Escherichia coli Peptide Binding Protein OppA Has a Preference for Positively Charged Peptides

The identification of oppA gene homologues as part of the oligopeptide transport system in mycoplasmas

The lack of an annotated oppA gene as part of many oligopeptide permease (opp) operons has questioned the necessity of the oligopeptide-binding domain (OppA) as a part of the Opp transport system in mycoplasmas. This study investigated the occurrence of an oppA gene as part of the oppBCDF operon in 42 mycoplasma genomes. Except for hemoplasma, all mycoplasmas were found to possess one or more copies of the oppBCDF operon and with the help of similarity searches their oppA genes could be identified. Phylogenetic analysis of the combined OppABCDF amino acid sequences allowed them to be grouped into three types. Each type has a unique set of conserved motifs, which are likely to reflect substrate preference and adaption strategies. Our approach allowed the identification of oppA gene homologues for all mycoplasma opp operons and thereby provides a method for re-evaluating the current annotation of oppA genes in mycoplasma genomes.

A Systematic Study of the Catalytic Behavior at Enzyme–Metal-Oxide Nanointerfaces

Metal-oxide nanoparticles with high surface area, controllable functionality and thermal and mechanical stability provide high affinity for enzymes when the next generation of biosensor applications are being considered. We report on the synthesis of metal-oxide-based nanoparticles (with different physical and chemical properties) using hydrothermal processing, photo-deposition and silane functionalization. Physical and chemical properties of the user-synthesized nanoparticles were investigated using scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), and Raman scattering, respectively. Thus, characterized metal-oxide-based nanoparticles served as nanosupports for the immobilization of soybean peroxidase enzyme (a model enzyme) through physical binding. The enzyme–nanosupport interface was evaluated to assess the optimum nanosupport characteristics that preserve enzyme functionality and its catalytic behavior. Our results showed that both the nanosupport geometry and its charge influence the functionality and catalytic behavior of the bio-metal-oxide hybrid system.

Structure and mode of peptide binding of pheromone receptor PrgZ

We present the crystal structure of the pheromone receptor protein PrgZ from Enterococcus faecalis in complex with the heptapeptide cCF10 (LVTLVFV), which is used in signaling between conjugative recipient and donor cells. Comparison of PrgZ with homologous oligopeptide-binding proteins (AppA and OppA) explains the high specificity of PrgZ for hydrophobic heptapeptides versus the promiscuity of peptide binding in the homologous proteins.

Purification and crystallization of the ABC-type transport substrate-binding protein OppA from Thermoanaerobacter tengcongensis

Di- and oligopeptide- binding protein OppAs play important roles in solute and nutrient uptake, sporulation, biofilm formation, cell wall muropeptides recycling, peptide-dependent quorum-sensing responses, adherence to host cells, and a variety of other biological processes. Soluble OppA from Thermoanaerobacter tengcongensis was expressed in Escherichia coli. The protein was found to be >95% pure with SDS-PAGE after a series of purification steps and the purity was further verified by mass spectrometry. The protein was crystallized using the sitting-drop vapour-diffusion method with PEG 400 as the precipitant. Crystal diffraction extended to 2.25 Å. The crystal belonged to space group C222(1), with unit-cell parameters of a=69.395, b=199.572, c=131.673 Å, and α=β=γ=90°.