Tapasin dependence of major histocompatibility complex class I molecules correlates with their conformational flexibility

Garstka, Malgorzata; Fritzsche, Susanne; Lenart, Izabela; Hein, Zeynep; Jankevicius, Gytis; Boyle, Louise H.; Elliott, Tim; Trowsdale, John; Antoniou, Antony N.; Zacharias, Martin; Springer, Sebastian

doi:10.1096/fj.11-190249

Cited by 63 publications

(79 citation statements)

References 42 publications

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“…The simplest explanation for this effect is that, in the presence of the dipeptides, the structure of class I is more conducive to the binding of full-length peptide. Recently, the α 1 /α 2 domain of class I molecules that lack high-affinity peptide was shown to be significantly structurally disordered (24)(25)(26), and we propose that the dipeptides bind into the F pocket region to alleviate this molecular disorder. Because of their low affinity to class I (in the lower millimolar range; Fig.…”

Section: Discussionmentioning

confidence: 90%

“…S3 B and C), GL and the other dipeptides would then be expected to exchange rapidly in and out of the binding groove, allowing high-affinity peptide to bind to a temporarily stabilized empty state. Interestingly, we have previously postulated that tapasin fulfils a similar role in vivo by supporting a stable open state that binds peptides more easily than the disordered empty state of a class I molecule (25).…”

Section: Discussionmentioning

confidence: 99%

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Dipeptides promote folding and peptide binding of MHC class I molecules

Saini

Ostermeir

Ramnarayan

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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MHC class I molecules bind only those peptides with high affinity that conform to stringent length and sequence requirements. We have now investigated which peptides can aid the in vitro folding of class I molecules, and we find that the dipeptide glycyl-leucine efficiently supports the folding of HLA-A*02:01 and H-2K b into a peptide-receptive conformation that rapidly binds high-affinity peptides. Treatment of cells with glycyl-leucine induces accumulation of peptide-receptive H-2K b and HLA-A*02:01 at the surface of cells. Other dipeptides with a hydrophobic second amino acid show similar enhancement effects. Our data suggest that the dipeptides bind into the F pocket like the C-terminal amino acids of a highaffinity peptide.antigen presentation | ligand exchange | chemical chaperones | endoplasmic reticulum | quality control M HC class I molecules are transmembrane proteins that are vital to the mammalian antiviral and antitumor immune response. They bind intracellular peptides in the lumen of the endoplasmic reticulum (ER) to transport them to the cell surface for inspection by cytotoxic T lymphocytes. To elicit a sustained immune response, peptides need to form stable complexes with class I molecules (1, 2), which means that they must conform to specific length and sequence requirements that were first identified by elution and sequencing, and then structurally understood by X-ray crystallography. Depending on the class I allotype, high-affinity peptides must be 8 to 10 aa long (such that the termini can form hydrogen bonding networks) and have defined side chains at particular positions that bind into specificity pockets at the bottom of the binding groove (3-5). This knowledge has been used to predict the binding affinity of any peptide sequence to a given class I allotype (6), and, together with theoretical simulations of the conformational movements of class I-peptide complexes, it has allowed the design of altered peptide ligands with higher binding affinities (7). The high-affinity peptides thus identified can be used to fold many bacterially expressed denatured class I molecules into their native state (8). Consequently, high-affinity peptides have been called the "essential third subunit of MHC class I" (9).In living cells, class I molecules bind high-affinity peptides with the help of several chaperone proteins, collectively called the peptide loading complex (PLC). Importantly, experiments in vivo and in vitro have shown that, in the presence of the PLC, peptide loading is iterative, i.e., class I molecules first bind suboptimal peptides (peptides that are too long, too short, or do not have the requisite anchor residues) and gradually exchange them for higher-affinity ones (10, 11). The idea that class I molecules can initially fold with such suboptimal peptides is indeed supported by the crystal structures of several class I molecules with octamer or pentamer peptides (12, 13).In our effort to determine the minimum peptide requirements for the folding of class I, we have analyzed even smaller p...

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Section: Discussionmentioning

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Dipeptides promote folding and peptide binding of MHC class I molecules

Saini

Ostermeir

Ramnarayan

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…Evaluation of association and dissociation parameters of a battery of peptides, containing targeted departures from the model, revealed that peptide acquisition by H-2K b takes place in two distinct phases. During the first phase, the peptide-binding groove of H-2K b accepts a wide range of candidates, including even amino acid side chains much larger than their optimal size, which implies significant flexibility in the anchor residue-accepting pockets (17,(19)(20)(21)(22). Following the initial association event, ill-suited peptides exhibit greater propensity for dissociation and are thus selected against.…”

Section: Discussionmentioning

confidence: 99%

“…Structural Flexibility in the Peptide-Binding Groove of H-2K b . The peptide-binding groove should be flexible to accommodate expanded anchors (17)(18)(19)(20)(21)(22) (Table S4). In all structures the peptides could be resolved and fit into the electron density (Fig.…”

Section: Association and Disassociation Kinetics Of 9-mer Peptide Varmentioning

confidence: 99%

The first step of peptide selection in antigen presentation by MHC class I molecules

Garstka¹,

Fish

Celie

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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MHC class I molecules present a variable but limited repertoire of antigenic peptides for T-cell recognition. Understanding how peptide selection is achieved requires mechanistic insights into the interactions between the MHC I and candidate peptides. We find that, at first encounter, MHC I H-2K b considers a wide range of peptides, including those with expanded N termini and unfitting anchor residues. Discrimination occurs in the second step, when noncanonical peptides dissociate with faster exchange rates. This second step exhibits remarkable temperature sensitivity, as illustrated by numerous noncanonical peptides presented by H-2K b in cells cultured at 26°C relative to 37°C. Crystallographic analyses of H-2K b -peptide complexes suggest that a conformational adaptation of H-2K b drives the decisive step in peptide selection. We propose that MHC class I molecules consider initially a large peptide pool, subsequently refined by a temperature-sensitive induced-fit mechanism to retain the canonical peptide repertoire.antigen presentation | peptide binding | anchor residues | dynamics | entropy M HC class I molecules present a wide array of peptides to cytotoxic T lymphocytes, allowing the immune system to scan for intracellular pathogens and mutated proteins. These peptides are not chosen at random, but rather are selected for their ability to bind to the polymorphic MHC class I peptidebinding groove. Antigenic peptide precursors are produced by the proteasome and further trimmed by cytosolic aminopeptidases. They are translocated into the endoplasmic reticulum (ER) lumen by the peptide transporter TAP that has broad peptide specificity. Peptides can be further trimmed in the ER lumen by ER aminopeptidases before selection by a defined MHC class I allele (reviewed in ref. 1). Only few peptides from a broad peptidome are presented by a given MHC class I allele. How a defined MHC I allele selects the correct peptides for presentation out of a large and diverse peptide pool is unclear.In principle, MHC class I molecules could consider only "optimal" peptides and ignore the remainder of the TAPtranslocated peptidome. Alternatively, MHC class I could bind all available peptides followed by a selection step for the optimal candidates for presentation. To discriminate between these scenarios, we studied peptide association (on-rates) and dissociation (off-rates) from the mouse MHC class I molecule H-2K b . To characterize the biophysical basis of discrimination between candidate peptides we complemented the kinetic data with five crystal structures of H-2K b with peptide variants. A comprehensive analysis of our in vitro data indicated that discrimination against suboptimal peptides by MHC class I may exhibit a strong temperature dependency, as illustrated by the H-2K b peptidome from cells cultured at 26°C versus 37°C. We thus arrive at a two-step model for peptide selection by MHC class I molecules, which explains how not so "empty MHC class I molecules come out in the cold" (2).

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“…Many class I allotypes require tapasin for any binding of high-affinity peptides and subsequent surface transport and are thus termed tapasin-dependent; others do not, or to a lesser degree. With regard to the tapasin dependence of the B27 subtypes, conflicting reports exist [22,[24][25][26][27][28], and generally, it is not well understood what makes a particular class I allotype tapasindependent or -independent [21].In this work, we have compared the conformational stabilities of the B*27:05 and B*27:09 subtypes through a combination of in silico, biochemical, and cellular approaches. We find that the disease-associated B*27:05 is much more conformationally disordered than B*27:09 in the empty and suboptimally loaded states, and that it requires tapasin, at least to a large extent, for its surface expression.…”

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confidence: 99%

F pocket flexibility influences the tapasin dependence of two differentially disease‐associated MHC Class I proteins

et al. 2015

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The human MHC class I protein HLA-B*27:05 is statistically associated with ankylosing spondylitis, unlike HLA-B*27:09, which differs in a single amino acid in the F pocket of the peptide-binding groove. To understand how this unique amino acid difference leads to a different behavior of the proteins in the cell, we have investigated the conformational stability of both proteins using a combination of in silico and experimental approaches. Here, we show that the binding site of B*27:05 is conformationally disordered in the absence of peptide due to a charge repulsion at the bottom of the F pocket. In agreement with this, B*27:05 requires the chaperone protein tapasin to a greater extent than the conformationally stable B*27:09 in order to remain structured and to bind peptide. Taken together, our data demonstrate a method to predict tapasin dependence and physiological behavior from the sequence and crystal structure of a particular class I allotype.Keywords: Ankylosing spondylitis r HLA-B27 r Major histocompatibility complex r Molecular dynamics r Natively unstructured proteins r Protein folding r Simulations Additional supporting information may be found in the online version of this article at the publisher's web-site Introduction MHC class I molecules are heterotrimeric proteins that transport antigenic peptides to the cell surface and present them to cytotoxic T cells. They consist of the transmembrane heavy chain (HC), the noncovalently associated light chain beta-2 microglobulin (β 2 m), and an antigenic peptide of eight to ten amino acids. The Correspondence: Prof. Sebastian Springer e-mail: s.springer@jacobs-university.de extracellular part of the heavy chain comprises the α 1 , α 2 , and α 3 domains. The α 1 and α 2 domains form the peptide-binding groove, a superdomain that consists of an antiparallel beta sheet surmounted by two alpha helices, between which the peptide binds [1,2].In the cell, peptide binding to class I is a multistep process within the ER. It involves the peptide-loading complex, which consists of the peptide transporter associated with antigen processing (TAP) that transports peptides from the cytosol into the ER lumen [3] and several chaperone proteins such as tapasin, which binds both to the class I molecule and TAP [4,5].C 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.eji-journal.eu Eur. J. Immunol. 2015. 45: 1248-1257 Molecular immunology 1249The sequence of peptides that can bind to class I is determined by interactions with the amino acid side chains of the peptide-binding groove. The high sequence polymorphism of the peptide-binding groove in human class I molecules (human leukocyte antigens, HLA-A, -B, and -C) means that different allotypes bind different peptides; thus, individual HLA allotypes-such as HLA-B27-support-specific immune responses and are statistically associated with disease [6,7]. Among the subtypes of HLA-B27 [8,9], HLA-B*27:05 (B*27:05) shows a very strong statistical association with spondyloarthropathies such as ankylosing spondylitis (AS), in contr...

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Tapasin dependence of major histocompatibility complex class I molecules correlates with their conformational flexibility

Cited by 63 publications

References 42 publications

Dipeptides promote folding and peptide binding of MHC class I molecules

Dipeptides promote folding and peptide binding of MHC class I molecules

The first step of peptide selection in antigen presentation by MHC class I molecules

F pocket flexibility influences the tapasin dependence of two differentially disease‐associated MHC Class I proteins

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