolite that Potently Activates Human T Cells

CDR3 binding chemistry controls TCR V-domain rotational probability and germline CDR2 scanning of polymorphic MHC

Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection

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