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Messenger-RNA-directed protein synthesis is accomplished by the ribosome. In eubacteria, this complex process is initiated by a specialized transfer RNA charged with formylmethionine (tRNA(fMet)). The amino-terminal formylated methionine of all bacterial nascent polypeptides blocks the reactive amino group to prevent unfavourable side-reactions and to enhance the efficiency of translation initiation. The first enzymatic factor that processes nascent chains is peptide deformylase (PDF); it removes this formyl group as polypeptides emerge from the ribosomal tunnel and before the newly synthesized proteins can adopt their native fold, which may bury the N terminus. Next, the N-terminal methionine is excised by methionine aminopeptidase. Bacterial PDFs are metalloproteases sharing a conserved N-terminal catalytic domain. All Gram-negative bacteria, including Escherichia coli, possess class-1 PDFs characterized by a carboxy-terminal alpha-helical extension. Studies focusing on PDF as a target for antibacterial drugs have not revealed the mechanism of its co-translational mode of action despite indications in early work that it co-purifies with ribosomes. Here we provide biochemical evidence that E. coli PDF interacts directly with the ribosome via its C-terminal extension. Crystallographic analysis of the complex between the ribosome-interacting helix of PDF and the ribosome at 3.7 A resolution reveals that the enzyme orients its active site towards the ribosomal tunnel exit for efficient co-translational processing of emerging nascent chains. Furthermore, we have found that the interaction of PDF with the ribosome enhances cell viability. These results provide the structural basis for understanding the coupling between protein synthesis and enzymatic processing of nascent chains, and offer insights into the interplay of PDF with the ribosome-associated chaperone trigger factor.

The plant hormone auxin is involved in almost every aspect of plant development; auxin homeostasis and auxin signaling are thus of crucial importance. The wider auxin family includes endogenous growth promoters, such as indole-3-acetic acid (IAA), and chemically diverse synthetic analogues; minor structural modifications afford growth inhibitors (antiauxins). As proper classification is of technological relevance (growth regulators, herbicides) we developed a classification by interaction similarity indices, based on the evaluation of two distinctive molecular conformations (planar and tilted) of indole-3-acetic acid in comparison with the optimized conformations of 50 compounds. Then we extended the method to a larger set of compounds using similarity of molecular interaction fields and lipophilicity predictions (log P). In addition to theoretical approaches based on the evaluation of molecular conformations of possible relevance for binding to the auxin receptor(s), we used experimental methods, such as X-ray structure analysis and spectroscopic methods to characterize the molecules of interest: alkylated IAAs, halogenated IAAs (F, Cl, Br), and dihalogenated IAAs. Systematic analysis of physico-chemical and structural properties provided indirect insight into the topology of the substrate-binding site of the, so far hypothetical, common auxin receptor. Our findings are in reasonable accord with the models proposed by previous researchers. The question of molecular fit to the receptor active site will, however, remain open until the coordinates of the first structurally characterized auxin binding protein, ABP1, will be in the public domain.