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Summary Mesothelioma is a cancer that typically originates in the pleura of the lungs. It rapidly invades the surrounding tissues, causing pain and shortness of breath. We compared cell lines injected either subcutaneously or intrapleurally and found that only the latter resulted in invasive and rapid growth. Pleural tumors displayed a transcriptional signature consistent with increased activity of nuclear receptors PPARα and PPARγ and with an increased abundance of endogenous PPAR-activating ligands. We found that chemical probe GW6471 is a potent, dual PPARα/γ antagonist with anti-invasive and anti-proliferative activity in vitro. However, administration of GW6471 at doses that provided sustained plasma exposure levels sufficient for inhibition of PPARα/γ transcriptional activity did not result in significant anti-mesothelioma activity in mice. Lastly, we demonstrate that the in vitro anti-tumor effect of GW6471 is off-target. We conclude that dual PPARα/γ antagonism alone is not a viable treatment modality for mesothelioma., Graphical abstract, Highlights • Pleural location stimulates mesothelioma invasion and proliferation • PPARα and PPARγ activation is associated with pleural mesothelioma invasion • Chemical probe GW6471 is a potent PPARα/γ antagonist in vitro • Dual inhibition of PPARα/γ does not have anti-mesothelioma activity in vivo, Biological sciences; Metabolomics; Transcriptomics

Flavoenzymes comprise a large class of proteins that carry out a diverse range of important redox chemistry. Although X-ray crystal structures of many flavoenzymes have been determined, there are still unresolved questions regarding the actual oxidation state of the flavin cofactors in these structures due to photoreduction by the ionizing radiation of the X-ray beam during the diffraction experiment. Additionally, the ability to visualize hydrogen atoms in X-ray structures is difficult due to the weak scattering capability of these atoms. Since hydrogen atoms affect the electrostatic nature of enzyme active sites and play important roles in the chemistry of key amino acid residues, visualizing the precise positions of these atoms provides a more detailed understanding of their role in enzyme catalysis. Single crystal neutron diffraction is an alternative method to structure determination, circumventing problems associated with photoreduction of the sample thus providing a clearer view of the structural features of a flavoenzyme in different redox states. Additionally, the larger neutron scattering factors for hydrogen and deuterium atoms enables one to visualize these atoms much more easily than from X-ray scattering measurements. In this chapter we give an overview of neutron and X-ray crystallography studies on the flavoenzyme, cholesterol oxidase and how the observations of unusual hydrogen atom positions provide insight into the redox chemistry of the flavin cofactor.

Summary The application of protein crystallography and two-dimensional NMR to study proteins which interact with DNA has provided detailed information about protein-DNA recognition and specificity. Numerous structural motifs have evolved to allow a diverse variety of interactions between proteins and DNA. These include motifs such as the helix-turn-helix, zinc finger, basic region leucine zipper, and ribbon-helix-helix, some of which are found in both prokaryotes and eukaryotes. DNA recognition is usually achieved through specific protein amino acid-DNA base pair interactions which can be mediated via water molecules, in either the major or minor grooves of the DNA. However, interactions between protein side chains and the phosphodiester backbone is a common feature of non-sequence-specific protein-DNA recognition. The flexibility and existence of DNA in a number of different conformations contributes significantly to the overall process of protein-DNA recognition. The enormous variety of protein structures and motifs which can interact with DNA probably reflects the diversity of biological function which requires the formation of protein-DNA complexes.