Peptide mimics of a tumor antigen induce functional cytotoxic T cells.

The ability to mimic peptide/peptide and/or peptide/carbohydrate structures may be important in generating cross-reactive antibodies for autoimmune and other diseases. We show that the peptide sequence DAHWESWL can mimic the conformation of the unrelated MUC1 peptide SAPDTRPAP(G). Mice immunized with mannan-MUC1-peptides make cytotoxic T lymphocytes (CTLs) and are protected from MUC1+ tumors. We show that the same specific anti-MUC1 responses can be produced by immunizing with the DAHWESWL peptide; furthermore, specific tumor protection is obtained in a manner similar to that with MUC1 immunization. The DAHWESWL peptide immunization leads to CTLs that recognize H2Dd and H2Ld but not H2b or human leukocyte antigens-group A (HLA-A) *0201 presented MUC1 peptides. However, mutation of the DAHWESWL peptide to a more HLA-A*0201-compatible structure with appropriate anchors (DLHWASWV), leads to the production of CTLs in HLA-A*0201 mice.

Human theta class glutathione transferase: the crystal structure reveals a sulfate-binding pocket within a buried active site.

BACKGROUND: Glutathione S-transferases (GSTs) comprise a multifunctional group of enzymes that play a critical role in the cellular detoxification process. These enzymes reduce the reactivity of toxic compounds by catalyzing their conjugation with glutathione. As a result of their role in detoxification, GSTs have been implicated in the development of cellular resistance to antibiotics, herbicides and clinical drugs and their study is therefore of much interest. In mammals, the cytosolic GSTs can be divided into five distinct classes termed alpha, mu, pi, sigma and theta. The human theta class GST, hGST T2-2, possesses several distinctive features compared to GSTs of other classes, including a long C-terminal extension and a specific sulfatase activity. It was hoped that the determination of the structure of hGST T2-2 may help us to understand more about this unusual class of enzymes. RESULTS: Here we present the crystal structures of hGST T2-2 in the apo form and in complex with the substrates glutathione and 1-menaphthyl sulfate. The enzyme adopts the canonical GST fold with a 40-residue C-terminal extension comprising two helices connected by a long loop. The extension completely buries the substrate-binding pocket and occludes most of the glutathione-binding site. The enzyme has a purpose-built novel sulfate-binding site. The crystals were shown to be catalytically active: soaks with 1-menaphthyl sulfate result in the production of the glutathione conjugate and cleavage of the sulfate group. CONCLUSIONS: hGST T2-2 shares less than 15% sequence identity with other GST classes, yet adopts a similar three-dimensional fold. The C-terminal extension that blocks the active site is not disordered in either the apo or complexed forms of the enzyme, but nevertheless catalysis occurs in the crystalline state. A narrow tunnel leading from the active site to the surface may provide a pathway for the entry of substrates and the release of products. The results suggest a molecular basis for the unique sulfatase activity of this GST.

Anatomy and evolution of proteins displaying the viral capsid jellyroll topology.

In this paper the anatomy of 25 structures containing a jellyroll motif, consisting of eight antiparallel beta-strands forming a so-called beta-barrel, was investigated. This involved performing a careful structural alignment based on hydrogen bonds for the equivalent regions of the tertiary folds and a subsequent analysis of conserved amino acids, equivalenced residue-residue contacts, and various parameters describing the size, shape and other geometrical characteristics of these regions. It was found that the jellyroll motif is best viewed as a two-sheet wedge structure rather than a barrel. The more conserved parameters are discussed. A model of evolutionary development for the jellyroll fold in the various protein and viral structures is proposed.

Prediction of protein folding pathways.

Recent 1H nuclear magnetic resonance (n.m.r.) hydrogen exchange experiments on five different proteins have delineated the secondary structures formed in trapped, partially folded intermediates. The early forming structural elements are identifiable through a technique described in this work to predict folding pathways. The method assumes that the sequential selection of structural fragments such as alpha-helices and beta-strands involved in the folding process is founded upon the maximal burial of solvent accessible surface from both the formation of internal structure and substructure association. The substructural elements were defined objectively by major changes in main-chain direction. The predicted folding pathways are in complete correspondence with the n.m.r. results in that the formed structural fragments found in the folding intermediates are those predicted earliest in the pathways. The technique was also applied to proteins of known tertiary structure and with fold similar to one of the five proteins examined by 1H n.m.r. The pathways for these structures also showed general consistency with the n.m.r. observations, suggesting conservation of a secondary structural framework or molten globule about which folding nucleates and proceeds.

Structural characteristics and stabilizing principles of bent beta-strands in protein tertiary architectures.

beta-Strands as constituents of beta-pleated sheets in protein tertiary structures often display considerable distortion from a purely extended conformation. The dislocation types are often characterized as "bulging," "twisting," and "bending." The former 2 properties have been extensively studied and classified. In this work an investigation of bent beta-structures is undertaken. The structural characteristics examined included the bending angles within and out of the principal strand plane, their distribution among various strand types such as parallel and antiparallel, the amino acid preferences at bend sites, and the usage of charged and polar residues for stabilization through interactive anchoring with other atoms of the beta-sheet within which the bent strand lies.

The Ubp6 family of deubiquitinating enzymes contains a ubiquitin-like domain: SUb.

A sequence motif that is Similar to Ubiquitin (SUb) has been identified in the Saccharomyces cerevisiae ubiquitin-specific protease Ubp6. SUb is conserved in all known Ubp6 homologues from a spectrum of eukaryotic species and is also present in a group of hypothetical proteins of unknown function (Unk1-3) present in sequence databases. An N-terminal deletion mutant of Ubp6 that lacks SUb is still capable of cleaving alpha-linked ubiquitin fusions, suggesting that SUb forms a separate domain to the catalytic core of Ubp6 and demonstrating that it is not required for in vitro cleavage activity. A homology model of the 78 N-terminal amino acids of human Ubp6, based on the known fold of ubiquitin, is presented. In human Ubp6, SUb shares only 20% sequence identity with ubiquitin. Even weaker similarity occurs between S. cerevisiae SUb and ubiquitin. The homology model supports a ubiquitin-like fold for SUb and suggests that two conserved Lys residues, corresponding to Lys48 and Lys63 of ubiquitin, are functionally important.

Mutagenic analysis of conserved arginine residues in and around the novel sulfate binding pocket of the human Theta class glutathione transferase T2-2.

The human Theta class glutathione transferase GSTT2-2 has a novel sulfatase activity that is not dependent on the presence of a conserved hydrogen bond donor in the active site. Initial homology modeling and the crystallographic studies have identified three conserved Arg residues that contribute to the formation of (Arg107 and Arg239), and entry to (Arg242), a sulfate binding pocket. These residues have been individually mutated to Ala to investigate their potential role in substrate binding and catalysis. The mutation of Arg107 had a significant detrimental effect on the sulfatase reaction, while the Arg242 mutation caused only a small reduction in sulfatase activity. Surprisingly, the Arg239 had an increased activity resulting from a reduction in stability. Thus, Arg239 appears to play a role in maintaining the architecture of the active site. Electrostatic calculations performed on the wild-type and mutant forms of the enzyme are in good agreement with the experimental results. These findings, along with docking studies, suggest that prior to conjugation, the location of 1-menaphthyl sulfate, a model substrate for the sulfatase reaction, is approximately midway between the position ultimately occupied by the naphthalene ring of 1-menaphthylglutathione and the free sulfate. It is further proposed that the Arg residues in and around the sulfate binding pocket have a role in electrostatic substrate recognition.

A roadmap for HLA-DR peptide binding specificities.

Peptide residue positional environments have previously been defined for class I MHC allelic products. These environments provide a less restrictive description of the traditional peptide binding pockets of class I molecules. When combined with the peptide anchor motifs that have been identified for some class I molecules, predictions as to likely motifs for other MHC molecules, which share the same potential environment can be made. Here, the same approach is used to derive peptide residue positional environments for class II MHC molecules. The environments are used to make predictions as to likely binding motifs for HLA-DR allelic products. The predictions are presented in the form of a Table and shown to have concordance with experimental results.

Polymorphism of phase II enzymes: identification of new enzymes and polymorphic variants by database analysis.

The Phase II enzymes of xenobiotic metabolism are characterized by a high level of substrate diversity and genetic polymorphism. Genetic polymorphism of the Phase II enzymes can be of substantial clinical significance as some variants have differences in substrate specificity, stability and levels of expression. Variation in these factors can give rise to abnormal drug metabolism and susceptibility to carcinogens and toxins. A new approach to the discovery of additional members of Phase II enzyme families and the identification of polymorphic variants using searches of the EST databases has been investigated. The examples provided demonstrate that relatively simple search strategies can be highly productive.

A roadmap for HLA-A, HLA-B, and HLA-C peptide binding specificities.

The high level of polymorphism in major histocompatibility complex (MHC) molecules leads to many allele-specific peptide binding repertoires that can generally be characterized by sequence motifs. Such motifs have previously been elucidated experimentally for several MHC molecules and shown to bind in specificity pockets in the antigen binding cleft. Here, a new and less restrictive description of the traditional antigen binding pockets is derived. These regions are referred to as peptide binding environments and are defined as those residues in a fixed neighborhood of the peptide residues in known crystal structure complexes. By examining the antigen binding environments from MHC molecules with known motifs, we made predictions as to likely motifs for other MHC molecules which share the same environments. The predictions are presented in the form of Tables and are pertinent to class I HLA-A, HLA-B, and HLA-C MHC sequences, and are shown to correlate well with experiments.

PASS: simple molecular graphics system for personal computers.

An interactive tool for displaying and manipulating molecular structures is presented. The system has a user friendly, menu driven interface and provides good quality graphics for viewing proteins. Full screen stereo viewing and a high degree of flexibility in the investigation of specific sites are among its key attributes. The low cost of the system allows it a diverse range of applicability.

Prediction of protein folding pathways: Bovine pancreatic trypsin inhibitor.

A previous theory for the prediction of protein folding pathways [1] is applied to bovine pancreatic trypsin inhibitor and the resulting sequence of folding events shown to corroborate well with available experimental data.

Stereo viewing on the PC/AT with EGA graphics.

Tachystoscopic stereo can be used to greatly enhance the performance and usability of low-cost molecular graphics systems. Here, a simple way to connect and control three-dimensional liquid-crystal glasses from a PC/AT with EGA graphics capabilities is described. The method makes elegant use of the screen's vertical retrace for synchronization purposes, allowing left and right views to be alternated every refresh cycle.

Correlating patterns in alignments of polymorphic sequences with experimental assays.

A general algorithm is presented for identifying sets of positions in multiple sequence alignments that best characterize an a priori partitioning such as those determined by inhibition studies or other experimental techniques. The algorithm explores combinations of polymorphic columns in the alignment and evaluates how well these sites reflect the original input partition. Partitions across the polymorphic columns are derived using a tree building procedure with conventional amino acid substitution matrices. Elucidation of those amino acids which govern the biochemical behaviour of a protein with a given substrate or inhibitor can provide insights towards an understanding of the tertiary conformation of the protein. Since it is likely that such positions will be spatially clustered in the protein fold, these positions may give rise to useful distance constraints for substantiating model protein structures. The method is exemplified using data for a set of human mu class glutathione S-transferases. A novel aspect for predicting the behaviour of new polymorphic sequences is also discussed.

Proteolytic processing of peptides in the lumen of the endoplasmic reticulum for antigen presentation by major histocompatibility class I.

We have tested the hypothesis that MHC class I molecules are actively involved as protease in the production of natural MHC class I ligands. First, the structure of a class I molecule was analyzed for homology with catalytic sites of known proteases. While several clusters of amino acids in the restriction element resembled protease active sites, structural discrepancies and the influence of nearby residues suggest that these sites are unlikely to have protease activity. Second, we have tested the presentation of viral cytotoxic T cell determinants with affinity for the same restriction element (H-2K(d) or K(k)), when targeted as tandem peptides into the endoplasmic reticulum. Peptide transporter-defective cells were used to exclude cleavage of the tandem peptides by cytosolic proteases. Cleavage by signal peptidase of the tandem peptides was ascertained. The C-terminal peptides in the tandem arrays were almost exclusively presented, suggesting that an aminopeptidase in the endoplasmic reticulum degraded the N-terminally positioned peptides. This result is inconsistent with an MHC class I-catalyzed cleavage following binding of longer peptides in the cleft of the restriction elements. Finally, we conclusively show that an aminopeptidase in the endoplasmic reticulum is also involved in antigen presentation in cells with a functional peptide transporter.

Easy adaptation of protein structure to sequence.

An investigation into the conservation of coarse, medium and fine grain structural properties has been performed over a data set of 175 protein tertiary structures in 34 different families, each characterized by a common core fold and a library of conserved sites formed for each family. It is shown that, while the conservation of coarse and medium grain properties correlates to the structural deviation between the proteins, fine grain properties are poorly conserved except in functional sites. This flexibility in fine grain properties suggests that folding can be viewed as an optimization process whereby side chains have freedom to position themselves as best as possible given environmental conformational constraints and that given a basic framework, the local structure is able to adapt easily to sequence variation. The conserved cores of the 34 families are used to estimate a minimal core size of 35% of the fold, consistent with buried residue considerations. Finally, conservation in side chain chi 1 torsion angles is combined with structural deviation, sequence deviation and resolution to suggest a set of example structure pairs suitable for testing automatic homology modelling programs.

Peptide binding motifs and specificities for HLA-DQ molecules.

HLA-DQ molecules have been associated with susceptibility to a number of autoimmune and other diseases, possibly through the peptide repertoire that can be presented by different allelic products. It is thus of importance to understand which peptides can be bound by different HLA-DQ allelic products. Recently, a model for HLA-DQ has been described and used to derive peptide positional environments for HLA-DQ allelic products. By combining the peptide positional environments with known HLA-DQ peptide binding motifs, a set of predictions of likely anchor motifs for many of the products of HLA-DQ allelic variants are made and presented in a table referred to as a roadmap for HLA-DQ peptide binding specificities.

The phospho-beta-galactosidase and synaptotagmin predictions.

Two bona fide consensus predictions of secondary and tertiary structure in a protein family, made and announced before experimental structures were known, are evaluated in light of the subsequently determined experimental structures. The first, for phospho-beta-galactosidase, identified the core strands of an 8-fold alpha-beta barrel, and identified the 8-fold alpha-beta barrel itself, which was found in the subsequently determined experimental structure to be the core folding domain. The second, for synaptotagmin, identified seven out of eight beta-strands in the structure correctly, missing only a noncore strand. Three preferred "topologies" were selected from several hundred thousand possible topologies of these seven predicted strands using a rule-based analysis. The subsequently determined experimental structure showed that these seven strands in synaptotagmin adopt one of the three preferred topologies. We were unable, however, to identify the correct topology from among these three topologies.

Structural comparison of major histocompatibility complex class I molecules and homology modelling of five distinct human leukocyte antigen-A alleles.

The peptide complexes of 19 major histocompatibility complex class I alpha 1 and alpha 2 domains have been compared to identify similarities that can be interpreted as constraints necessary for the function or stability of the molecule. It was found that nearly half of the residues maintained their side-chain conformations (or had no side chain), with the remaining residues being highly solvent exposed and/or polymorphic. Seven hydrogen bonds between the molecule and peptide are conserved in all the structures and serve to orientate the ends of the peptide in the binding groove. Furthermore, the general orientations of most residue side chains in the peptide are similar. Based on these constraints, homology models for the distinct human leukocyte antigen-A alleles A*0302, A*2403, A*2603, A*3101 and A*8001 have been constructed and the implications for peptide binding discussed. The models provide a useful framework from which to engineer allele-specific peptides with a high binding affinity.

Database analysis and gene discovery in pharmacogenetics.

The global genome research effort has resulted in the creation of extensive DNA and protein sequence databases that are a valuable resource for the identification of new genes and polymorphic variants of enzymes of pharmacogenetic interest. Previously undescribed members of gene families with novel functions and substrate specificities can be identified by database searching and sequence alignment strategies. Since the expressed sequence tag (EST) database contains sequences from many individuals, it can be searched for evidence of polymorphisms that can significantly influence enzyme function. The different approaches to these forms of analysis are reviewed and illustrated with examples from the glutathione transferase gene family.