Current challenges in software solutions for mass spectrometry-based quantitative proteomics

This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.

A Chemical Genetic Screen for Modulators of Asymmetrical 2,2′-Dimeric Naphthoquinones Cytotoxicity in Yeast

BACKGROUND: Dimeric naphthoquinones (BiQ) were originally synthesized as a new class of HIV integrase inhibitors but have shown integrase-independent cytotoxicity in acute lymphoblastic leukemia cell lines suggesting their use as potential anti-neoplastic agents. The mechanism of this cytotoxicity is unknown. In order to gain insight into the mode of action of binaphthoquinones we performed a systematic high-throughput screen in a yeast isogenic deletion mutant array for enhanced or suppressed growth in the presence of binaphthoquinones. METHODOLOGY/PRINCIPAL FINDINGS: Exposure of wild type yeast strains to various BiQs demonstrated inhibition of yeast growth with IC(50)s in the microM range. Drug sensitivity and resistance screens were performed by exposing arrays of a haploid yeast deletion mutant library to BiQs at concentrations near their IC(50). Sensitivity screens identified yeast with deletions affecting mitochondrial function and cellular respiration as having increased sensitivity to BiQs. Corresponding to this, wild type yeast grown in the absence of a fermentable carbon source were particularly sensitive to BiQs, and treatment with BiQs was shown to disrupt the mitochondrial membrane potential and lead to the generation of reactive oxygen species (ROS). Furthermore, baseline ROS production in BiQ sensitive mutant strains was increased compared to wild type and could be further augmented by the presence of BiQ. Screens for resistance to BiQ action identified the mitochondrial external NAD(P)H dehydrogenase, NDE1, as critical to BiQ toxicity and over-expression of this gene resulted in increased ROS production and increased sensitivity of wild type yeast to BiQ. CONCLUSIONS/SIGNIFICANCE: In yeast, binaphthoquinone cytotoxicity is likely mediated through NAD(P)H:quonine oxidoreductases leading to ROS production and dysfunctional mitochondria. Further studies are required to validate this mechanism in mammalian cells

Comparison of CC triple and double bonds as spacers in push-pull chromophores

We report the synthesis and properties of two series of homologous donor–acceptor (D–A) chromophores in which N,N-dimethylanilino (DMA) or N,N-dihexylanilino (DHA) donors and dicyanovinyl acceptors are separated by up to four C≡C triple-bond spacers or up to three C=C double-bond spacers. The intramolecular charge-transfer (CT) interactions of the new D–A oligoynes and the known all-trans D–A oligoenes were investigated by X-ray crystallography, electrochemistry, UV/Vis spectroscopy, and theoretical calculations. In both series, the optical and electrochemical HOMO–LUMO gaps decrease with increasing spacer length. The HOMO–LUMO gaps for the D–A oligoynes and oligoenes with a given spacer length are nearly identical. The effect of the spacer length was found to level-off for spacers with more than six carbon atoms. The third-order optical nonlinearity of both series of molecules was determined by measuring the rotational averages of the third-order polarizabilities rot by degenerate four-wave mixing

Comparison of CC triple and double bonds as spacers in push-pull chromophores

We report the synthesis and properties of two series of homologous donor–acceptor (D–A) chromophores in which N,N-dimethylanilino (DMA) or N,N-dihexylanilino (DHA) donors and dicyanovinyl acceptors are separated by up to four C≡C triple-bond spacers or up to three C=C double-bond spacers. The intramolecular charge-transfer (CT) interactions of the new D–A oligoynes and the known all-trans D–A oligoenes were investigated by X-ray crystallography, electrochemistry, UV/Vis spectroscopy, and theoretical calculations. In both series, the optical and electrochemical HOMO–LUMO gaps decrease with increasing spacer length. The HOMO–LUMO gaps for the D–A oligoynes and oligoenes with a given spacer length are nearly identical. The effect of the spacer length was found to level-off for spacers with more than six carbon atoms. The third-order optical nonlinearity of both series of molecules was determined by measuring the rotational averages of the third-order polarizabilities rot by degenerate four-wave mixing