In bacteria, translation of all the ribosomal protein cistrons in the spc operon mRNA is repressed by the binding of the product of one of them, S8, to an internal sequence at the 5# end of the L5 cistron. The way in which the first two genes of the spc operon are regulated, retroregulation, is mechanistically distinct from translational repression by S8 of the genes from L5 onward. A 2.8 resolution crystal structure has been obtained of Escherichia coli S8 bound to this site. Despite sequence differences, the structure of this complex is almost identical to that of the S8/helix 21 complex seen in the small ribosomal subunit, consistent with the hypothesis that autogenous regulation of ribosomal protein synthesis results from conformational similarities between mRNAs and rRNAs. S8 binding must repress the translation of its own mRNA by inhibiting the formation of a ribosomal initiation complex at the start of the L5 cistron.

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Structural bioinformatics provides new tools for investigating protein-protein interactions at the molecular level. We present two types of structural descriptors for efficiently representing and comparing protein-protein binding sites and surface patches. The descriptors are based on distributions of distances between five types of functional atoms, thereby capturing the spatial arrangement of physicochemical properties in 3D space. Experiments with the method are performed on two tasks: (1) detection of binding sites with known similarity from homologous proteins, and (2) scanning of the surfaces of two non-homologous proteins for similar regions.

Proteomics computational analyses suggest that baculovirus GP64 superfamily proteins are class III penetrenes

Research article Structural footprinting in protein structure comparison: the impact of structural fragments

Research article Improving protein structure similarity searches using domain boundaries based on conserved sequence information

Abstract not found

Research article Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements

1 The FFAT motif is a targeting signal responsible for localizing a number of proteins to the cytosolic surface of the endoplasmic reticulum (ER) and to the nuclear membrane. FFAT motifs bind to the highly conserved protein VAP-33, which is tethered to the cytoplasmic face of the ER by a C-terminal transmembrane domain. We find that VAP proteins bind FFAT motifs through a highly conserved N-terminal Major Sperm Protein (MSP) homology domain with 1:1 stoichiometry. We have solved crystal structures of the rat VAP-A MSP homology domain alone and in complex with an FFAT motif. The co-crystal structure was used to design a VAP mutant that disrupts rat and yeast VAP-FFAT interactions in vitro. The FFAT binding-defective mutant also blocked function of the VAP homologue Scs2p in yeast. Finally, overexpression of the FFAT binding-defective VAP in COS7 cells dramatically altered ER morphology. Our data establish the structural basis of FFAT-mediated ER targeting and suggest that FFAT targeted proteins play an important role in determining ER morphology.

Research article Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1