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BackgroundCytotoxic T-lymphocytes (CTLs) recognize complexes of short peptides with major histocompatibility complex (MHC) class I molecules. MHC molecules are polymorphic, and the products of different MHC alleles bind to different subsets of peptides. This is due to differences in the shape of the peptide-binding groove on the surface of the MHC protein, especially the 'pockets' into which anchor residues at each end of the peptide fit. Non-peptidic ligands for class I molecules may be useful clinically.ResultsBy applying computer-aided design methods guided by X-ray structures, we designed and synthesized several MHC class I ligands, based on known peptide ligands, in which the tricyclic, aromatic compound phenanthridine replaced the central amino acids of the peptides. These semi-peptidic fluorescent ligands bound with high affinity and with allelic specificity to the peptide-binding groove of different MHC class I molecules, forming crystallizable complexes.ConclusionsSpecificity for binding to different MHC class I molecules can be imparted to the common phenanthridine element by judicious choice of terminal peptidic elements from either nonamer or decamer peptides. The phenanthridine-based ligands have a long bound half-life, as do antigenic peptides.

Results reveal that among the glycosaminoglycans heparin binds with high affinity to the surface antigen circumsporozoite protein of malaria sporozoites. Data indicate that a decasaccharide represents the minimum sized sequence that can bind to circumsporozoite.

The structure of a complex of human T-cell receptor (TCR), viral Tax peptide and a major histocompatibility complex (MHC) molecule HLA-A2 contains diagonal binding of TCR. Variable loops in the TCR structure bury a majority of the peptide and MHC molecule. The diagonal orientation and binding mode of TCR is similar to that observed in all general class I and class II molecules. Orientation of the loops, their interaction with Tax and HLA-A2, and TCR's signalling and specificity are discussed.

X-ray crystallographic studies of human class I major histocompatibility complex molecule HLA-Aw68, from which alpha3 domain has been protelytically deleted, reveal no changes in structure with domain removal. Both altered and unaltered molecules exhibit similar complexation with a decameric peptide, implying that peptide binding does not require the alpha3 domain.

Three-dimensional structural analysis of the decamer peptide from class I major histocompatibility complex (MHC) molecules reveals that longer peptides can also bind to the carboxy-terminal residue present in the peptide binding site. Redistribution of protein side chains facilitates the easy exit of the peptide. Stability measurements in the MHC during thermal denaturation to define the energetic impact of modified binding mode show that peptide binding is stable even at physiological temperature during denaturation.

X-ray crystallography was used for analyzing complexes of five peptides from human immunodeficiency virus-1 (HIV-1), influenza A virus, human T lymphotrophic virus type and B virus proteins bound to human class I major histocompatibility complex (MHC) molecule human antigen, HLA-A2. The structure of an MHC-bound peptide seems to be an extremely complicated function of its total sequence, and is responsive even to marginal reference differences.

Hfq proteins in Gram-negative bacteria play important roles in bacterial physiology and virulence, mediated by binding of the Hfq hexamer to small RNAs and/or mRNAs to post-transcriptionally regulate gene expression. However, the physiological role of Hfqs in Gram-positive bacteria is less clear. Bacillus anthracis, the causative agent of anthrax, uniquely expresses three distinct Hfq proteins, two from the chromosome (Hfq1, Hfq2) and one from its pXO1 virulence plasmid (Hfq3). The protein sequences of Hfq1 and 3 are evolutionarily distinct from those of Hfq2 and of Hfqs found in other Bacilli. Here, the quaternary structure of each B. anthracis Hfq protein, as produced heterologously in Escherichia coli, was characterized. While Hfq2 adopts the expected hexamer structure, Hfq1 does not form similarly stable hexamers in vitro. The impact on the monomer-hexamer equilibrium of varying Hfq C-terminal tail length and other sequence differences among the Hfqs was examined, and a sequence region of the Hfq proteins that was involved in hexamer formation was identified. It was found that, in addition to the distinct higher-order structures of the Hfq homologs, they give rise to different phenotypes. Hfq1 has a disruptive effect on the function of E. coli Hfq in vivo, while Hfq3 expression at high levels is toxic to E. coli but also partially complements Hfq function in E. coli. These results set the stage for future studies of the roles of these proteins in B. anthracis physiology and for the identification of sequence determinants of phenotypic complementation. [ABSTRACT FROM AUTHOR]

Coenzyme F420 is a deazaflavin hydride carrier with a lower reduction potential than most flavins. In Mycobacterium tuberculosis ( Mtb), F420 plays an important role in activating PA-824, an antituberculosis drug currently used in clinical trials. Although F420 is important to Mtb redox metabolism, little is known about the enzymes that bind F420 and the reactions that they catalyze. We have identified a novel F420-binding protein, Rv1155, which is annotated in the Mtb genome sequence as a putative flavin mononucleotide (FMN)-binding protein. Using biophysical techniques, we have demonstrated that instead of binding FMN or other flavins, Rv1155 binds coenzyme F420. The crystal structure of the complex of Rv1155 and F420 reveals one F420 molecule bound to each monomer of the Rv1155 dimer. Structural, biophysical, and bioinformatic analyses of the Rv1155-F420 complex provide clues about its role in the bacterium. [ABSTRACT FROM AUTHOR]