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.

As part of molecular recognition studies on the phytohormone indole-3-acetic acid (IAA) a series of alkylated IAAs has been examined. Phenyl-ring substitution (alkyl = methyl and ethyl) at positions 4-, 6- or 7- as well as pyrrole substitution at the 2-site resulted in the six compounds which are analyzed: 2-Me-IAA, 4-Me-IAA, 6-Me-IAA, 7-Me-IAA, 4-Et-IAA and 6-Et-IAA. The structure-activity relationships investigated include those between the geometrical parameters of the molecular structures determined by X-ray analysis, the growth-promoting activities in the Avena coleoptile straight-growth bioassay and relative lipophilicities calculated from retention times on a reversed-phase HPLC column and from R(F) values in reversed-phase TLC. Lipophilicities are correlated with the moments of inertia, average polarizability, molecular mass, and the van der Waals radii of the ring substituents. The influence of substitution on the electronic properties of the indole ring and its geometry is discussed on the basis of the UV and 1H NMR spectra.

The physiological properties of the phytohormone (auxin) indole-3-acetic acid (IAA) and its ring substituted derivatives have so far been rationalized by a number of contradictory hypotheses based on incomplete structural data deduced mainly by inspection of molecular models. In order to give more evidence for structure–activity relationships of monohalogenated IAA's, the molecular structures of the natural auxin 4-CI-IAA as well as 5-CI-IAA, 6-CI-IAA, 7-CI-IAA and 5-Br-IAA have been compared, as revealed by X-ray analysis, and molecular mechanics and dynamics. The influence of the substitution site and the size of the halogen atom and bioactivity is discussed. The typical structural feature of the molecules studied is the slight distortion of part of the indole nucleus around C7: bond length C6—C7 1.368 (6) Å and C6—C7—C71 117.6 (3)° (average values of five structures and seven molecules). The conformations of monohalogenated indole-3-acetic acid molecules, characteristic for auxins, are defined by rotations about two bonds only: one describes the relative orientation of a side chain towards the indole moiety and the second the orientation of the carboxylic group. The results of X-ray structure analysis, and molecular mechanics and dynamics revealed the folded shape of the molecules in all compounds studied. Ab initio calculations showed that the planar conformation can be adopted as well. Crystal data at 297 K for 4-CI-IAA, 6-CI-IAA, 7-CI-IAA and 5-Br-IAA, and at 220 K for 5-CI-IAA, using Mo Kα radiation (λ = 0.71073 Å), and CuKα (λ = 1.5418 Å) for 6-CI-IAA, are as follows: 4-CI-IAA, C10H8ClNO2, Mr = 209.63, monoclinic, P21/c, a = 7.313 (4), b = 17.156 (4), c = 7.640 (4) Å, β = 92.71 (5)°, V = 957.5 (1) Å3, Z = 4, Dx = 1.454 g cm−3, μ = 3.7 cm−1, F(000) = 432, R = 0.037, wR = 0.039 for 1040 symmetry-independent [I ≥ 3σ(I)] reflections; 5-CI-IAA, C10H8ClNO2, monoclinic, P21/c, a = 19.141 (4), b = 5.154 (2), c = 10.323 (3) Å, β = 116.23 (2)°, V = 913.5 (1) Å3, Z = 4, Dx = 1.524  g cm−3, μ = 3.8 cm−1, F(000) = 432, R = 0.039, wR = 0.042 for 1184 symmetry-independent [I≥ 3σ(I)] reflections; 6-CI-IAA, C10H8ClNO2, orthorhombic, Pbca, a = 61.08 (1), b = 12.115 (7), c = 7.674 (5) Å, V = 5679 (5) Å3, Z = 24, Dx = 1.471 g cm−3, μ = 33.9 cm−1, F(000) = 2592, R = 0.052, wR = 0.052 for 3030 symmetry-independent [I ≥ σ(I)] reflections; 7-CI-IAA, C10H8ClNO2, monoclinic, P21/c, a = 20.244 (5), b = 4.829 (2), c = 10.728 (4) Å, β = 116.30 (1)°, V = 940 (1) Å3, Z = 4, Dx = 1.481 g cm−3, μ = 3.7 cm−1, F(000) = 432, R = 0.042, wR = 0.029 for 889 symmetry-independent [I ≥ 3σ(I)] reflections; 5-Br-IAA, C10H8BrNO2, Mr = 254.08, triclinic, P{\bar 1}, a = 5.645 (3), b = 9.713 (4), c = 10.019 (4) Å, α = 116.02 (3), β = 92.67 (5), γ = 100.12 (4)°, V = 481.2 (5) Å3, Z = 2, Dx = 1.754 g cm−3, μ = 42.0 cm−1, F(000) = 252, R = 0.029, wR = 0.020 for 1865 symmetry-independent [I ≥ 3σ(I)] reflections.

In the title compound, the coordination geometry of the CoIII atom is only slightly distorted from regular octahedral, and the racemic nature of the material was confirmed by X‐ray structure analysis.

The conformational characteristics of a flexible totally protected C-terminal dipeptide fragment (Boc-Phe-Leu-OBzl) of enkephalin are studied using X-ray data, molecular modelling and data retrieved from the Cambridge Structural Database. The dipeptide crystallizes with seven conformers in the asymmetric unit. C(27)H(36)N(2)O(5), T = 133 K, monoclinic, P2(1), a = 13.706 (3), b = 22.800 (3), c = 30.674 (5) Å, beta = 97.15 (3) degrees, V = 9511 (3) Å(3), Z = 14, D(c) = 1.145 Mg m(-3). Six of the seven molecules exhibit folded conformations with hydrophobic groups disposed at the opposite side of the peptide backbone. The characteristic Phi(1) and Psi(1) angles of the Phe residue and Phi(2) of the Leu fragment are in the allowed region defined in the Ramachandran diagram. However, they do not belong to the family of the lowest energy conformations. In the crystal, molecules are interconnected via N-H.O hydrogen bonds of peptide groups forming an infinite sheet similar to a parallel beta-sheet. Molecular dynamics simulations performed in vacuo reproduce the conformers and rotamers detected in the solid state.