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.     

Contribution to the certification of B,Cd, Cu,Mg and Pb in a synthetic water sample,by use of isotope-dilution ICP-MS,for Comparison 12 of the International Measurement Evaluation Programme

The contribution of the Institute for Reference Materials and Measurements to the certification of the B, Cd, Cu, Mg, and Pb content of a synthetic water sample used in Comparison 12 of the International Measurement Evaluation Programme (IMEP-12) is described. The aim of the IMEP programme is to demonstrate objectively the degree of equivalence and quality of chemical measurements of individual laboratories on the international scene by comparing them with reference ranges traceable to the SI (Système International d'Unités). IMEP is organized in support of European Union policies and helps to improve the traceability of values produced by field chemical measurement laboratories. The analytical procedure used to establish the reference values for the B, Cd, Cu, Mg, and Pb content of the IMEP-12 sample is based on inductively coupled plasma-isotope-dilution mass spectrometry (ICP-IDMS) applied as a primary method of measurement. The measurements performed for the IMEP-12 study are described in detail. Focus is on the element boron, which is particularly difficult to analyze by ICP-MS because of potential problems of low sensitivity, high mass discrimination, memory effects, and abundance sensitivity. For each of the certified amount contents presented here a total uncertainty budget was calculated using the method of propagation of uncertainties according to ISO (International Organization for Standardization) and Eurachem guidelines. For all investigated elements with concentrations in the low micro g kg(-1) and mg kg(-1) range (corresponding to pmol kg(-1) to the high micro mol kg(-1) level), SI-traceable reference values with relative expanded uncertainties ( k=2) of less than 2 % were obtained.     

Molecular dynamics study of gas hydrate formation

Long-time-scale molecular dynamics simulations are presented of the spontaneous formation of methane hydrate at a methane/liquid water interface. The water film was prepared at 300 K, 30 bar and showed no significant hydrate order. On crash cooling to 250 K, 300 bar (about 20 K subcooling), the system showed a rapid growth of hydrate clusters. Contrary to popular models for hydrate nucleation, the clusters formed first as two-dimensional arrangements and only later into three-dimensional cage structures; the results are, however, consistent with the local order model proposed recently. The hydrate clusters showed clear signatures of the type II hydrate structure even though the type I structure is the thermodynamically stable form for methane hydrate; this is in accord with the results of recent diffraction experiments.     

Determination of the intrinsic site pK(a) value and cooperativity of the symmetrical hexadentate chelator N,N',N'-tris[2-(3-hydroxy-2-oxo-1,2-dihydropyridin-1-yl)acetamido]ethylamine

The three overlapping pK(a) values of N,N',N'-tris[2-(3-hydroxy-2-oxo-1,2-dihydropyridin-1-yl)acetamido]ethylamine, a tripodal hexadentate chelator formed from three 3-hydroxy-2(1H)-pyridinone moieties amide linked to tris-(2-aminoethyl)amine, were determined by simultaneous spectrophotometric and potentiometric titration. The data was analysed by non-linear regression with constraints to deal with (a) the highly correlated absorptivities and (b) the highly correlated pK(a) values. The three pK(a) values were optimized first from the spectrophotometric data (absorbance vs. pH) by non-linear regression to a model in which the molar absorptivity of the ith species ((i)) was constrained by the correlation equation (i) = epsilon (0) + (epsilon (3) - epsilon (0))i 3 with i = 0, 1, 2, 3, where (3) and (0) represent the molar absorptivities of the most protonated and least protonated species, respectively. The molar absorbitivity of the four species defined by three pK(a) values is, therefore, linearly related to proton stoichiometry. The pK(a) values were then optimized from the potentiometric data (pH vs. titrant volume) by non-linear regression to a model in which the three pK(a) values were constrained by the correlation equation pK(a(i)) = pK(a(int)) + b(i - 1) + (i - 2)log(3) where i = 1, 2 or 3. This expresses the three pK(a) values in terms of only two optimizable parameters, the intrinsic site pK(a) (pK(a(int))) and the interaction energy between sites (b). The fixed term (i - 2)log(3) accounts for the statistical effect on the pK(a) values of three equivalent ionizable sites. The modified analytical derivatives required for optimization of these parameters by the Gauss-Newton-Marquardt algorithm and the merits of optimizing pK(a) values with these two correlation equations are discussed. The optimized pK(a) values were 9.31 +/- 0.01, 8.75 +/- 0.01 and 8.19 +/- 0.01. The separation between pK(a) values is 0.58 comprising 0.477 for the statistical effect and 0.081 for the interaction energy while the intrinsic site pK(a) is 8.672 +/- 0.005. The tertiary amine at the centre of the tripodal backbone has a pK(a) of 5.88 +/- 0.03.