We describe here the identification and characterization of two novel enzymes belonging to the IlvD/EDD protein family, the D-xylonate dehydratase from Caulobacter crescentus, Cc XyDHT, (EC 4.2.1.82), and the L-arabonate dehydratase from Rhizobium leguminosarum bv. trifolii, Rl ArDHT (EC 4.2.1.25), that produce the corresponding 2-keto-3-deoxy-sugar acids. There is only a very limited amount of characterization data available on pentonate dehydratases, even though the enzymes from these oxidative pathways have potential applications with plant biomass pentose sugars. The two bacterial enzymes share 41 % amino acid sequence identity and were expressed and purified from Escherichia coli as homotetrameric proteins. Both dehydratases were shown to accept pentonate and hexonate sugar acids as their substrates and require Mg(2+) for their activity. Cc XyDHT displayed the highest activity on D-xylonate and D-gluconate, while Rl ArDHT functioned best on D-fuconate, L-arabonate and D-galactonate. The configuration of the OH groups at C2 and C3 position of the sugar acid were shown to be critical, and the C4 configuration also contributed substantially to the substrate recognition. The two enzymes were also shown to contain an iron-sulphur [Fe-S] cluster. Our phylogenetic analysis and mutagenesis studies demonstrated that the three conserved cysteine residues in the aldonic acid dehydratase group of IlvD/EDD family members, those of C60, C128 and C201 in Cc XyDHT, and of C59, C127 and C200 in Rl ArDHT, are needed for coordination of the [Fe-S] cluster. The iron-sulphur cluster was shown to be crucial for the catalytic activity (kcat) but not for the substrate binding (Km) of the two pentonate dehydratases.
The bacteriophage 434 repressor regulates gene expression by binding with differing affinities to the six operator sites on the phage chromosome. The symmetrically arrayed outer eight base pairs (four in each half-site) of these 14-base-pair operators are highly conserved but the middle four bases are divergent. Although these four base pairs are not in contact with repressor, operators with A.T or T.A base pairs at these positions bind repressor more strongly than those bearing C.G or G.C, suggesting that these bases are important for the repressor's ability to discriminate between operators. There is evidence that the central base pairs influence operator function by constraining the twisting and/or bending of DNA. Here we show that there is a relationship between the intrinsic twist of an operator, as determined by the sequence of its central bases, and its affinity for repressor; an operator with a lower affinity is undertwisted relative to an operator with higher affinity. In complex with repressor, the twist of both high- and low-affinity operators is the same. These results indicate that the intrinsic twist of DNA and its twisting flexibility both affect the affinity of 434 operator for repressor.
We report on the synthesis, kinetics of proteolysis by trypsin, and morphological characterization of a novel lipidated decapeptide that spontaneously self-assembles in aqueous solutions into 0.5 μm diameter hollow tubules and helices that range in length from tens to hundreds of micrometers depending on formation conditions. We also report on an improved method for the tritioacetylation of peptides. Tight molecular packing of the peptide−amphiphile into a crystalline bilayer array forces tight packing between peptide headgroups, which was found to significantly protect the peptides from proteolysis by trypsin. Relief of this steric hindrance between peptide headgroups caused by solubilization of the bilayer into detergent micelles accelerated the rate of trypsin hydrolysis by 32,000-fold. Raman spectroscopy and circular dichroism spectropolarimetry were used to gain molecular-level insight into the difference between hydrolysis rates. Results obtained from these studies suggest that differences in molecular packing and conformation of the peptide headgroups in crystalline tubular and dispersed micellar phases determine the extent of proteolytic protection. Protection from proteolysis is considered a useful feature of lipidated peptide tubules for their potential use as a depot of bioactive peptides and other labile prodrugs at defined biological sites for sustained release.
The first study of enzymatic hydrolysis of phospholipid tubules is reported. Phosphatidylcholines with acyl chains containing diacetylene groups are known to form tubular microstructures in which the lipids are tightly packed and crystalline. These tubules can be used to probe the role of microstructural form in the mechanics of interfacial enzymatic degradation by such enzymes as phospholipase A2 (PLA2). Hydrolysis by PLA2 may occur most rapidly in regions having the greatest number of bilayer packing defects, such as those that must be found at tubule ends. A microstructure that degrades primarily from its ends should exhibit zero-order kinetics, because the area of the degrading tubule and remains constant as the length of the microstructure decreases. Free fatty acid concentration was measured to follow the generation of PLA2 hydrolysis products in suspensions of diacetylenic phospholipid tubules. The kinetics of tubule hydrolysis were essentially zero-order until conversion was complete, as predicted. However, microscopy of partially hydrolyzed tubules revealed the formation of multiple discrete anionic product domains along the length of degrading tubules as well as in insoluble reaction product microstructures. Furthermore, the rate of tubule hydrolysis was only moderately enhanced by increasing the number of tubule ends, which is consistent with the conclusion that tubule ends are not the only sites of hydrolysis. A model that reconciles the overall kinetics with the morphological evidence is proposed.
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