No abstract

A new optical sensor based on covalent immobilization of a newly synthesized calcium-selective, long-wavelength, fluorescent indicator has been constructed, with a response dynamic range optimal for physiological measurements. Immobilization occurs via photoinitiated copolymerization of the indicator with acrylamide on the distal end of a silanized 125 micrograms diameter multimode optical fiber. The working lifetime of this sensor is limited only by photobleaching of the indicator. Due to the inherent hydrophilic nature of the acrylamide polymer, the response time of this new sensor is governed by simple aqueous diffusion of the ionic calcium. This results in sensor response times fast enough to monitor some concentration fluctuations at physiological rates. The ability to monitor calcium concentration fluctuations in a high background level of magnesium is also demonstrated with a calculated selectivity of 10(-4.5).

Correct identification of protein post-translational modifications (PTMs) is crucial to understanding many aspects of protein function in biological processes. G-PTM-D is a recently developed technique for global identification and localization of PTMs. Spectral file calibration prior to applying G-PTM-D, and algorithmic enhancements in the peptide database search significantly increase the accuracy, speed, and scope of PTM identification. We enhance G-PTM-D by using multinotch searches and demonstrate its effectiveness in identification of numerous types of PTMs including high-mass modifications such as glycosylations. The changes described in this work lead to a 20% increase in the number of identified modifications and an order of magnitude decrease in search time. The complete workflow is implemented in MetaMorpheus, a software tool that integrates the database search procedure, identification of coisolated peptides, spectral calibration, and the enhanced G-PTM-D workflow. Multinotch searches are also shown to be useful in contexts other than G-PTM-D by producing superior results when used instead of standard narrow-window and open database searches.

We have studied the dynamics of directed, multistep energy transport in a class of fractal-like dendrimeric molecules. For particular forms of these highly branched phenylacetylene dendrimers, both theory and experiment put the lowest excitation energy at the center (locus) of the supermolecule. This results in a structurally symmetric and ordered exciton funnel, with a well-directed energy gradient. We have designed and synthesized a derivative of these dendrimers with a perylene moiety at the locus, which acts as an energy trap for the directed exciton funnel. Spectroscopic evidence indicates transfer efficiency of 98% from the photoabsorbing dendrimer backbone to the perylenic trap.

Summary Emerging evidence suggests that protein acetylation is a broad-ranging regulatory mechanism. Here we utilize acetyl-peptide arrays and metabolomic analyses to identify substrates of mitochondrial deacetylase Sirt3. We identified ornithine transcarbamoylase (OTC) from the urea cycle, and enzymes involved in β-oxidation. Metabolomic analyses of fasted mice lacking Sirt3 (sirt3−/−) revealed alterations in β-oxidation and the urea cycle. Biochemical analysis demonstrated that Sirt3 directly deacetylates OTC and stimulates its activity. Mice under caloric restriction (CR) increased Sirt3 protein levels, leading to deacetylation and stimulation of OTC activity. In contrast, sirt3−/− mice failed to deacetylate OTC in response to CR. Inability to stimulate OTC under CR led to a failure to reduce orotic acid levels, a known outcome of OTC deficiency. Thus, Sirt3 directly regulates OTC activity and promotes the urea cycle during CR, and the results suggest that under low energy input, Sirt3 modulates mitochondria by promoting amino-acid catabolism and β-oxidation.