A unique region in bacteriophage t7 DNA polymerase important for exonucleolytic hydrolysis of DNA.

A crystal structure of the bacteriophage T7 gene 5 protein/Escherichia coli thioredoxin complex reveals a region in the exonuclease domain (residues 144-157) that is not present in other members of the E. coli DNA polymerase I family. To examine the role of this region, a genetically altered enzyme that lacked residues 144-157 (T7 polymerase (pol) Delta144-157) was purified and characterized biochemically. The polymerase activity and processivity of T7 pol Delta144-157 on primed M13 DNA are similar to that of wild-type T7 DNA polymerase implying that these residues are not important for DNA synthesis. The ability of T7 pol Delta144-157 to catalyze the hydrolysis of a phosphodiester bond, as judged from the rate of hydrolysis of a p-nitrophenyl ester of thymidine monophosphate, also remains unaffected. However, the 3'-5' exonuclease activity on polynucleotide substrates is drastically reduced; exonuclease activity on single-stranded DNA is 10-fold lower and that on double-stranded DNA is 20-fold lower as compared with wild-type T7 DNA polymerase. Taken together, our results suggest that residues 144-157 of gene 5 protein, although not crucial for polymerase activity, are important for DNA binding during hydrolysis of polynucleotides.

Proteomic analysis of thioredoxin-targeted proteins in Escherichia coli.

Thioredoxin, a ubiquitous and evolutionarily conserved protein, modulates the structure and activity of proteins involved in a spectrum of processes, such as gene expression, apoptosis, and the oxidative stress response. Here, we present a comprehensive analysis of the thioredoxin-linked Escherichia coli proteome by using tandem affinity purification and nanospray microcapillary tandem mass spectrometry. We have identified a total of 80 proteins associated with thioredoxin, implicating the involvement of thioredoxin in at least 26 distinct cellular processes that include transcription regulation, cell division, energy transduction, and several biosynthetic pathways. We also found a number of proteins associated with thioredoxin that either participate directly (SodA, HPI, and AhpC) or have key regulatory functions (Fur and AcnB) in the detoxification of the cell. Transcription factors NusG, OmpR, and RcsB, not considered to be under redox control, are also associated with thioredoxin.

Proximity effects in monolayer films: kinetic analysis of amide bond formation at the air-water interface using (1)H NMR spectroscopy.

The kinetics of amide bond formation in a monolayer film has been studied by proton NMR spectroscopy. Compression of a hexadecyl thioester of N-acetyl glycine (1) and a hexadecyl amide of glycine (2) at the air-water interface produces a single dipeptide product (4) that remains at the surface once formed. Extraction of the reaction mixture from the interface, followed by (1)H NMR spectroscopy, provides quantitative data on the rate of product formation. The kinetics of this reaction was examined as a function of surface pressure, subphase pH, and temperature. The monolayer provides an effective molarity for the reaction of approximately 500 M as compared to the bimolecular reaction of 1 and 4 in chloroform solution. The first-order rate constant for the reaction of 1 and 2 in the monolayer is less than 70-fold slower than k(cat) for condensation of the first amide bond in the enzymatic synthesis of the cyclic antibiotic gramicidin S by gramicidin S synthetase. Activation energies of the reaction were extracted from the temperature dependence of the rate constants of the reaction and are 9.9 +/- 1.0 and 2.1 +/- 0.2 kcal/mol for the chloroform solution and monolayer reactions, respectively. The pK(a) of 2 in the monolayer was estimated to be approximately 0.5 pK(a) units lower than that of related amines in solution. The lower pK(a) at the interface as compared to that in solution may be ascribed to increased electrostatic repulsion at the interface relative to solution. The rate of reaction in the monolayer was also followed by monitoring changes in surface area as a function of time. The rate constant for the reaction of 1 and 4 as determined by changes in surface area differs significantly from the rate determined by NMR. The results indicate that measurements of surface area versus time may yield erroneous rate constants for reactions in monolayers.