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Brief Definitive Reports |


Department of Microbiology and the
Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75235
| Abstract |
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Key Words: major histocompatibility complex class Ib Qa-1b surface plasmon resonance peptide binding
Most MHC class I molecules are capable of binding a large array of individual peptides (1). In contrast, the murine class Ib molecule, Qa-1b, predominantly binds a single species (2, 3). We refer to this peptide as Qdm (for Qa-1 determinant modifier; reference 2), and it is derived from amino acids 3–11 of class Ia D-region–encoded molecules. HLA-E, which differs from Qa-1b in 55 of 181 residues in the
Cloning Soluble Qa-1b for the Production of Soluble Molecules.
Production of Soluble Qa-1b.
SPR.
1 and
2 domains, binds leader peptides from human class Ia molecules that are very similar to the murine class Ia leader peptide bound by Qa-1b (4). HLA-E and Qa-1b, unlike other class Ia molecules, have serines rather than the conserved residues threonine and tryptophan at positions 143 and 147 in the "F" pocket, respectively. In the "B" pocket, HLA-E and Qa-1b also share the key residues methionine and alanine at positions 45 and 67, respectively. The HLA-E crystal structure reveals that side chains of five of the nine amino acids of the bound peptide protrude into the pockets of the HLA-E groove (5). Based on this structure of HLA-E, it would be predicted that only a few substitutions in the native Qdm peptide would be tolerated for binding to Qa-1b. This use of multiple anchors would also account for our previous finding that the Qdm peptide binds to Qa-1b with a very high affinity (6). Here, we test this issue by examining the ability of class I leader– derived peptides from several mammalian species to bind Qa-1b and define a minimum Qa-1b binding peptide. Using surface plasmon resonance (SPR), we find that Qa-1b binds class I leader peptides from almost all species tested. Unlike most class Ia molecules, the binding of peptide to Qa-1b requires the retention of multiple amino acids from the native Qdm peptide sequence. The fact that this single peptide dominates the occupancy of Qa-1b/HLA-E may also be related to the functional properties of these molecules, since recent data show that HLA-E interacts with CD94/NKG2 receptors on NK cells to deliver an inhibitory signal (7, 8).
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Materials and Methods
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Abstract
Materials and Methods
Results
Discussion
References
Cells.
Drosophila melanogaster cells (S2 cells) cultured at room temperature in Schneider's medium (Life Technologies, Inc., Gaithersburg, MD) supplemented with 10% fetal bovine serum (Hyclone, Logan, UT) were cotransfected with pRMHa-3/Qa-1b truncated (12 µg), pRMHa-3/β2-microglobulin (β2m) murine (12 µg), and phshsneo (1µg) using the calcium-phosphate precipitation method (9).
Total mRNA isolated from spleen cells of a C57BL/6 mouse (RNA STAT-60; Tel-Test, Inc., Friendswood, TX) was the template in the synthesis of first strand cDNA with reverse transcriptase (SuperScript II RT; Life Technologies, Inc.) that used oligo(dT)12–18 as a primer. Qa-1b cDNA was synthesized by PCR with oligonucleotides 5'-GTGAGGATGTTGCTTTTTGCCC and 5'-TCATGCCTTCTGAGGCCAGTC. The truncated Qa-1b (consisting of the leader,
1,
2, and
3 domains with an attached [His]6-tag) cDNA was cloned into the modified vector pRMHa-3 (9). sH2-M3 was a gift from Dr. Johann Deisenhofer (University of Texas Southwestern Medical Center at Dallas).
Soluble (s)Qa-1b from the supernatant of stably transfected Drosophila cells was concentrated 10-fold, loaded onto a C10/10 column packed with 6 ml of Ni-Nta agarose (QIAGEN Inc., Chatsworth, CA) and eluted with 150 mM imidazole (pH 7.4). The protein was further purified by ion exchange chromatography (Mono Q; Amersham Pharmacia Biotech, Inc., Piscataway, NJ).
All binding experiments were performed on a Biacore 2000 (Biacore International AB, Uppsala, Sweden) at 25°C. Cysteine-substituted analogue peptides of Qdm were immobilized to the biosensor surface (Sensor Chip CM5; Biacore International AB) using an approach similar to that described by Khilko et al. (10). The peptides were immobilized via thioether coupling to the biosensor flow cell, and Qa-1b was run over it in the soluble phase. In brief, upon activation of the surface with N-hydroxylsuccinimide (NHS)-N-ethyl-N'(dimethylaminopropyl)carbodiimide (EDC), amino groups were generated by a 10-min injection of 1 M ethylenediamine (pH 8.5; Sigma Chemical Co., St. Louis, MO). This was followed by a 4-min introduction of reactive maleimido groups from 50 mM sulfo-SMCC (Pierce Chemical Co., Rockford, IL) in 25 mM sodium bicarbonate, pH 8.5. The cysteine-substituted peptide analogue QdmC5 (200 µM in 10 mM sodium acetate, pH 5.0, except in Fig. 1, B and C, where the QdmC5 concentration was 500 µM) was run over the biosensor surface for 10 min. Unreacted maleimido groups were inactivated by a 2-min exposure to 0.1 M sodium hydroxide. All immobilization steps were performed using a flow rate of 5 µl/min, except the step in which cysteine-substituted peptides were run at 2 µl/ min. The flow rate for peptide binding experiments was 1 µl/min.
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| Results |
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To study antigen binding to the Qa-1b molecule, recombinant sQa-1b/β2m dimers were generated in D. melanogaster (S2) cells following established protocols (11, 12). Truncated Qa-1b molecules secreted by stably transfected cells were purified on Ni-coated beads followed by anion exchange. Both heavy chain and β2m were visible on Coomassie-stained SDS-PAGE (Fig. 1 A).
Binding of Qa-1b to Immobilized Qdm Peptide Is Specific and Concentration Dependent.
Due to the SPR limitations in detecting the binding of small molecular weight peptides to immobilized class I molecules, we decided to attach the peptide to the chip. In the following experiments, we used QdmC5 (arginine
cysteine substitution at position 5), which readily bound to the biosensor chip and in turn was bound by sQa-1b (Fig. 1, B and C). This binding is specific, since sM3 (Fig. 1 B) and sCD1 (not shown) failed to bind. Binding of Qa-1b to immobilized QdmC5 was blocked by adding QdmC5 or Qdm in solution, but not irrelevant control peptides (YPHFMPTNL) or (PMLTMCHAL), the latter of which contains the putative Qa-1b peptide anchors methionine at P2 and leucine at P9 (Fig. 1 C).
Trimming and Extending Qdm at the COOH Terminus Affects Its Binding to Qa-1b.
Since peptides in solution can compete with immobilized QdmC5 for binding to soluble Qa-1b, we used this approach to further analyze the peptide binding characteristics of this molecule. The Qdm nonamer peptide completely blocked binding at concentrations between 200 nM and 20 µM (Fig. 1 D). Extending the Qdm peptide by adding a leucine at position 10 (10-mer) results in decreased binding relative to the nonamer at 20 and 2 µM concentrations, and almost no binding at 200 nM. Trimming the Qdm peptide at the COOH end to an 8-mer gives a similar result. A 7-mer lost virtually all of its binding ability. We also tested the entire 24 amino acid leader of Dd from which the Qdm peptide is derived, and found that it failed to block the binding of Qa-1b to immobilized peptides. Finally, we generated two more nonamers from the leader or Dd. Instead of spanning from residues 3 to 11, these peptides span amino acids 1–9 (MGAMAPRTL) and 4–12 (MAPRTLLLL). They both failed to bind to Qa-1b.
Qa-1b Binds Peptides Derived from the Leader Segment of Human Class I Molecules.
Since HLA-E and Qa-1b share unique features in their peptide binding grooves, we tested whether Qa-1b can bind the same human class I–derived peptides that bind to HLA-E. We found that all of the tested peptides except for the one originating from the leader of HLA-A3 bound to Qa-1b (Fig. 2). All of the peptides that bound to both Qa-1b and HLA-E have very similar sequences that are derived from positions 3–11 of the leader. Peptides with a threonine
methionine change at P2 (HLA-B27, -35) bound less well, and this was more evident in experiments where the inhibiting peptides were titrated at lower concentrations (data not shown).
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The Minimal Requirements for Peptide Binding to Qa-1b.
We next determined the minimum requirement for ligand binding to Qa-1b by synthesizing a number of peptides in which glycines were introduced in different positions (Table 2). We used glycine instead of alanine because the native Qdm sequence contains two alanines. Of the minimal peptides we tested, those with two or three nonglycine residues showed no (GMGGGGGGL, GMGGRGGGL) or very little binding (GMGGGGLGL, GMGGGGGLL) (Table 2). However, a peptide with four of nine native residues GMGGGGLLL blocked >50% of binding of sQa-1b to immobilized QdmC5 peptide at the highest concentration tested (20 µM). However, when this peptide was titrated, we noted relatively little blocking activity at 2 µM and none at 200 nM, in marked contrast to the titration seen when more homologous peptides were tested (Fig. 3 A). This indicates that methionine at P2 and the three COOH-terminal leucines are sufficient for detectable although relatively very weak binding to Qa-1b. Side chains of other amino acids in Qdm also play a role in the overall peptide binding. There is apparently a fine balance in their contribution which is dependent on the neighboring residues, since a peptide with five native residues (GMGGRGLLL) binds better to Qa-1b than a peptide with six native residues (GMGPRGLLL).
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| Discussion |
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We have attempted to determine the minimum motif required for peptide binding to Qa-1b. Since only one peptide has been eluted from the groove of this molecule, it is not possible to assign anchor residues in the conventional manner. In addition to embedding principal anchors, methionine at P2 and leucine at P9, we needed to introduce two more wild-type residues in the polyglycine chain, leucines at P7 and P8, to observe detectable binding. However, the binding of this pentaglycine analogue was still considerably weaker than that of native Qdm, suggesting that side chains of other residues also contribute to the overall interaction. Although it is possible that binding of the minimal peptide with fewer anchor residues could have been found had we used a backbone other than glycine (13), several other minimal peptides with glycine backbones have been used successfully to identify anchors that participate in binding to class I molecules (14, 15).
Thus, the finding that Qdm requires multiple anchors would explain the dominance of a single peptide in its groove. The data presented here, together with the recent crystal structure of HLA-E bound to its peptide (5), suggest that Qa-1b and HLA-E can only bind Qdm-like peptides with high efficiency. However, it cannot be ruled out that their occupancy by these peptides is a result of a restrictive peptide antigen processing and/or presentation pathway. It is interesting to note that the common ligand that Qa-1b and HLA-E bind is derived from a conserved part of class I leader segments that are expendable in the mature protein and thus would not affect selection for polymorphic peptide binding residues.
Boyson et al. (16) pointed out that a comparison of the rates of synonymous and nonsynonymous nucleotide substitutions in the peptide binding region versus the remainder of the molecule indicates that the peptide binding groove of HLA-E and its homologues in macaques has been conserved for over 36 million years, when the two last shared a common ancestor. Yeager et al. have communicated that, although not orthologous, Qa-1b and HLA-E might have evolved similar functions through convergent evolution at the amino acid sequence level of the peptide binding region (17). Regardless of whether molecular-level convergence or evolutionary conservation of the peptide binding region accounts for the specificity of these grooves, this conservation of specificity suggests a crucial immunological function for these molecules. In this regard, it has recently been shown that HLA-E is a ligand for CD94/ NKG2 receptors on NK cells; interaction of HLA-E with this receptor protects target cells from NK-mediated lysis (7, 8). Although this has not yet been demonstrated for Qa-1b, it is likely that it interacts with its murine CD94/ NKG2 counterpart in a similar manner. Class I molecules in mice could, through Qa-1b, control the activity of NK cells which would be signaled upon interaction with cell surface–expressed Qa-1b. Decreased expression and/or processing of class I molecules would decrease the expression of Qa-1b, which would in turn result in a changed activity level of NK cells.
It is conceivable that occasionally Qa-1b–bound class I–derived peptides could be replaced, or that some of the peptide binding grooves might be initially occupied by other self- or pathogen-derived peptides which would be presented to T cells. Future studies should show whether Qa-1b is recognized by NK cell receptors, and what role peptides play in the response.
| Acknowledgments |
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Submitted: 13 April 1998
Revised: 18 June 1998
| References |
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1 Hunt DF, Henderson RA, Shabanowitz J, Sakaguchi K, Michel H, Sevilir N, Cox AL, Appella E & Engelhard VH. Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry, Science, 1992, 255, 1261–1263.
2 Aldrich CJ, DeCloux A, Woods AS, Cotter RJ, Soloski MJ & Forman J. Identification of a TAP-dependent leader peptide recognized by alloreactive T cells specific for a class Ib antigen, Cell, 1994, 79, 649–658.[Medline]
3 DeCloux A, Woods AS, Cotter RJ, Soloski MJ & Forman J. Dominance of a single peptide bound to the class Ib molecule, Qa-1b, J Immunol, 1997, 158, 2183–2191.[Abstract]
4 Braud V, Jones EY & McMichael A. The human major histocompatibility complex class Ib molecule HLA-E binds signal sequence-derived peptides with primary anchor residues at position 2 and 9, Eur J Immunol, 1997, 27, 1164–1169.[Medline]
5 O'Callaghan CA, Tormo J, Willcox BE, Braud VM, Jakobsen BK, Stuart DI, McMichael AJ, Bell JI & Jones EY. Structural features impose tight peptide binding specificity in the nonclassical MHC molecule HLA-E, Mol Cell, 1998, 1, 531–541.[Medline]
6 Kurepa Z & Forman J. Peptide binding to the class Ib molecule, Qa-1b, J Immunol, 1997, 158, 3244–3251.[Abstract]
7 Braud VM, Allan DSJ, O'Callaghan CA, Sodestrom K, D'Andrea A, Ogg GS, Lazetic S, Young NT, Bell JI, Phillips JH, Lanier LL & McMichael AJ. HLA-E binds to natural killer receptors CD94/NKG2A, B and C, Nature, 1998, 91, 795–799.[Medline]
8 Borrego F, Ulbrecht M, Weiss EH, Coligan JE & Brooks AG. Recognition of human histocompatibility leukocyte antigen (HLA-A)-E complexed with HLA class I signal sequence–derived peptides by CD94/NKG2 confers protection from natural killer cell–mediated lysis, J Exp Med, 1998, 187, 813–818.
9 Bunch TA, Grinblat Y & Goldstein LSB. Characterization and use of the Drosophila metallothionein promoter in cultured Drosophila melanogastercells, Nucleic Acids Res, 1988, 16, 1043–1061.
10 Khilko SN, Corr M, Boyd LF, Lees A, Inmaa JK & Margulies DH. Direct detection of major histocompatibility complex class I binding to antigenic peptides using surface plasmon resonance, J Biol Chem, 1993, 268, 15425–15434.
11 Matsumura M, Saito Y, Jackson MR, Song ES & Peterson PA. In vitro peptide binding to soluble empty class I major histocompatibility complex molecules from transfected Drosophila melanogastercells, J Biol Chem, 1992, 267, 23589–23595.
12 Wang CR, Castano AR, Peterson PA, Slaughter C, Lindahl KF & Deisenhofer J. Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3, Cell, 1995, 82, 655–664.[Medline]
13 Maryanski JL, Verdini AS, Weber PC, Salemme FR & Corradin G. Competitor analogs for defined T cell antigens: peptides incorporating a putative binding motif and polyproline or polyglycine spaces, Cell, 1990, 60, 63–72.[Medline]
14 Parker KC, Bednarek MA, Hull LK, Utz U, Cunningham B, Zweerink HJ, Biddison WE & Coligan JE. Sequence motifs important for peptide binding to the human MHC molecule, HLA-A2, J Immunol, 1992, 149, 3580–3587.[Abstract]
15 DiBrino M, Parker KC, Shiloach J, Knierman M, Lukszo J, Turner RV, Biddison WE & Coligan JE. Endogenous peptides bound to HLA-A3 possess a specific combination of anchor residues that permit identification of potential antigenic peptides, Proc Natl Acad Sci USA, 1993, 90, 1508–1512.
16 Boyson JE, McAdam SN, Gallimore A, Golos TG, Liu X, Gotch FM, Hughes AL & Watkins DI. The MHC E locus in macaques is polymorphic and is conserved between macaques and humans, Immunogenetics, 1995, 41, 59–68.[Medline]
17 Yeager M, Kumar S & Hughes AL. Sequence convergence in the peptide-binding region of primate and rodent MHC class Ib molecules, Mol Biol Evol, 1997, 14, 1035–1041.[Abstract]
18 Braud VM, Allan DSJ, Wilson D & McMichael AJ. TAP- and tapasin-dependent HLA-E surface expression correlates with the binding of an MHC class I leader peptide, Curr Biol, 1997, 8, 1–10.[Medline]
19 Crew MD, Bates LM, Douglass CA & York JL. Expressed Peromyscus maniculatus(Pema) MHC class I genes: evolutionary implications and the identification of a gene encoding a Qa1-like antigen, Immunogenetics, 1996, 44, 177–185.[Medline]
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