The JI
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     
 

This Article
Right arrow Abstract Freely available
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow Request Permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Chu, F.
Right arrow Articles by Gao, G. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chu, F.
Right arrow Articles by Gao, G. F.
The Journal of Immunology, 2007, 178: 944-952.
Copyright © 2007 by The American Association of Immunologists, Inc.

First Glimpse of the Peptide Presentation by Rhesus Macaque MHC Class I: Crystal Structures of Mamu-A*01 Complexed with Two Immunogenic SIV Epitopes and Insights into CTL Escape1

Fuliang Chu*,||, Zhiyong Lou{dagger}, Yu Wai Chen*, Yiwei Liu{dagger}, Bin Gao*, Lili Zong*,{ddagger},§, Abdul Hamid Khan*,||, John I. Bell, Zihe Rao{dagger} and George F. Gao2,*,¶

* Center for Molecular Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China; {dagger} Laboratory of Structural Biology, Tsinghua University, Beijing, People’s Republic of China; {ddagger} Department of Obstetrics and Gynaecology, Zhujiang Hospital, Nanfang Medical University, Guangzhou, People’s Republic of China; § Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, Oxfordshire, United Kingdom; Nuffield Department of Clinical Medicine, University of Oxford, Oxford, Oxfordshire, United Kingdom; and || Graduate School, Chinese Academy of Sciences, Beijing, People’s Republic of China


   Abstract
Top
 Abstract
Introduction
 Materials and Methods
 Results
 Discussion
 Disclosures
 References
 
The infection of rhesus macaques (Macaca mulatta) by the SIV is the best animal model for studying HIV infection and for AIDS vaccine development. A prevalent MHC class I allele, Mamu-A*01, is known to correlate with containment of SIV, which has been extensively explored in studies of CTL-based vaccination concepts. We determined the crystal structures of Mamu-A*01 complexed with two immunodominant SIV epitopes: the nonamer CM9 of group-specific Ag (Gag, 181–189; CTPYDINQM) and the octamer TL8 of transcription activator (Tat, 28–35; TTPESANL). The overall structures of the two Mamu-A*01 complexes are similar to other MHC class I molecules. Both structures confirm the presence of an absolutely conserved proline anchor residue in the P3 position of the Ag, bound to a D pocket of the Mamu-A*01 H chain with optimal surface complementarity. Like other MHC/peptide complex structures, the P2 and C-terminal residues of the epitopes are also important for anchoring to the MHC molecule, whereas the middle residues form an arch and their side chains are directed into solvent. These two structures reveal details of how Mamu-A*01 interacts with two well-studied epitopes at the atomic level. We discuss the structural basis of CTL escape, based on molecular models made possible by these two structures. The results we present in this study are most relevant for the rational design of Mamu-A*01-restricted CTL epitopes with improved binding, as a step toward development of AIDS vaccines.


   Introduction
Top
 Abstract
 Introduction
Materials and Methods
 Results
 Discussion
 Disclosures
 References
 
Human immunodeficiency virus is the causative agent of AIDS, which currently poses one of the greatest global threats to human health. According to the World Health Organization, the population infected with HIV rose in 2004 to its highest level ever: an estimated 36–44 million (World Health Organization, http://www.unaids.org/wad2004/report.html). This fact underscores the urgent need for an effective AIDS vaccine. Despite vigorous research efforts, preventive (sterilizing) immunization based on raising neutralizing Abs against HIV components has proved fruitless (1, 2, 3). In contrast, it is known that the host CTL responses provide powerful defense to contain the virus postinfection (4, 5), and CTL-based immunization is currently the most promising approach toward vaccine development (6). At present, the most relevant animal model for investigating HIV pathology is the SIV infection of the nonhuman primate rhesus monkeys, with both the viruses and the infected hosts being genetically close (7, 8, 9, 10). SIV and HIV have high nucleotide sequence homology, a similar tropism for CD4+ T cells, and induce similar pathologies (5, 7, 9). Moreover, immune system components of rhesus monkeys and humans are highly conserved. For example both have MHC and TCR genes that present the same regions of lentiviral Gag and Env proteins (7, 11, 12, 13, 14). At the molecular level, it has been reported that the binding motif of the peptide to MHC class I molecules between human and rhesus monkeys is conserved in general (15), although Mamu-A*01 shows a special preference for P3 proline as anchor residue, which is not a case for any other known human HLAs (15). For all of these reasons, the SIV/rhesus model has been extensively explored as an invaluable tool for vaccine evaluation (16, 17).

Among the host CTL defense system of rhesus monkey, an allele of class I MHC, Mamu-A*01, has been associated with slow progression to AIDS-like syndrome (18, 19, 20, 21), and animals that expressed this allele show the best control over SIV replication (22). Systematic studies were performed to discover its epitopes and their specific CTLs (7, 23, 24). Two well-characterized epitopes, "TL8" from the SIV transcriptional transactivator (Tat) protein (residues 28–35, TTPESANL; note that in some studies, the "SL8," STPESANL, sequence was used) and "CM9" from the SIV group-specific Ag (Gag) protein (residues 181–189, CTPYDINQM) have been found to be immunodominant, and CTLs specific for these two epitopes are detected in the acute stage of SIV infection (7, 25, 26, 27). Following the initial peak expression, TL8-specific CTLs declined precipitously after the acute phase, whereas CM9-specific CTLs remained at a constant level throughout the chronic phase of infection (25, 27). Unfortunately, these powerful host defense mechanisms also impose strong selective pressure on the evolution of the viruses (27, 28, 29). TL8 escape variants were detectable during the very early stage of infection, whereas CM9 escape variants appeared much later (27, 30). Eventually, the mutants will dominate the virus population and result in the progression to AIDS, as reported in both rhesus monkey and human hosts (27). Evasion of the host immune system via CTL escape was found to be a major obstacle in CTL-based vaccine strategies (27, 31, 32, 33).

The availability of the SIV/rhesus model makes it possible to perform systematic studies on CTL escape. A number of escape mutants of various Mamu-A*01-restricted epitopes, including CM9 and TL8, were documented (20, 26). As a step toward delineating the molecular basis of CTL escape, we undertook structural studies to reveal how Mamu-A*01 binds these two very different SIV peptides for presentation to the TCR. Previously, several studies have probed the interactions and structures of peptide and class I MHC molecules (pMHC)3 from human and mice (34, 35, 36, 37, 38). This is the first nonhuman primate pMHC structure ever solved, and the results show that the nonamer and octamer peptides bind to the Mamu-A*01 in a similar way with P3 as an anchor residue. The results we describe in this study provide a structural basis for T cell immune escape and have implications in the rational design of CTL-based vaccines against AIDS.


   Materials and Methods
Top
 Abstract
 Introduction
 Materials and Methods
Results
 Discussion
 Disclosures
 References
 
Peptide synthesis

The Gag (181–189) CTPYDINQM peptide (denoted CM9) and Tat (28, 29, 30, 31, 32, 33, 34, 35) TTPESANL peptide (denoted TL8) were synthesized and purified by HPLC reverse phase chromatography (SciLight Biotechnology). The purities of the peptides are >90% as assessed by HPLC (data not shown).

Crystallization and data collection

The overexpression and purification of Mamu-A*01 and beta2-microglobulin (beta2m) and the crystallization of the Mamu-A*01/CM9 complex has been reported previously (39). The Mamu-A*01/TL8 complex was prepared by the same procedures. Crystals of the Mamu-A*01/CM9 and Mamu-A*01/TL8 complexes were obtained under the optimized condition (0.1 M Tris (pH 8.5), 1.8 M ammonium sulfate) in 8 wk. Data for the CM9 and TL8 crystals were collected on a Rigaku R-AXIS IV++ image plate with a Rigaku MM007 rotation Cu K{alpha} anode home x-ray generator at 40 kV and 20 mA ({lambda} = 1.5418Å). The crystals were soaked for several minutes in the reservoir solution supplemented with 20% glycerol as a cryoprotectant and then flash cooled directly in liquid nitrogen. Diffraction data collected at 100 K to 2.8 Å were processed using the program HKL2000 (40) (Table I).


View this table:
[in this window]
[in a new window]

  		Table I. Data collection and refinement statistics

 
Structure determination and refinement

The structures of the Mamu-A*01/CM9 and Mamu-A*01/TL8 complexes belong to the I422 space group. The structure of Mamu-A*01/CM9 was solved by molecular replacement using the HLA-B*5301 molecule (Protein Data Bank code: 1A1M; with the peptide excluded) as a search model, using the program CNS (38, 41). Two clear solutions in both the rotation and translation functions correspond to the two molecules in the asymmetric unit. Residues that differ between Mamu-A*01 and the search model were manually rebuilt in the program O (42) under the guidance of Fo-Fc and 2Fo-Fc electron density maps. After refinement of the model with the CNS program using simulated annealing, energy minimization, restrained individual B factors, and the addition of 343 water molecules, the respective working R factor and Rfree dropped from 0.45 and 0.42 to 0.23 and 0.28 for all data from 50 to 2.8 Å. The course of refinement was monitored by calculating Rfree based on a subset containing 5% of the total number of unique reflections. The final model of Mamu-A*01 in complex with CM9 was subsequently used to solve the structure of the Mamu-A*01/TL8 complex by molecular replacement. After the same refinement steps and the addition of 309 water molecules, the working R factor and Rfree dropped from 0.27 and 0.31 to 0.22 and 0.26. The coordinate errors estimated by Luzzati plot in CNS (41), and for the Mamu-A*01/CM9 and the Mamu-A*01/TL8 complex structures are 0.41Å and 0.35 Å, respectively. The average real-space fit values, calculated by the O program (42), for the Mamu-A*01/CM9 and the Mamu-A*01/TL8 complex structures are 0.95 and 0.94, respectively. Model geometries were verified using the program PROCHECK (43). The atomic coordinates of these two crystal structures have been deposited in the Protein Data Bank with accession nos. 1ZLN and 1ZVS.


   Results
Top
 Abstract
 Introduction
 Materials and Methods
 Results
Discussion
 Disclosures
 References
 
Overall structures of Mamu-A*01/peptide complexes

Both of the complex crystal structures contain residues 1 to 276 of the Mamu-A*01 H chain, residues 1 to 99 of human beta2m, and SIV peptides (CM9 or TL8). The overall structure of Mamu-A*01 is similar to other class I MHC molecules, with a H chain consisting of the characteristic {alpha}1/{alpha}2 and {alpha}3 domains, and the beta2m chain (Fig. 1). Mamu-A*01 shares significant sequence homology with other MHC molecule, including ~85% sequence identities among primates and 70% with mice (Fig. 2). We compared the structure of the Mamu-A*01/CM9 complex with representative structures of human and mouse origins. The root-mean-squared (r.m.s.) deviations between Mamu-A*01/CM9 and other class I MHC molecules for superposition over all C{alpha} atoms are below 1.6 Å. In the two complex structures reported in this study, the respective Mamu-A*01 molecules have a r.m.s. deviation of 0.58 Å for all C{alpha} atoms, suggesting that the two Mamu-A*01 molecules are identical within the limits of experimental error. Detailed interaction between the bound peptides and the Mamu-A*01 H chain are listed in Table II.


Figure 1
View larger version (49K):
[in this window]
[in a new window]

  		FIGURE 1. Overview of Mamu-A*01 structure with peptide-CM9. The H chain, composed of the {alpha}1, {alpha}2, and {alpha}3 domains, is shown in ribbon representation and colored purple. The L chain (beta2m) is shown in ribbon representation and colored light blue; the peptide is shown in stick model colored by atom types (C, yellow; N, blue; O, red; S, green).

 

Figure 2
View larger version (128K):
[in this window]
[in a new window]

  		FIGURE 2. Structure-based sequence alignment of Mamu-A*01 and 11 different types of MHC class I molecules, including Mamu-A*02, HLA-A*0101, HLA-A*0201, HLA-A*1101, HLA-A*2402, HLA-B*5301, HLA-Cw4, Patr-A*0101, Patr-A*0201, H-2Kb, and H-2Kd. Black arrows above the alignment indicate beta-strands; cylinders denote {alpha}-helices. Residues highlighted in red are absolutely conserved, whereas those highlighted in yellow are highly (>80%) conserved. Green numbers denote residues that form disulfide-bonds. The alignment was generated using the program Clustal X (56 ) and drawn with ESPript (57 ).

 

View this table:
[in this window]
[in a new window]

  		Table II. Hydrogen bonds and van der Waals interactions between SIV peptides and Mamu-A*01 residues

 
Conformations of the bound peptides

The electron densities for the bound peptides CM9 and TL8 are well-defined inside the peptide-binding grooves of Mamu-A*01 (Fig. 3, A and B). The side chains of the central residues of both peptides are directed into solvent and make few contacts with residues in the {alpha}1 and {alpha}2 helical domains of the Mamu-A*01 H chain (Fig. 3, A and B). Both peptides make extensive polar and nonpolar contacts with residues of Mamu-A*01 (Table II).


Figure 3
View larger version (47K):
[in this window]
[in a new window]

  		FIGURE 3. Electron densities of bound SIV peptides. Shown here are final 2Fo-Fc-stimulated annealing omit maps contoured at 1.0 {varsigma}. Only the densities corresponding to the peptides are drawn. The peptides are shown as stick models colored by atom types (C, yellow; N, blue; O, red; S, green), and all peptide residues are labeled. The peptides are shown in stick representation and colored yellow. Parts of the {alpha}1 helix and beta sheet of Mamu-A*01 are shown in ribbon representation and colored purple. A, CM9 peptide; B, TL8 peptide. Figs. 3, 4, and 6 were generated by Bobscript (58 ) and Raster3D (59 ).

 
By superimposing the binding domains of these complexes, we found that the TL8 and CM9 peptides adopt similar extended conformations with the P2, P3, and C-terminal residues in near-identical positions to serve as anchor residues to the Mamu-A*01-binding groove (Fig. 4A). In the central region of CM9, from P4 to P6, the backbone of the peptide arches out of the binding groove. The TL8 peptide is one residue shorter and the effects of arching of its central residues (P4 and P5) are not as pronounced as those of CM9. To accommodate an extra residue, the P4 and P5 residues of CM9 follow a small zigzag across the width of the binding groove.


Figure 4
View larger version (28K):
[in this window]
[in a new window]

  		FIGURE 4. Comparisons of SIV and HIV peptide antigenic conformations. Side view superpositions of the different peptides are shown here to compare the position of the anchor residues that tether the peptide to the MHC surface, and the exposed residues that are most likely to be involved in TCR binding. The peptides are shown as stick models colored by atom types (N, blue; O, red; S, green) with carbon atoms colored differently for each peptide: yellow for TL8, purple for CM9, and green for TL9. A, Superposition of the CM9 and TL8 peptides. B, Superposition of the CM9, with TL9 (PDB ID, 1A1M) peptides.

 
The P3 anchor residue, the C-terminal residues, and P2 residue are totally buried. The P4, P5, and P8 residues of CM9 and P4, P5, and P7 residues of TL8 remain solvent accessible after binding, with relative solvent accessibilities varying from ~40% to 80% (Table III).


View this table:
[in this window]
[in a new window]

  		Table III. Accessible surface area (ASA) calculations of bound SIV epitopesa

 
P3 anchor residue

It has been known for some time that proline in the P3 position is an absolutely conserved feature shared by all Mamu-A*01-restricted epitopes reported to date (7, 15, 23, 24). The two Mamu-A*01/peptide complex models provide a structural explanation for this observation. The peptide-binding groove of Mamu-A*01 contains a well-defined hydrophobic pocket (D pocket) that is optimal for binding the P3 proline side chain, constituted by the side chains of residues Tyr9, Arg97, and Tyr159; and the allele-specific residues Val99 and Met156 (Fig. 5). In addition, the pyrrolidine ring of the P3 proline stacks against the aromatic ring of Tyr159, with a nearest distance of 2.9 Å, and offers extra stability (Fig. 5). These data argue for a stringent stereochemical requirement for proline in position P3: a more bulky residue cannot be accommodated, whereas a smaller residue cannot form the optimal hydrophobic interactions required for binding.


Figure 5
View larger version (83K):
[in this window]
[in a new window]

  		FIGURE 5. Binding of TL8 peptide with emphasis of Pocket D. The molecule surface of Mamu-A*01 is shown in gray, Pocket D in green, and the peptide is represented as stick model colored in yellow. The residues of TL8 peptide and the important residues forming the Pocket D in Mamu-A*01 are labeled. Pocket A–F are labeled in red letters. The P3 proline is the core of hydrophobic interactions. The pyrrolidine ring of P3-Pro is parallel to the phenyl ring of Tyr159. Species-specific residues Val99 and Met156 are shown in the pocket. Tyr9 and Val99 are forming the bottom of Pocket D, while Arg97 are forming the other side. The figure was generated by Pymol (http://www.pymol.org/).

 
In most MHC class I molecules, tyrosine in position 99 is conserved, except in H-2Kb, where its counterpart is serine, which can form hydrogen bonds. However, in Mamu-A*01 and H-2Dd, the residues at position 99 are valine and alanine, respectively. The side chains of valine and alanine are relatively small, which provide more space to accommodate the P3 proline side chain of the peptide. Furthermore, valine and alanine cannot form hydrogen bonds. As in H-2Ld, in pocket B, position 63 is alanine, which cannot form any hydrogen bonds to P2-Pro. Thus, we postulate that it is the nonpolar residues at position 99 that ensure the P3 proline to packs in the right place complementary to the pocket (34, 38, 44, 45). Similarly, in H-2Dd, which also has an absolute preference for proline as the third residue of the epitope (34), it has alanine, another residue with a small hydrophobic side chain, at position 99.

C terminus anchor residue

The F pocket of Mamu-A*01 is deep and hydrophobic, formed by the absolutely conserved residues Tyr84, Tyr123, Thr143, Lys146, and Trp147, (Figs. 2 and 6, A and B), as well as the less conserved residues Asn77, Thr80, Leu95, and Tyr116. The carboxylate group of the CM9 C terminus makes two hydrogen bonds with Tyr84 and Thr143 and extends deeply into the hydrophobic pocket together with the side chain of P9-Met, which firmly anchors the C terminus of the peptide (Fig. 6A). In contrast to CM9, the TL8 peptide binds to Mamu-A*01 with a C-terminal P8-Leu that has its side chain slightly reoriented from the CM9 P9-Met side chain (Fig. 6, A and B).


Figure 6
View larger version (23K):
[in this window]
[in a new window]

  		FIGURE 6. Network of hydrogen bonds at the C- and N-terminal ends of the binding groove. The backbone of Mamu-A*01 is represented as purple ribbon; the residues of the peptides is shown as golden stick, and relevant residues of Mamu-A*01 are shown as stick models colored by atom types (N, blue; O, red; S, green) with carbon atoms of peptides in yellow and those of Mamu-A*01 in green. Hydrogen bonds are illustrated as dotted lines. Water molecules are shown as red spheres indicated by red letter W. A, Pocket F for CM9. Only P7, P8, P9, and one water molecule (W348) are shown. B, Pocket F for TL8. Only P7, P8, and one water molecule (W24) are shown. C, Pocket A for CM9. Only P1-Cys, P2-Thr, and P3-Pro are shown. D, Pocket A for TL8. Only P1-Cys, P2-Thr, and P3-Pro are shown.

 
Compared with the human and mouse MHC complex structures, the residues forming the F pocket of Mamu-A*01, Tyr84, Thr143, and Asp77 are rather conserved. These residues usually form hydrogen bonds to the C-terminal residues. There are water molecule-mediated hydrogen bonds with Asp77 and Thr80 (Table II and Fig. 6, A and B). The pattern of C-terminal hydrogen bonds in the Mamu-A*01/peptide complexes is very similar to those of human and mouse complexes. Like most class I MHC molecules, the F pocket of Mamu-A*01 can accept aliphatic P-omega side chains (Leu, Met, Ile, and Val) (46).

Unique P2 residue

The B pockets of MHC class I molecules including Mamu-A*01, HLA-A*0101, and HLA-B*5801 are constituted by a conserved peptide-binding motif with Met/Thr at residue 45, Asn at residue 66, and Met at residue 67. There is a strong preference for a small residue, either threonine, serine, or alanine, in the P2 position of the peptide (15, 24). From the two Mamu-A*01/peptide structures reported in this study, the P2-Thr residues are found to be in contact with these three residues’ conserved peptide-binding motif residues (Table II). In addition, two bulky tyrosine residues Tyr7 and Tyr9 on the bottom of the pocket protrude upwards and define a small volume to accommodate the P2 side chain. In both of the Mamu-A*01 complex structures, we found that the side chains of P2-Thr form hydrogen bonds with Glu63 and Asn66 (Fig. 6, C and D, and Table II). Presumably serine in position P2 can be accommodated in the way as a threonine, thus maintaining these two hydrogen bonds.

Buried P1 residue

In both complex structures, the N-terminal (P1) residue of each peptide is buried in pocket A with a reduction of >160 Å2 in accessible surface area (Table III). The main-chain atoms of this residue contribute to the overall binding of the peptides. Pocket A is formed by the residues Met5, Tyr7, Tyr167, and Tyr171, which are highly conserved in most class I molecules (Fig. 2). The amino group of the P1 residue of CM9 forms hydrogen bonds with both Tyr7 and Tyr171 of Mamu-A*01, whereas the carbonyl group of this residue forms a hydrogen bond with Tyr159. The P1 residue of TL8 is able to adopt a similar conformation and interacts with these same tyrosine residues (Fig. 6, C and D). Hydrogen bonding with the N-terminal residue of the bound epitope is a recurring theme among class I MHC molecules (24, 37). Therefore, we conclude that the hydrogen bonding pattern of the N-terminal residue of the bound peptide, similar to the C-terminal residues, is relatively conserved.

Interactions of the middle residues in the peptide and the roles of water molecules

In CM9, the P6-Ile and P7-Glu residues show no interaction with the floor of the binding pocket (the beta-sheet) and they are largely buried, having relative solvent accessibilities of 23 and 28%, respectively (Table III). In some human pMHC complexes (of HLA-A*1101), the side chains of residues in the central P6 (of nonamer) or P7 (of decamer) positions are directed into the binding pocket and contribute significant secondary interactions to anchor the peptide (47). With Mamu-A*01, however, the equivalent residues (P6 and P7 of CM9; P6 of TL8) adopt different conformations. Instead of pointing downwards, their side chains extend parallel to the beta-sheet floor of the binding groove and make van der Waals interactions with the {alpha}1 and {alpha}2 helices of Mamu-A*01 (Fig. 3 and Table II).

In the Mamu-A*01/CM9 structure, water molecule W348 mediates four important hydrogen bonds between the Mamu-A*01 residues Glu70 and Arg97 and the CM9 residue P7-Gln within the C and E pockets (Table II and Fig. 6A). In the Mamu-A*01/TL8 complex, water molecules W24 form three hydrogen bonds between the TL8 residue P8-Leu, and the Mamu-A*01 residues Asn77 and Thr80 within the F pocket (Table II and Fig. 6B). The locations of the two water molecules are not conserved between the two structures.


   Discussion
Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
Disclosures
 References
 
The structures reported in this study provide detailed information regarding peptide presentation by the rhesus monkey Mamu-A*01, an important MHC allele that has been used in many systematic investigations into SIV infection. These are the first-ever solved nonhuman primate pMHC complex structures and allow many published functional data to be interpreted from a structural perspective. Apart from AIDS, nonhuman primate models are invaluable in studying other human diseases, such as rheumatoid arthritis, hepatitis, malaria, etc. (15).

SIV epitopes bind to Mamu-A*01 with a two-point anchorage resembling the motif of binding by several known human and mouse class I MHC molecules, including HLA-A*01, HLA-B*08, and H-2Db (7, 24). Similar to other pMHC complex structures, the SIV epitopes have the characteristic P2 and C-terminal anchor residues in the peptide-binding motif. The unique structural feature of the Mamu-A*01-restricted epitope is an absolute requirement for proline in the P3 position as one of its major anchor residues (23). Precedents for P3 anchors have been reported in the context of both the murine (H-2Dd) and human (HLA-A*01 and -B*08) MHC molecules (7, 24). Interestingly, the murine structure also has a P3-Pro anchor that is stabilized by the ring stacking with MHC residue Tyr159 (34).

In addition to interactions between protein and peptide atoms, water molecules have been shown to be important in bridging hydrogen bonds in almost every MHC peptide structure determined to date, including the two structures we solved in this study (48). Our structural observations provide two examples of water molecules contributing additional hydrogen bonds and fine-tuning the binding interface between a MHC molecule and its epitopes.

It is interesting to compare the structure of the CM9 (CTPYDINQM) peptide reported in this study here with that of a highly similar HIV-2 epitope (TPYDINQML, TL9) that is part of the complex with HLA-B*53 (38). The HIV-2 epitope is identical in sequence to SIV Gag 182–190 (i.e., CM9 shifted by one residue to the C-terminal), such that CM9 and TL9 are related by a single-residue offset relative to each other. Despite having eight of their nine residues in common, the two nonamers have totally different conformations when induced to fit into optimal binding to their respective MHC molecules (Fig. 4B). Therefore, it cannot be inferred that epitopes with similar sequences bind to MHC molecules with similar peptide conformations. In a previous study, it was found that HIV-2-derived TL9 binds 25-fold weaker than CM9 to Mamu-A*01 (7).

Similarly, another interesting epitope that is highly related to CM9 is Gag CL10 (CTPYDINQML), which is essentially CM9 plus one extra residue at the C terminus. CL10 is restricted by a distinctly different CTL clone (7), but it binds to Mamu-A*01 with a similar affinity to CM9 (7). The bound conformation of the CL10 epitope may result in a different C-terminal anchorage from CM9.

For the CM9 peptide, residues P4-Tyr, P5-Asp, and P8-Gln show the highest degree of solvent exposure (Table III) and are the best candidates for TCR binding. For TL8, residues P4-Glu, P5-Ser, and P7-Asn also display a high degree of solvent exposure. In the crystal structures of HLA-A*1101 complexed with two HIV epitopes, the side chains of the P4, P5, P7, and P8 residues (for the nonamer peptide), or the P4, P5, P8, and P9 residues (for the decamer peptide) have the highest solvent exposure and are proposed as the best candidates for TCR recognition (47). We examined previous work on natural and artificial mutations of SIV/HIV to gain insights into the TCR binding site on the Mamu-A*01/peptide structures. It has been shown that alanine substitutions in either the P7 or P8 positions of a HLA-A*11-restricted peptide eliminate TCR recognition without affecting the binding affinity, whereas substitutions at P4 and P5 have no effect (47, 49). These results for the human MHC class I homologue are in striking contrast to those of Mamu-A*01. A recombinant SIV that has an alanine substitution at the CM9 P8-Gln residue (Gag Q188A; also known as "Q53A") behaves very much like the wild-type virus and stimulates CM9-specific CTL responses (50). This argues against P8-Gln of CM9 playing a role in TCR binding. In contrast, a naturally occurring P5-Ser to leucine (Tat S32L) variant is resistant to CTL lysis while its binding to Mamu-A*01 is not lost, suggesting that this residue is important in TCR recognition (26). Taken together, residues in the P4 and P5 positions are the more likely determinants for TCR binding, whereas the involvement of residues at the C terminus are debatable. It is noteworthy that the work on HLA-A11 was performed using a CTL clone, whereas the work on Mamu-A*01 was conducted using a cell line. Therefore, it should be possible to isolate a CTL clone from this cell line that recognizes the P8-residue. Studies using these specific conditions should be performed in the future to address these issues.

MHC class I molecules bind the dimeric CD8{alpha}{alpha} coreceptor mainly via its {alpha}3 domain (51, 52). It can be inferred that the CD8 binding site of Mamu-A*01 is also located on this surface because the {alpha}3 domain of Mamu-A*01 is highly conserved (Figs. 1 and 2).

The SIV/rhesus monkey model has contributed significantly to our current understanding of the effects of CTL escape. The evasion of CTL responses can occur at two levels: either the mutated epitope does not bind to the MHC molecule, or the pMHC complex is no longer recognized by the TCR. The two Mamu-A*01-restricted epitopes we used in this study have been extensively studied and their escape variants have been characterized.

CTL escape variants of CM9 are rare and they arise at a later stage of infection, consistent with CM9 being derived from a structurally and/or functionally constrained part of Gag where mutations cannot be tolerated (28). Most consistently, the T182I variant (P2 location of the epitope; or "T47I" in some studies) is the only one that turned up in several investigations (20, 31, 53). According to a previous study, the T182I mutation of CM9 leads to decrease in binding to Mamu-A*01 by two orders of magnitude (24, 31). We studied the Mamu-A*01/CIPYDINQM complex and observed a dramatically reduced complex yield in refolding experiments (F. Chu, G. F. Gao, unpublished results), suggesting a significantly reduced binding affinity. From the Mamu-A*01/CM9 structure, pocket B is simply not large enough to accommodate the isoleucine side chain that is just slightly bigger. Furthermore, the two hydrogen bonds contributed by P2-Thr are lost as a result of mutation.

In contrast, escape variants of TL8 restricted by Mamu-A*01 are diversified and they appear very early postinfection, implying that this part of the Tat protein is nonessential and can tolerate mutations without compromising survival (26, 27, 30). Although the most dramatic loss in binding to Mamu-A*01 was caused by mutations in the P2 and P8 anchor positions, CTL escape can be achieved by mutations in any of the eight residues (26). In this study, we discuss the structural consequences of several predominant mutations, namely, T28P (P1 residue, also known as "S28P" in some studies), T29I (P2), S32L (P5), L35Q, L35P, and P35R (P8 residue) (26, 30). The Tat T29I mutation is analogous to the Gag T182I mutation at the P2 location, resulting in a side chain that is unable to fit in the B pocket, as discussed above. From the Mamu-A*01/TL8 structure, the P8-Leu residue is an important residue that is completely buried in the F pocket (Table III), which has a strong preference for hydrophobic residues in the C-terminal anchor position (24). Replacement of P8-Leu with either proline, arginine, or glutamine would result in a loss of this optimal C-terminal anchorage due to the mutant side chain being too bulky, or sterically unfit, or due to burial of polar or charged atoms. The T28P (P1 position) and S32L (P5 position) mutants are 2- and 7-fold weaker in binding, respectively. As revealed by the Mamu-A*01/TL8 structure, the P1 and P5 residues do not contribute significantly to the stability of the complex. Presumably, these two mutations would compromise the shape complementarity at the protein-peptide interface but will not abolish binding. It is more likely that these two mutants escape CTL via evasion of TCR recognition.

The two SIV epitopes used in this study could represent two very different strategies for viral control: TL8-specific CTLs are stimulated by very low concentration of the epitope (high "functional avidity") and are therefore promising in initial containment of acute infection (29), whereas the CM9-specific CTLs may force the virus to escape with a severely compromised fitness and the weakened viruses may subsequently be controlled by secondary measures (27). The two structures reported are most relevant in providing a detailed molecular understanding of the specific CTL escape, one of the major obstacles in current AIDS vaccine research. From the electron density for TL8, we observe a relatively flat peptide in the middle of the epitope, and position P5 is occupied by serine with a short side chain. In CM9, its counterpart is isoleucine in position P6. As reported by Price et al. (54), TCR CDR3 usages for many TL8 epitope-restricted CTL clones used arginine in the middle of the CDR3. This arginine has been shown, in a HLA-A2-restricted TCR recognition, to insert into a notch formed on the Ag surface between the largely flat peptide and the MHC class I {alpha}2 helix (55). This pattern of recognition of TL8 may limit the flexibility of Ag recognition and facilitates viral escape. The T cell response is mainly stimulated by the interaction of the epitope with the CDR3, but different immunodominant epitopes induce different responses. Based on this, a vaccine with a spectrum of different peptide epitopes, including the future mutant variants, would offer a stronger immune response. This strategy should be tested for the TL8 and its escape mutant S5L immunization in the rhesus model. Furthermore, the structures reported in this study also pave the way for rational vaccine design, e.g., by virtual screening in silico.


   Acknowledgments
 
We thank Prof. Norman L. Letvin and Dr. Marcelo Kuroda from Harvard Medical School for providing us with the Mamu-A*01 plasmid. We are grateful to Prof. Po Tien and Dr. Minghai Zhou for their assistance. We also thank Dr. Justin L. Merritt from University California Los Angeles School of Dentistry and Dr. Mark Bartlam from Tsinghua University for their critical reading of the manuscript. Dr. Yu Wai Chen (Randall Division of Cell and Molecular Biophysics, King’s College London, London, U.K.) is a visiting professor at the Laboratory of Molecular Immunology and Molecular Virology, Institute of Microbiology, Chinese Academy of Sciences.


   Disclosures
Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Disclosures
References
 
The authors have no financial conflict of interest.


   Footnotes
 
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

1 This work was supported by a grant from Chinese Academy of Sciences Knowledge Innovation Project Grant no. KSCX2-SW-227, a grant from the National Basic Research Program (Project 973) of the Ministry of Science and Technology of the People’s Republic of China (Grant no. 2006CB504204), and grants from National Natural Science Foundation of China (Grant nos. 30440020 and 30671903). G.F.G. is a distinguished young investigator of the Natural Science Foundation of China (Grant no. 30525010). Back

2 Address correspondence and reprint requests to Dr. George F. Gao, Center for Molecular Immunology, Institute of Microbiology, Chinese Academy of Sciences, 13 Beiyitiao, Zhongguancun, Beijing 100080, People’s Republic of China. E-mail address: gaof{at}im.ac.cn Back

3 Abbreviations used in this paper: pMHC, peptide and class I MHC molecule complex; beta2m, beta2-microglobulin; r.m.s., root-mean-squared. Back

Received for publication November 17, 2005. Accepted for publication October 27, 2006.


   References
Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Disclosures
 References
 

  1. Friedrich, T. C., A. B. McDermott, M. R. Reynolds, S. Piaskowski, S. Fuenger, I. P. De Souza, R. Rudersdorf, C. Cullen, L. J. Yant, L. Vojnov, et al 2004. Consequences of cytotoxic T-lymphocyte escape: common escape mutations in simian immunodeficiency virus are poorly recognized in naive hosts. J. Virol. 78: 10064-10073. [Abstract/Free Full Text]
  2. Poignard, P., E. O. Saphire, P. W. Parren, D. R. Burton. 2001. gp120: Biologic aspects of structural features. Annu. Rev. Immunol. 19: 253-274. [Medline]
  3. Wagner, R., V. J. Teeuwsen, L. Deml, F. Notka, A. G. Haaksma, S. S. Jhagjhoorsingh, H. Niphuis, H. Wolf, J. L. Heeney. 1998. Cytotoxic T cells and neutralizing antibodies induced in rhesus monkeys by virus-like particle HIV vaccines in the absence of protection from SHIV infection. Virology 245: 65-74. [Medline]
  4. Kuroda, M. J., J. E. Schmitz, W. A. Charini, C. E. Nickerson, M. A. Lifton, C. I. Lord, M. A. Forman, N. L. Letvin. 1999. Emergence of CTL coincides with clearance of virus during primary simian immunodeficiency virus infection in rhesus monkeys. J. Immunol. 162: 5127-5133. [Abstract/Free Full Text]
  5. Stott, J., N. Almond. 1995. Assessing animal models of AIDS. Nat. Med. 1: 295-297. [Medline]
  6. Kaufmann, S. H., A. J. McMichael. 2005. Annulling a dangerous liaison: vaccination strategies against AIDS and tuberculosis. Nat. Med. 11: S33-S44. [Medline]
  7. Allen, T. M., J. Sidney, M. F. del Guercio, R. L. Glickman, G. L. Lensmeyer, D. A. Wiebe, R. DeMars, C. D. Pauza, R. P. Johnson, A. Sette, D. I. Watkins. 1998. Characterization of the peptide binding motif of a rhesus MHC class I molecule (Mamu-A*01) that binds an immunodominant CTL epitope from simian immunodeficiency virus. J. Immunol. 160: 6062-6071. [Abstract/Free Full Text]
  8. Bontrop, R. E., N. Otting, B. L. Slierendregt, J. S. Lanchbury. 1995. Evolution of major histocompatibility complex polymorphisms and T-cell receptor diversity in primates. Immunol. Rev. 143: 33-62. [Medline]
  9. Johnson, R. P.. 1996. Macaque models for AIDS vaccine development. Curr. Opin. Immunol. 8: 554-560. [Medline]
  10. Sauermann, U.. 2001. Making the animal model for AIDS research more precise: the impact of major histocompatibility complex (MHC) genes on pathogenesis and disease progression in SIV-infected monkeys. Curr. Mol. Med. 1: 515-522. [Medline]
  11. Boyson, J. E., C. Shufflebotham, L. F. Cadavid, J. A. Urvater, L. A. Knapp, A. L. Hughes, D. I. Watkins. 1996. The MHC class I genes of the rhesus monkey. Different evolutionary histories of MHC class I and II genes in primates. J. Immunol. 156: 4656-4665. [Abstract]
  12. Levinson, G., A. L. Hughes, N. L. Letvin. 1992. Sequence and diversity of rhesus monkey T-cell receptor beta chain genes. Immunogenetics 35: 75-88. [Medline]
  13. Voss, G., N. L. Letvin. 1996. Definition of human immunodeficiency virus type 1 gp120 and gp41 cytotoxic T-lymphocyte epitopes and their restricting major histocompatibility complex class I alleles in simian-human immunodeficiency virus-infected rhesus monkeys. J. Virol. 70: 7335-7340. [Abstract/Free Full Text]
  14. Watkins, D. I.. 1995. The evolution of major histocompatibility class I genes in primates. Crit. Rev. Immunol. 15: 1-29. [Medline]
  15. Dzuris, J. L., J. Sidney, E. Appella, R. W. Chesnut, D. I. Watkins, A. Sette. 2000. Conserved MHC class I peptide binding motif between humans and rhesus macaques. J. Immunol. 164: 283-291. [Abstract/Free Full Text]
  16. Kindt, T. J., V. M. Hirsch, P. R. Johnson, S. Sawasdikosol. 1992. Animal models for acquired immunodeficiency syndrome. Adv. Immunol. 52: 425-474. [Medline]
  17. Smith, S. M.. 2002. HIV vaccine development in the nonhuman primate model of AIDS. J. Biomed. Sci. 9: 100-111. [Medline]
  18. Miller, M. D., H. Yamamoto, A. L. Hughes, D. I. Watkins, N. L. Letvin. 1991. Definition of an epitope and MHC class I molecule recognized by gag-specific cytotoxic T lymphocytes in SIVmac-infected rhesus monkeys. J. Immunol. 147: 320-329. [Abstract]
  19. Muhl, T., M. Krawczak, P. ten Haaft, G. Hunsmann, U. Sauermann. 2002. MHC class I alleles influence set-point viral load and survival time in simian immunodeficiency virus-infected rhesus monkeys. J. Immunol. 169: 3438-3446. [Abstract/Free Full Text]
  20. O’Connor, D. H., B. R. Mothe, J. T. Weinfurter, S. Fuenger, W. M. Rehrauer, P. Jing, R. R. Rudersdorf, M. E. Liebl, K. Krebs, J. Vasquez, et al 2003. Major histocompatibility complex class I alleles associated with slow simian immunodeficiency virus disease progression bind epitopes recognized by dominant acute-phase cytotoxic-T-lymphocyte responses. J. Virol. 77: 9029-9040. [Abstract/Free Full Text]
  21. Zhang, Z.-Q., T.-M. Fu, D. R. Casimiro, M.-E. Davies, X. Liang, W. A. Schleif, L. Handt, L. Tussey, M. Chen, A. Tang, et al 2002. Mamu-A*01 allele-mediated attenuation of disease progression in simian-human immunodeficiency virus infection. J. Virol. 76: 12845-12854. [Abstract/Free Full Text]
  22. Mothe, B. R., J. Weinfurter, C. Wang, W. Rehrauer, N. Wilson, T. M. Allen, D. B. Allison, D. I. Watkins. 2003. Expression of the major histocompatibility complex class I molecule Mamu-A*01 is associated with control of simian immunodeficiency virus SIVmac239 replication. J. Virol. 77: 2736-2740. [Abstract/Free Full Text]
  23. Allen, T. M., B. R. Mothe, J. Sidney, P. Jing, J. L. Dzuris, M. E. Liebl, T. U. Vogel, D. H. O’Connor, X. Wang, M. C. Wussow, et al 2001. CD8+ lymphocytes from simian immunodeficiency virus-infected rhesus macaques recognize 14 different epitopes bound by the major histocompatibility complex class I molecule mamu-A*01: implications for vaccine design and testing. J. Virol. 75: 738-749. [Abstract/Free Full Text]
  24. Sidney, J., J. L. Dzuris, M. J. Newman, R. P. Johnson, A. Kaur, K. Amitinder, C. M. Walker, E. Appella, B. Mothe, D. I. Watkins, A. Sette. 2000. Definition of the Mamu A*01 peptide binding specificity: application to the identification of wild-type and optimized ligands from simian immunodeficiency virus regulatory proteins. J. Immunol. 165: 6387-6399. [Abstract/Free Full Text]
  25. Allen, T. M., L. Mortara, B. R. Mothe, M. Liebl, P. Jing, B. Calore, M. Piekarczyk, R. Ruddersdorf, D. H. O’Connor, X. Wang, et al 2002. Tat-vaccinated macaques do not control simian immunodeficiency virus SIVmac239 replication. J. Virol. 76: 4108-4112. [Abstract/Free Full Text]
  26. Allen, T. M., D. H. O’Connor, P. Jing, J. L. Dzuris, B. R. Mothe, T. U. Vogel, E. Dunphy, M. E. Liebl, C. Emerson, N. Wilson, et al 2000. Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature 407: 386-390. [Medline]
  27. Goulder, P. J., D. I. Watkins. 2004. HIV and SIV CTL escape: implications for vaccine design. Nat. Rev. Immunol. 4: 630-640. [Medline]
  28. McMichael, A., P. Klenerman. 2002. HIV/AIDS. HLA leaves its footprints on HIV. Science 296: 1410-1411. [Abstract/Free Full Text]
  29. O’Connor, D. H., T. M. Allen, T. U. Vogel, P. Jing, I. P. DeSouza, E. Dodds, E. J. Dunphy, C. Melsaether, B. Mothe, H. Yamamoto, et al 2002. Acute phase cytotoxic T lymphocyte escape is a hallmark of simian immunodeficiency virus infection. Nat. Med. 8: 493-499. [Medline]
  30. O’Connor, D., T. Friedrich, A. Hughes, T. M. Allen, D. Watkins. 2001. Understanding cytotoxic T-lymphocyte escape during simian immunodeficiency virus infection. Immunol. Rev. 183: 115-126. [Medline]
  31. Barouch, D. H., J. Kunstman, M. J. Kuroda, J. E. Schmitz, S. Santra, F. W. Peyerl, G. R. Krivulka, K. Beaudry, M. A. Lifton, D. A. Gorgone, et al 2002. Eventual AIDS vaccine failure in a rhesus monkey by viral escape from cytotoxic T lymphocytes. Nature 415: 335-339. [Medline]
  32. Chen, Z. W., A. Craiu, L. Shen, M. J. Kuroda, U. C. Iroku, D. I. Watkins, G. Voss, N. L. Letvin. 2000. Simian immunodeficiency virus evades a dominant epitope-specific cytotoxic T lymphocyte response through a mutation resulting in the accelerated dissociation of viral peptide and MHC class I. J. Immunol. 164: 6474-6479. [Abstract/Free Full Text]
  33. Friedrich, T. C., E. J. Dodds, L. J. Yant, L. Vojnov, R. Rudersdorf, C. Cullen, D. T. Evans, R. C. Desrosiers, B. R. Mothe, J. Sidney, et al 2004. Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nat. Med. 10: 275-281. [Medline]
  34. Achour, A., K. Persson, R. A. Harris, J. Sundback, C. L. Sentman, Y. Lindqvist, G. Schneider, K. Karre. 1998. The crystal structure of H-2Dd MHC class I complexed with the HIV-1-derived peptide P18–I10 at 2.4 A resolution: implications for T cell and NK cell recognition. Immunity 9: 199-208. [Medline]
  35. Bjorkman, P. J., M. A. Saper, B. Samraoui, W. S. Bennett, J. L. Strominger, D. C. Wiley. 1987. Structure of the human class I histocompatibility antigen, HLA-A2. Nature 329: 506-512. [Medline]
  36. Bouvier, M., D. C. Wiley. 1994. Importance of peptide amino and carboxyl termini to the stability of MHC class I molecules. Science 265: 398-402. [Abstract/Free Full Text]
  37. Persson, K. S., G. Schnieder. 2000. Three-dimensional structures of MHC class I-peptide complexes: implications for peptide recognition. Arch. Immunol. Ther. Exp. 48: 135-142.
  38. Smith, K. J., S. W. Reid, K. Harlos, A. J. McMichael, D. I. Stuart, J. I. Bell, E. Y. Jones. 1996. Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53. Immunity 4: 215-228. [Medline]
  39. Chu, F., Z. Lou, B. Gao, J. I. Bell, Z. Rao, G. F. Gao. 2005. Complex assembly, crystallization and preliminary X-ray crystallographic studies of rhesus macaque MHC Mamu-A*01 complexed with an immunodominant SIV-Gag nonapeptide. Acta Crystallograph Sect. F Struct. Biol. Cryst. Commun. 61: 614-616. [Medline]
  40. Otwinoski, Z. M., W. Minor. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326.
  41. Brunger, A. T., P. D. Adams, G. M. Clore, W. L. DeLano, P. Gros, R. W. Grosse-Kunstleve, J. S. Jiang, J. Kuszewski, M. Nilges, N. S. Pannu, et al 1998. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54: 905-921. (Pt. 5). [Medline]
  42. Jones, T. A., J. Y. Zou, S. W. Cowan, M. Kjeldgaard. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47: 110-119. (Pt. 2).
  43. Laskowski, R. A., D. S. Moss, J. M. Thornton. 1993. Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol. 231: 1049-1067. [Medline]
  44. Balendiran, G. K., J. C. Solheim, A. C. Young, T. H. Hansen, S. G. Nathenson, J. C. Sacchettini. 1997. The three-dimensional structure of an H-2Ld-peptide complex explains the unique interaction of Ld with beta-2 microglobulin and peptide. Proc. Natl. Acad. Sci. USA 94: 6880-6885. [Abstract/Free Full Text]
  45. Smith, K. J., S. W. Reid, D. I. Stuart, A. J. McMichael, E. Y. Jones, J. I. Bell. 1996. An altered position of the {alpha}2 helix of MHC class I is revealed by the crystal structure of HLA-B*3501. Immunity 4: 203-213. [Medline]
  46. Zhang, C., A. Anderson, C. DeLisi. 1998. Structural principles that govern the peptide-binding motifs of class I MHC molecules. J. Mol. Biol. 281: 929-947. [Medline]
  47. Li, L., M. Bouvier. 2004. Structures of HLA-A*1101 complexed with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle, secondary anchor residue. J. Immunol. 172: 6175-6184. [Abstract/Free Full Text]
  48. Fremont, D. H., E. A. Stura, M. Matsumura, P. A. Peterson, I. A. Wilson. 1995. Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove. Proc. Natl. Acad. Sci. USA 92: 2479-2483. [Abstract/Free Full Text]
  49. Threlkeld, S. C., P. A. Wentworth, S. A. Kalams, B. M. Wilkes, D. J. Ruhl, E. Keogh, J. Sidney, S. Southwood, B. D. Walker, A. Sette. 1997. Degenerate and promiscuous recognition by CTL of peptides presented by the MHC class I A3-like superfamily: implications for vaccine development. J. Immunol. 159: 1648-1657. [Abstract]
  50. Peyerl, F. W., H. S. Bazick, M. H. Newberg, D. H. Barouch, J. Sodroski, N. L. Letvin. 2004. Fitness costs limit viral escape from cytotoxic T lymphocytes at a structurally constrained epitope. J. Virol. 78: 13901-13910. [Abstract/Free Full Text]
  51. Gao, G. F., J. Tormo, U. C. Gerth, J. R. Wyer, A. J. McMichael, D. I. Stuart, J. I. Bell, E. Y. Jones, B. K. Jakobsen. 1997. Crystal structure of the complex between human CD8{alpha}{alpha} and HLA-A2. Nature 387: 630-634. [Medline]
  52. Kern, P. S., M. K. Teng, A. Smolyar, J. H. Liu, J. Liu, R. E. Hussey, R. Spoerl, H. C. Chang, E. L. Reinherz, J. H. Wang. 1998. Structural basis of CD8 coreceptor function revealed by crystallographic analysis of a murine CD8{alpha}{alpha} ectodomain fragment in complex with H-2Kb. Immunity 9: 519-530. [Medline]
  53. Peyerl, F. W., D. H. Barouch, W. W. Yeh, H. S. Bazick, J. Kunstman, K. J. Kunstman, S. M. Wolinsky, N. L. Letvin. 2003. Simian-human immunodeficiency virus escape from cytotoxic T-lymphocyte recognition at a structurally constrained epitope. J. Virol. 77: 12572-12578. [Abstract/Free Full Text]
  54. Price, D. A., S. M. West, M. R. Betts, L. E. Ruff, J. M. Brenchley, D. R. Ambrozak, Y. Edghill-Smith, M. J. Kuroda, D. Bogdan, K. Kunstman, et al 2004. T cell receptor recognition motifs govern immune escape patterns in acute SIV infection. Immunity 21: 793-803. [Medline]
  55. Stewart-Jones, G. B., A. J. McMichael, J. I. Bell, D. I. Stuart, E. Y. Jones. 2003. A structural basis for immunodominant human T cell receptor recognition. Nat. Immunol. 4: 657-663. [Medline]
  56. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882. [Abstract/Free Full Text]
  57. Gouet, P., X. Robert, E. Courcelle. 2003. ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 31: 3320-3323. [Abstract/Free Full Text]
  58. Esnouf, R. M.. 1997. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graph. Model. 15: 132-134. 112–133. [Medline]
  59. Merritt, E. A., D. J. Bacon. 1997. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277: 505-524. [Medline]
  60. Hubbard, S. J., S. F. Campbell, J. M. Thornton. 1991. Molecular recognition: conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J. Mol. Biol. 220: 507-530. [Medline]



This article has been cited by other articles:


Home page
 JEMHome page
D. A. Price, T. E. Asher, N. A. Wilson, M. C. Nason, J. M. Brenchley, I. S. Metzler, V. Venturi, E. Gostick, P. K. Chattopadhyay, M. Roederer, et al.
Public clonotype usage identifies protective Gag-specific CD8+ T cell responses in SIV infection
J. Exp. Med., April 13, 2009; 206(4): 923 - 936.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
E.-Y. Kim, R. S. Veazey, R. Zahn, K. J. McEvers, S. H. C. Baumeister, G. J. Foster, M. D. Rett, M. H. Newberg, M. J. Kuroda, E. P. Rieber, et al.
Contribution of CD8+ T Cells to Containment of Viral Replication and Emergence of Mutations in Mamu-A*01-Restricted Epitopes in Simian Immunodeficiency Virus-Infected Rhesus Monkeys
J. Virol., June 1, 2008; 82(11): 5631 - 5635.
[Abstract] [Full Text] [PDF]

This Article
Right arrow Abstract Freely available
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow Request Permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Chu, F.
Right arrow Articles by Gao, G. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chu, F.
Right arrow Articles by Gao, G. F.

HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS