Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3′O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. Our multidisciplinary approach tackled an extremely challenging protein–glycopolymer complex and delineated a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity.

Combining genetic, biochemical and computational approaches, we elucidated the molecular mechanisms underlying the recognition of Listeria wall teichoic acid by bacteriophage-encoded SH3b repeats.     

The use of bis(diphenylphosphino)amines with N-aryl functionalities in selective ethylene tri- and tetramerisation

A systematic study was conducted on the Cr catalysed tri- and tetramerisation of ethylene using bis(diphenylphosphino)amine ligands with N-aryl functionality. This study revealed that the oligomerisation reaction product selectivity is primarily dependent on the structure and size of the N-aryl groups.

Addition of sufficient steric bulk to the N-phenyl group via ortho-alkyl substitution increased the combined 1-hexene and 1-octene selectivity (overall alpha selectivity) to above 82% at an overall 1-octene selectivity of 56%. The introduction of a single carbon spacer between the N-atom and the aryl-moiety, as well as the addition of branching on this carbon, resulted in further selectivity improvements, achieving an overall 1-octene selectivity of 64% and an overall alpha selectivity of 84%. This was obtained at catalyst productivities in excess of 1,000,000 g/g Cr/h.     

Preparation and dilute solution properties of model gemini nonionic surfactants

Dimeric poly(ethylene oxide) surfactants (or nonionic gemini surfactants) with the structure (Cn-2H2n-3CHCH2O(CH2CH2O)mH)2(CH2)6 (or GemnEm), where n is the alkyl length and m is the average number of ethylene oxides per head group, were synthesized. Surfactants were synthesized with alkyl chain lengths n = 12, 14, and 20 and m = 5, 10, 15, 20, and 30. Water solubilities and cloud temperatures at 1 wt% were determined by measuring turbidity as a function of temperature. Cloud temperatures increase with m and decrease with n, as observed for conventional surfactants. For large m the cloud temperatures were all above 100 degrees C. Surfactants with small m (i.e., n = 12, 14, m = 5 and n = 20, m = 10) were insoluble at room temperature, forming two-phase mixtures. Critical micelle concentrations (CMCs) were measured using a pyrene fluorescence method and are all in the range of 10(-7) to 10(-6) M, with the lowest values from the surfactants with large n and small m. CMCs of mixtures with both anionic and nonionic conventional (monomeric) surfactants were well described by an ideal mixing model.     

Intermolecular potential and second virial coefficient of the water-hydrogen complex

We construct a rigid-body (five-dimensional) potential-energy surface for the water-hydrogen complex using scaled perturbation theory (SPT). An analytic fit of this surface is obtained, and, using this, two minima are found. The global minimum has C2v symmetry, with the hydrogen molecule acting as a proton donor to the oxygen atom on water. A local minimum with Cs symmetry has the hydrogen molecule acting as a proton acceptor to one of the hydrogen atoms on water, where the OH bond and H2 are in a T-shaped configuration. The SPT global minimum is bound by 1097 microEh (Eh approximately 4.359744 x 10(-18) J). Our best estimate of the binding energy, from a complete basis set extrapolation of coupled-cluster calculations, is 1076.1 microEh. The fitted surface is used to calculate the second cross virial coefficient over a wide temperature range (100-3000 K). Three complementary methods are used to quantify quantum statistical mechanical effects that become significant at low temperatures. We compare our results with experimental data, which are available over a smaller temperature range (230-700 K). Generally good agreement is found, but the experimental data are subject to larger uncertainties.     

Development of Molecular Mechanics Torsion Parameters for alpha,beta-Cyclopropyl Ketones and Conformational Analysis of Bicyclo[m.1.0]alkan-2-ones

Conformations of cyclopropyl methyl ketone have been studied using ab initio methods in an effort to quantify the effects of conjugative overlap between the cyclopropane ring and an adjacent ketone carbonyl. Results were comparable with previous experimental and theoretical studies. Cyclopropyl methyl ketone exhibits a global energy minimum in the s-cis conformer and a local energy minimum near the s-trans conformer. The potential energy curve obtained was used to derive torsion parameters which were employed in molecular mechanics studies of the conformations of the set of bicyclo[m.1.0]alkan-2-ones having larger ring sizes from five- to 16-membered. Similar conformations for the cyclopropyl ketone substructure are observed for all the medium and large ring systems examined. Possible synthetic ramifications of local conformational anchoring by this functional group array are discussed.     

Substituted pyridines

5-Methyl-4-phenyl-2-styryipyridine has been oxidized to 5-methyl-4-phenylpyridinie-2-carboxylic acid. The decarboxylation of this acid has given 3-methyl-4-phenylpyrldine. To prove the structure of -(5-methyl-4-phenyl-2-pyridyl)acetophenone, it has been converted into 2, 5-dimethyl-4-phenylpyridine. The reaction of benzyl chloride with the lithium derivative of 2, 5-dimethyl-4-phenylpyridine has been studied. 3,7-Dimethyl-2-azafluorene has been obtained from 2,5-dimethyl-4-p-tolylpyridine.     

New routes to beta-cycloalkylalanine derivatives using serine-derived organozinc reagents

Two distinct routes to beta-cycloalkylalanine derivatives have been developed. The first route employs the reaction of the iodoalanine-derived zinc-copper reagent 2 with cycloalk-1-en-3-yl phosphates, and the second uses the palladium-catalysed coupling of the iodoalanine-derived zinc reagent 1 with cycloalkenyl triflates; in each case, catalytic hydrogenation of the unsaturated product leads to the protected beta-cycloalkylalanine. The latter route allows access to a range of cycloalkyl derivatives, with ring sizes of 5-8. beta-(1-Methyl-1-cyclohexyl)alanine may be prepared using reaction of the zinc-copper reagent 2 with 3-methyl-2-cyclohexenyl chloride, followed by hydrogenation. The corresponding cyclopentyl derivative may be prepared by reaction of the same zinc-copper reagent 2 with diethyl geranylphosphate, followed by ring-closing metathesis and hydrogenation.