2 Department of Immunology, The Scripps Research Institute, Department of Molecular Biology, La Jolla, CA 92037
3 The Skaggs Institute for Chemical Biology, The Scripps Research Institute, Department of Molecular Biology, La Jolla, CA 92037
Address correspondence to Ian Wilson, Dept. of Molecular Biology, BCC206, The Scripps Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037. Phone: 858-784-9706; Fax: 858-784-2980; E-mail: wilson{at}scripps.edu
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Abstract |
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Key Words: ß T cell receptor antigen alloreactivity complementarity determining regions TCR-MHC recognition
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Introduction |
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Class I MHCs, which consist of an MHC heavy chain and a ß2-microglobulin light chain, are 45-kD antigen-presenting glycoproteins expressed universally in nucleated cells. Peptides are bound to class I MHCs in an extended conformation with conserved hydrogen bonding to the peptide backbone N and C termini (24). The peptide side chains interact with six pockets in the peptide binding groove designated A to F (5). Frequent polymorphisms therein lead to MHC-specific peptide-binding motifs. Allelic variation in MHC I genes, arising from germline gene conversion (for a review, see reference 6), is the primary cause of graft rejection and graft-versus-host disease, the clinical manifestations of alloreactive TCR recognition.
The murine H-2Kb class I gene encodes a classical transplantation antigen within the MHC multigene cluster on chromosome 17. H-2Kbm proteins are naturally occurring mutants of the H-2Kb gene and were originally identified in skin graft experiments by correlating precise amino acid changes with altered histocompatibility (6). Most H-2Kbm molecules are characterized by clusters of amino acid substitutions, as many as five, occurring in one of either of the two amino-terminal heavy chain domains, 1 and
2 (6). H-2Kbm3 contains two mutations in the
1 domain. Substitution of serine for aspartate at position 77 determines the alloreactive phenotype, whereas replacement of alanine for lysine at position 89 determines the serologic phenotype (7). H-2Kb is responsible for positive selection of 2C TCR-bearing cytolytic T lymphocytes in transgenic mice, whereas H-2Kbm3 expression results in negative selection (8). dEV8 is a self-peptide derived from MLRQ, a component of the mitochondrial NADH ubiquinone complex, that, when bound to H-2Kbm3, is an alloligand for the 2C TCR (9).
Despite starkly contrasting biological properties, surface plasmon resonance measurements of 2C binding to H-2KbdEV8 and H-2Kbm3dEV8 demonstrate that, in an isolated system, the difference in affinities and binding kinetics of 2C for these pMHCs is remarkably small (10). Although puzzling, this is not entirely unexpected. Some studies have reported good correlation between binding kinetics and the degree of T cell activation, i.e., strong agonists tend to have longer half lives than do antagonists (for a review, see reference 11), but an absolute correlation between binding kinetics and biological effect has not been experimentally observed (12, 13). However, the question remains as to how well these measurements reflect the nature of TCRpMHC interactions in the presence of accessory molecules, such as CD8 (1417), on the surface of the cell, and within the specialized environment of the immunological synapse (18). In addition, recent studies suggest that activated T cells have markedly increased avidity for pMHCs when compared with their naive counterparts (19).
The TCR is a cell surface glycoprotein consisting of two disulfide-linked polypeptide chains, and ß, whose binding orientation relative to the MHC-peptide binding groove was determined by crystallography to be approximately diagonal (20, 21, 2325; for a review, see reference 22). Each chain has four possible complementarity determining regions (CDRs) with CDRs 1, 2, and 4 being germline encoded and CDR3, the most variable, being formed during thymic development by D to J and V to D gene rearrangements in the ß-chain and V to J gene rearrangements in the
-chain. Generally, the
- and ß-chain CDR3 loops form the majority of direct contacts to the peptide in TCRpMHC interactions while the CDRs 1, 2, and, sometimes, 4 primarily contact the
1- and
2-helices that straddle the MHC peptide-binding groove. Thus far, four independent high resolution TCR crystal structures (
3.2 Å) have been reported with their respective class I MHCs (20, 21, 2628). Two independent TCRs bound to their respective class II MHCs have also been reported (2931). In crystal structures of the A6 TCR bound to four distinct peptideHLA-A2 complexes, no correlation was found between structure and biological activities that ranged from strong agonism to weak antagonism (32), raising the question as to how astonishingly dissimilar biological effects can be manifested by vanishingly small changes within the TCRpMHC interface. Likewise, the structure of the 2C/H-2KbSIYR depicted very similar overall binding between a weak agonist and a superagonist, with functionally significant changes restricted to interaction of the P4 and P6 residues of the peptide with a "hot spot" around the TCR CDR3
and CDR3ß (18). The BM3.3 TCR in complex with the H-2KbpBM1 MHC-peptide ligand revealed that, in the allogeneic interaction, the diagonal orientation of the TCR with respect to the antigen binding interface is preserved (28). However, comparison with the specific equivalent syngeneic complex was not possible as its structure has not yet been determined. This study enables, for the first time, a comparative analysis of the structures of a single TCR bound to both self and nonself MHC in the presence of the same bound peptide.
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Materials and Methods |
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Protein Expression, Purification, and Crystallization.
Protein was overexpressed and purified as described previously (10). 2C and H-2Kbm3dEV8 were mixed in 1:1 molar ratio (0.2 mM), and crystals of the 2C/H-2Kbm3dEV8 complex were obtained by sitting drop vapor diffusion at 4°C with a 1:1 mixture of protein and mother liquor containing 0.1 M Tris-acetate pH 6.9, 12.5% PEG4000, and 20% glycerol.
Data Collection and Refinement Methods.
Crystals were cryocooled to -170°C in a nitrogen stream. X-ray diffraction data were collected at beamline 91 of the Stanford Synchrotron Radiation Laboratory (SSRL) on a MAR345 image plate using a monochromatic wavelength of 1.0 Å. The 2C/H-2Kbm3dEV8 crystals are isomorphous with the previously reported 2C/H-2KbSIYR crystals (18) in the orthorhombic space group P21212. The structure was determined by direct refinement using the coordinates of the 2C/H-2KbSIYR complex as a model (PDB code 1G6R). The structure was initially refined by rigid body methods using the seven independent TCR and MHC domains against the maximum likelihood target (35). Iterative cycles of torsion angle dynamics using a maximum likelihood target function and slow-cooling temperature protocols with the program CNS (35) were combined with manual model adjustment. Bulk solvent correction with a flat model and anisotropic correction were used throughout the refinement. The model was rebuilt in density modified, composite omit, and A-weighted 3Fo-2Fc and Fo-Fc maps (36) using the program O (37). A final round of refinement was conducted in REFMAC5 using TLS parameters (38), yielding an Rcryst of 28.2% and an Rfree of 31.1%. Progress of the refinement was assessed by continuously monitoring continuously Rfree for cross validation (39), and avoiding divergence between Rcryst and Rfree. One of the two independent copies of the TCR in the asymmetric unit is highly disordered, as found in other 2C/pMHC crystals (18, 26). The high Wilson B factor derived from the diffraction intensities correlates with the overall average B value of the model. Analysis of the final model with PROCHECK (40) shows no outliers and 83.7% and 65.6% of residues in the most favored regions of the Ramachandran plot in the first and second complex, respectively. Shape complementarity (SC) coefficients, excluding water molecules (41), were calculated using SC as implemented in CCP4 (42) with a 1.7 Å probe. Buried surface area was calculated using the program MS with a 1.7 Å probe (43). Hydrogen bonds and TCR-pMHC contacts were identified using the programs HBPLUS (44) and CONTACSYM (45).
Crystals of H-2KbdEV8 and H-2Kbm3dEV8 were grown as described previously (46) and cryocooled after soaking in mother liquor supplemented with 20% glycerol. Diffraction data for H-2Kb dEV8 and H-2Kbm3dEV8 were collected on the MAR345 image plate detector at beamline 91 at SSRL and an in-house 30 cm MAR image plate detector, respectively. All data (see Table I) were integrated and reduced with DENZO and SCALEPACK (47). The H-2KbdEV8 structure was determined by molecular replacement (AMORE [48]) using H-2KbSEV9 (PDB code 1VAB) as an overall search model. After rigid-body refinement of individual domains the H-2Kb molecules were refined using slowcool protocols as implemented in X-PLOR version 3.85 (49). Solvent mask correction was applied throughout the refinement, and Rcryst and Rfree values were used to monitor the refinement progress. The model was then subjected to several rounds of alternating slowcool/positional refinement and manual model adjusting/rebuilding using the program O (37). The structure was refined to 1.7 Å with an Rcryst and Rfree of 20.6% and 25.1%, respectively (see Table I). The structure of H-2Kbm3dEV8 was determined by molecular replacement using H-2KbdEV8 as a search model and was refined to 2.1 Å with a protocol similar to that used for the refinement of H-2KbdEV8 to Rcryst and Rfree values of 20.6 and 25.8%, respectively (see Table I). Fig. 1 was created with Insight II (Molecular Simulations, Inc.). Figs. 2 and 3 were created with BOBSCRIPT (50) and RASTER3D (51). Fig. 4 was created with GRASP (52).
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Results |
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The resolution of the unliganded H-2KbdEV8 was also extended to 1.75 Å from the original 2.3 Å (26). The structure was determined by molecular replacement using wild-type H-2Kb coordinates (1VAB; reference 2) as a search model and refined to 1.75 Å with Rcryst and Rfree values of 20.6 and 25.1%, respectively. The H-2KbdEV8 structure includes 401 water molecules, 4 carbohydrate residues, and 2 phosphate ions. The H-2Kbm3dEV8 structure was determined by molecular replacement using this new H-2KbdEV8 structure as a model and refined to 2.15 Å with Rcryst and Rfree values of 20.6 and 25.8%, respectively. The structure includes 278 water molecules, 4 carbohydrate residues, and 1 phosphate ion.
Comparison of the Unliganded Syngeneic and Allogeneic pMHCs.
The peptide-binding 1
2 domains of H-2KbdEV8 and H-2Kbm3dEV8 superimpose with an r.m.s. deviation of 0.48 Å for all main-chain atoms. The peptide is bound by both MHCs in an extended conformation (Fig. 1 A) with the side chains of anchor residues Phe-P5 and Val-P8 binding in the C and F pockets, respectively. In H-2KbdEV8, the side-chain torsion angles at
1 and
2 of Tyr-P6 are 71° and 10°, respectively, while in H-2Kbm3dEV8, a substantial rotation to angles of 175° at
1 and 90° at
2 results in displacement of the hydroxyl oxygen by 9.4 Å (Figs. 1 A, 2 A, and 2 B). Of interest, a previous modeling study predicted a difference in the orientation of this side chain, although in those studies the P6 side-chain rotamers in the syngeneic and allogeneic complexes were reversed (53) relative to those observed in the actual crystal structures. The torsion angle at
1 of Ser-P7 in H-2KbdEV8 is 75°, compared with 57° in H-2Kbm3dEV8 (Figs. 1 A, 2 A, and 2 B). The root mean square (r.m.s.) deviation for the peptide main-chain atoms is only 0.47 Å, but the largest deviation occurs in the four COOH-terminal residues (r.m.s. deviation 0.60 Å) and represents a shift in the peptide backbone toward the
1-helix of H-2Kbm3. Although the side chain of H-2Kbm3 Ser77 is shorter than that of H-2Kb Asp77, the hydrogen bond from the MHC side-chain hydroxyl to the main-chain nitrogen of P8 is preserved (Fig. 2 B) by a displacement of P7 and P8 backbone nitrogens by 0.9 Å and 0.5 Å, respectively, toward the
1-helix, which bears the Asp77Ser mutation.
Other structural rearrangements occur in the vicinity of Ser77 in H-2Kbm3. A different rotamer of Ser73 (1 = 72°) is found in the H-2KbdEV8 compared with H-2Kbm3dEV8 (
1 = 179°; Fig. 2, A and B). In H-2KbdEV8, the hydroxyl of Ser73 is rotated away from the Asp77 side chain, forming a hydrogen bond with the carbonyl oxygen of P5 (Fig. 2 A). In H-2Kbm3dEV8, Ser73 O
hydrogen bonds to the amide nitrogen of Ser-P7 beneath which two waters (W2 and W7) are buried (Fig. 2 B), partially filling space vacated by the Asp77Ser substitution. In H-2KbdEV8, one water (W2) molecule is buried beneath Ser-P7 (Fig. 2 A). A water molecule (W1) coordinated by Asp77 and Thr80 side chains and the Val-P8 terminal carboxylate in most H-2Kb structures (PDB codes 1FZJ, 1FZK, 1FZO, 1KGB, 1VAC, 1VAB, 1G7Q, 1G7P), is absent in the allogeneic mutant (Fig. 2 B). In this H-2KbdEV8 structure, W1 is slightly beyond hydrogen bonding distance from the Asp77 carboxylate, but close enough for a polar interaction (3.8 Å; Fig. 2 A).
Comparison of Allogeneic and Syngeneic TCRpMHC Complexes.
The 2C/H-2Kbm3dEV8 complex (Fig. 3) has the same gross structural features as previously described for other class Irestricted TCRpMHC structures with the TCR binding the pMHC in a diagonal orientation and the variable domains contacting the pMHC via their CDR loops (21, 2628). TCR V-pMHC contacts are clustered in the neighborhood of the NH2-terminal half of the bound peptide, while the TCR Vß-pMHC contacts are focused on the COOH-terminal region of the peptide. 2C binds H-2KbdEV8 and H-2Kbm3dEV8 in a remarkably similar fashion (Fig. 3) with an r.m.s. deviation of 1.07 Å for all main-chain atoms of the V
and Vß variable domains. The pMHC-contacting CDR loops for both V
and Vß superimpose with an overall r.m.s. deviation for all main-chain atoms of 1.08 Å with the majority of contacts between the 2C and H-2KbdEV8 being conserved in the allogeneic complex. The greatest individual r.m.s. deviations are found in CDR3
and CDR3ß (1.11 and 1.18 Å, respectively; Table II), CDRs that were previously identified as forming a functional hot spot for 2C TCR recognition (18). The CDR3
loop C
atoms at Ala101 and Ala103 are displaced by 1.83 Å and 1.15 Å, respectively, in the allogeneic complex. In both complexes, the dEV8 is bound in a similar orientation (compare Fig. 1 A versus 1 B, Fig. 3) with an r.m.s. deviation for all atoms of 0.90 Å and for main-chain atoms of 0.66 Å. The three COOH-terminal residues of the peptide, proximal to the Asp77Ser mutation have an increased r.m.s deviation of 0.82 Å for backbone atoms.
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A water molecule (W15), not previously observed, mediates contact between the N of Lys-P4 and the hydroxyl of Ser93. Unambiguous density places the amide side-chain oxygen of the TCR
-chain Gln1 within hydrogen bonding distance of the backbone nitrogens of both Gly99 and Phe100 of the CDR3
. Contacts between the CDR3
loop and the pMHC are similar with the side chain of Lys-P4 protruding out from the MHC binding groove and into a pocket bounded by CDR3
and CDR3ß.
For CDR1ß, a water (W16) is within hydrogen bonding distance of the carbonyl oxygen of Asn28, the side-chain hydroxyl of Tyr-P6, and the carbonyl oxygen of H-2Kbm3 Lys146. As opposed to the wild-type structure, the hydrogen bonding partner of the Asn30 amide side-chain nitrogen is the backbone carbonyl oxygen of Ser-P7, not its side-chain O.
The resolution (2.5 Å) of the BM3.3/H-2KbpBM1 structure also allowed delineation of numerous waters in the TCRpMHC interface (28). The similar resolution of 2C/H-2Kbm3dEV8 thus allows for comparison of water-mediated contacts in the two structures. 12 waters mediate contact between the TCR and the MHC in BM3.3/H-2KbpBM1, while 6 waters mediate contact in 2C/H-2Kbm3dEV8; none are equivalent in both structures. Four waters in the peptide-binding groove are conserved between the allogeneic BM3.3/H-2KbpBM1 and the 2C/H-2Kbm3dEV8 structures, but none mediates contact with the TCR in both structures.
TCRpMHC Interface and Complementarity.
Although the Asp77Ser mutation in the H-2Kb heavy chain might have abolished the hydrogen bond between the side chain of residue 77 and the amide nitrogen of Leu-P8 (26), the hydrogen bond between these residues is preserved (compare Fig. 2, C and D). Movement of the peptide main chain toward the 1-helix maintains the Ser77 hydrogen bond with Leu-P8 and also brings O
of Ser-P7 within hydrogen bonding distance of heavy chain Ser73 O
(Fig. 2 D). The plane of the Trp147 indole ring is now rotated such that its indole nitrogen, along with the N
2 of Asn30 in the CDR1ß loop, can make a hydrogen bond to the backbone carbonyl oxygen of Ser-P7. In the lower resolution wild-type complex, N
2 of CDR1ß Asn30 is more than 5 Å distant from the carbonyl oxygen of Ser-P7 (Fig. 2 C). It was postulated that N
2 of Asn30 may hydrogen bond to the O
of Ser-P7 in the wild-type structure (26), but, at this resolution, the geometry and distance are not ideal for such a bond (Fig. 2 C). The novel hydrogen bond between N
2 of CDR1ß Asn30 and the peptide in the 2C/H-2Kbm3dEV8 complex is also absent in the 2C/H-2KbSIYR superagonist complex. Thus, local changes to the peptide and MHC in the vicinity of the Asp77Ser mutation actually promote a more intimate union between the TCR CDR1ß loop and the pMHC.
In the 2C/H-2KbdEV8 structure, a total of 981 Å2 of pMHC surface area is buried by the TCR with 232 Å2 (23.6%) contributed by the peptide. In the 2C/H-2Kbm3dEV8 structure, 2C buries 965 Å2 of pMHC surface area, approximately equal to that buried in the 2C/H-2KbSIYR complex, with 256 Å2 (26.5%) contributed by the peptide. Thus, even though the overall pMHC buried surface area is smaller in the mutant complex, the contribution of the peptide is slightly greater. Despite a smaller pMHC buried surface in the mutant complex, the shape complementarity (Sc) coefficient (41) is significantly higher for the mutant (0.62) than for the wild-type complex (0.41; see Fig. 5 A) and, surprisingly, even greater than that of the 2C/H-2KbSIYR superagonist complex (0.49).
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Comparison of Liganded and Unliganded H-2Kbm3dEV8.
As in the syngeneic structures, the side-chain of Tyr-P6 in H-2Kbm3dEV8 must shift to accommodate the CDR1ß loop of 2C. However, in contrast to the equivalent wild-type structures (Fig. 1 C), the 1 and
2 angles of P6 change little between the bound and unbound H-2Kbm3dEV8 (Fig. 1 D), and the bulky aromatic ring of the side chain is repositioned only by a local lateral movement of the peptide main chain toward the
2-helix, which is also seen in the syngeneic complex. The C
carbon of P6 is displaced by 1.5 Å toward the
2-helix. However, relative to the syngeneic complex, the P7 backbone nitrogen is pulled closer to the
1-helix in order to preserve the hydrogen bond from MHC residue 77 to the peptide in the alloreactive complex. Despite significant local changes in the disposition of the peptide, buried waters hydrogen bonded to the carbonyl oxygen of Phe-P5 (W6) and the amide nitrogen of Tyr-P6 (W5) are conserved (Fig. 2, B and D) with coordinates being shifted the same distance and in the same direction as the peptide main chain. The side-chain conformation of Glu152 in the
2-helix must be reorganized to avoid clashing with the main-chain shift in the peptide.
The Ser-P7 1 angle is rotated 172° in the unliganded H-2Kbm3dEV8 to -48° in the liganded molecule (Fig. 1, B versus D). In the allogeneic pMHC, movement of the peptide main chain toward the
2-helix upon TCR ligation increases the distance between the hydroxyl of Ser73 and the amide nitrogen of Ser-P7 with which it forms a hydrogen bond (Fig. 2 B). This increase in the hydrogen bonding distance may weaken the bond sufficiently such that O
of Ser73 preferentially hydrogen bonds with O
of Ser-P7 (Fig. 2 D). However, what causes the dissolution of the hydrogen bond between O
of Ser-P7 and the terminal carboxyl of Val-P8 (compare Fig. 2, B and D) in the liganded H-2Kbm3dEV8 is not clear.
Stability of H-2Kb and H-2Kbm3 Complexes.
In competitive binding assays, dEV8 was shown to bind H-2Kbm3 with greater affinity than H-2Kb at both 23°C (1.3 versus 11.1 nM, respectively) and 37°C (30.4 versus 90.1 nM, respectively; Table III). As a control, binding to the peptide OVA8 was measured for both H-2Kb and H-2Kbm3. The affinity of H-2Kbm3 for OVA8 was less than that for H-2Kb at both 23°C (13.3 versus 4.5 nM, respectively) and 37°C (160.2 versus 82.2 nM, respectively). This would indicate that the increase in affinity of H-2Kbm3 for dEV8 is likely not a reflection of an increase in affinity for peptides in general.
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Discussion |
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One model proposed to explain the frequency of alloreactive T cells is dependent on presentation of a unique set of self-peptides by allogeneic MHC molecules (56). The H-2Kbm3 system would appear to be in disagreement with this peptide-dependent hypothesis because presentation of the same peptide results in both positive and negative selection depending on the allelic variant of the MHC by which it is presented. However, the mutations in the MHC alter the disposition of the peptide such that the TCR may be "seeing" an altered view of the peptide when presented by the mutant MHC. Thus, although the peptide is chemically identical in the syngeneic and allogeneic pMHC molecules, from the perspective of the TCR, it may be unique when considered in the context of the syngeneic and allogeneic pMHCs. The structural data presented here, therefore, can be reconciled with this model. A second hypothesis, based on allogeneic TCRs directly discriminating between the polymorphic changes in the -helices of the allogeneic MHC (57), does not fit in this case, as the definitive alloreactive mutation in H-2Kbm3 is buried in the peptide-binding groove and does not directly contact the TCR.
Numerous reports have identified water molecules as compensatory elements in proteinprotein interactions, occupying positions vacated by mutated side chains. In keeping with this observation, an additional water molecule is found in the cavity partially vacated by the aspartate to serine mutation at position 77 in the heavy chain in H-2Kbm3dEV8. In the H-2Kbm1VSV8 complex, a water molecule reestablishes hydrogen bonding to the peptide where it has been abolished by the Glu152Ala mutation (58). In the complexes of the HyHEL-5 (54) and D1.3 (59) antibodies bound to lysozyme, buried water molecules occupy cavities formed by Arg68Lys and Asp18Ala mutations, respectively. In the Phe78Ser mutant of Rac (60), a member of the RHO GTPase family, and in the Leu41Ala mutant of ROP (61), an RNA-binding protein involved in plasmid replication, waters occupy analogous positions. In H-2KbdEV8, the water molecule bound to the carbonyl oxygen of Tyr6 in the peptide is coordinated by O2 of heavy chain Asp77. In H-2Kbm3dEV8, the conserved water bound to the Tyr6 carbonyl is coordinated by a second water which occupies the cavity expanded by the Asp77Ser mutation. The novel cavity-filling water in turn bridges the hydroxyl oxygens of MHC heavy chain Ser73 and Ser77. Thus, the H-2Kbm3dEV8 complex is another example of the important accessory role of solvent in stabilizing protein-ligand interfaces, as well as playing a direct role in the ligand receptor recognition.
Thus far, only limited data are available delineating the role of bound water in the TCRpMHC interface. The BM3.3/H-2KbpBM1 structure was the first to reveal an extensive network of bound waters in a TCRpMHC interface (28), although waters were originally identified in the 2C/H-2KbdEV8 complex (26). The unusual conformation and size of the CDR3 loop in BM3.3/H-2KbpBM1 complex creates a cavity which is filled by
30 water molecules. The structure of 2C/H-2Kbm3dEV8 complex also highlights numerous waters in the TCRpMHC interface. As more TCRpMHC structures are determined to higher resolution, the role of waters in TCRpMHC binding will be elucidated, much as it was in the case of antibodyantigen recognition. Higher resolution structures of antibodyantigen complexes have demonstrated that bound waters participate extensively in shaping the complementary surfaces of the antibody and antigen (6266).
The BM3.3/H-2KbpBM1 structure formally established that, in an allogeneic interaction, the TCRpMHC binding orientation is still diagonal (28); however, as the structure for the corresponding TCR/self-ligand complex has not yet been determined, the degree of similarity with the syngeneic complex cannot be ascertained. The 2C/H-2Kbm3dEV8 complex confirms the observation that allogeneic TCRpMHC interactions are oriented diagonally and, furthermore, demonstrates that the structural differences between an allogeneic and syngeneic interaction can be exceedingly subtle. In the BM3.3/H-2KbpBM1 and 2C/H-2Kbm3dEV8 interactions, ß-chainpMHC contacts are increased and become emphasized. However, with only two allogeneic structures available, whether this correlates with alloreactivity itself remains conjecture. Of note, the H-2LdQL9 alloligand has been predicted to increase substantially the interactions with the 2C ß-chain through a COOH-terminal bulge in the peptide formed to accommodate a prominent ridge in the floor of the H-2Ld binding groove (67). However, it is apparent that relatively innocuous, even buried, polymorphisms can alter the presentation of the peptide itself, and, hence, lead to alloreactive TCR specificity and biological outcome.
Although the overall change in individual structures, as measured by r.m.s. deviations, appears minimal, shape complementarity coefficients and buried surface area calculations, as well as the distribution of TCRpMHC contacts, indicate that the summation of changes amounts to a subtle, but global shift, in the nature of TCR binding such that ß-chainpMHC interactions become a more dominant feature. The 2C/H-2Kbm3dEV8 is the first structure for which an analysis of this type has been possible, pointing to the importance of accumulating more structural information that addresses the question as to how TCRs distinguish between syngeneic and allogeneic ligands. Such information will provide invaluable insights into immunological phenomena that directly affect human health and disease.
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Acknowledgments |
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This work was supported by National Institutes of Health grant AI-42266 (I.A. Wilson), National Institutes of Health grants CA-58896 (I.A. Wilson) and AI-42267, (L. Teyton), National Institutes of Health training fellowship AI-07244 (J.G. Luz), a post-doctoral fellowship from the German Academic Exchange Service and Skaggs Institute (M.G. Rudolph), and a CJ Martin Fellowship (987071) from the National Health and Medical Research Council of Australia and The Austin Research Institute. This is manuscript number 14170-MB from the Scripps Research Institute. Coordinates of 2C/H-2Kbm3dEV8, H-2Kbm3dEV8, and H-2KbdEV8 have been deposited in the PDB with accession codes 1JTR, 1LEK, and 1LEG, respectively.
Submitted: September 27, 2001
Revised: March 12, 2002
Accepted: March 25, 2002
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Footnotes |
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K.C. Garcia's present address is Department of Microbiology and Department of Immunology, Stanford University School of Medicine, Fairchild D319, 299 Campus Dr., Stanford, CA 94305-5124.
V. Apostolopoulos's present address is The Austin Research Institute, Immunology and Vaccine Laboratory, Studley Rd., Heidelberg, Victoria 3084, Australia.
* Abbreviations used in this paper: pMHC, peptide-MHC; r.m.s., root mean square; SC, shape complementarity.
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References |
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