Outer membrane protein OmpF involved in the transportation of polypyridyl ruthenium complexes into Escherichia coli

Alkyne Functionalization of a Photoactivated Ruthenium Polypyridyl Complex for Click-Enabled Serum Albumin Interaction Studies

Studying metal-protein interactions is key for understanding the fate of metallodrugs in biological systems. When a metal complex is not emissive and too weakly bound for mass spectrometry analysis, however, it may become challenging to study such interactions. In this work a synthetic procedure was developed for the alkyne functionalization of a photolabile ruthenium polypyridyl complex, [Ru(tpy)(bpy)(Hmte)](PF₆)₂, where tpy = 2,2′:6′,2′′-terpyridine, bpy = 2,2′-bipyridine, and Hmte = 2-(methylthio)ethanol. In the functionalized complex [Ru(HCC-tpy)(bpy)(Hmte)](PF₆)₂, where HCC-tpy = 4′-ethynyl-2,2′:6′,2′′-terpyridine, the alkyne group can be used for bioorthogonal ligation to an azide-labeled fluorophore using copper-catalyzed “click” chemistry. We developed a gel-based click chemistry method to study the interaction between this ruthenium complex and bovine serum albumin (BSA). Our results demonstrate that visualization of the interaction between the metal complex and the protein is possible, even when this interaction is too weak to be studied by conventional means such as UV–vis spectroscopy or ESI mass spectrometry. In addition, the weak metal complex-protein interaction is controlled by visible light irradiation, i.e., the complex and the protein do not interact in the dark, but they do interact via weak van der Waals interactions after light activation of the complex, which triggers photosubstitution of the Hmte ligand.

A “clickable” and photosubstitutionally active ruthenium complex has been prepared that bears a terminal alkyne group. In the dark, the saturated coordination sphere of the complex prevents it from interacting with serum albumin. Upon photosubstitution of one ligand, the complex interacts with the protein via weak interactions that were visualized using copper-catalyzed “click” chemistry postfunctionalization with an azide fluorophore on polyacrylamide gel electrophoresis. These studies demonstrate that the metal-protein interaction is triggered by light irradiation.

In silico identification of vaccine candidates against Klebsiella oxytoca

Klebsiella oxytoca causes several diseases in immunocompromised as well as healthy individuals. Increasing resistance to a number of antibiotics makes treatment options limited. Prevention using vaccine could be an important solution to get rid of infections caused by Klebsiella oxytoca. In recent time, genome based approaches have contributed significantly in vaccine development. Our aim was to identify the most conserved and immunogenic antigens that can be considered as potential vaccine candidates. KEGG database was used to find out pathways unique to the bacteria. Subcellular localization of the protein sequences taken from the selected 36 pathways were predicted using PSORTb v3.0.2 and CELLO v2.5. Prediction of B cell epitope and the probability of the antigenicity were evaluated by using IEDB and Vaxijen respectively. BLASTp was done to find out the similarity of the selected proteins with the human proteome. Proteins failing to comply with the set parameters were filtered at each step. Finally, we identified 6 surface exposed proteins as potential vaccine candidates against Klebsiella oxytoca.

Inductive properties of polypyridyl ruthenium complexes significantly regulate various protein distributions in Escherichia coli

Ruthenium complexes with similar octahedral structures but different intrinsic inductive properties significantly influence the total cellular protein distributions, which may affect different metabolic pathways. A systematic study of the relationship between ruthenium complexes and Escherichia coli was undertaken, using two-dimensional gel electrophoresis analysis and the identification of various proteins by mass data mining. Based on the low similarities (<40%) between the total protein distributions, the inductive properties of the ruthenium complexes are relevant to the formation of the protein-Ru interaction in addition to the Ru-DNA interaction. Two major protein functions in E. coli BL21 that were reduced by compound 1 were oxidoreductases and transporters, corresponding to 29% and 25% of the 24 down-regulated proteins. The main biological processes of the proteins down-regulated by compound 1 were related to carbohydrate reactions, including in transport, tricarboxylic acid (TCA) cycle, glycolysis, and gluconeogenesis. All four ruthenium complexes shared similar up-regulated proteins, including clpB and kpyk1, and down-regulated similar proteins, including ompA and ybbN. This result supports that the presence of Ru-protein interactions is a major factor affecting bacteria growth, and particularly transport and carbohydrate-related reactions.