Experimental and Theoretical Electron Paramagnetic Resonance (EPR) Study on the Temperature-Dependent Structural Changes of Methylsulfanylmethane

Methylsulfonylmethane (or dimethyl sulfone), a naturally produced and vitally important organosulfur compound in living organisms, was irradiated with gamma rays, and the produced radicals were investigated using electron paramagnetic resonance spectroscopy at different temperatures. The structure and behavior of the radical changed when the temperatures varied. The hyperfine splitting of the CH3 group was small, and the 33S splitting was relatively high between 80 and −50 °C. When the temperature was between −50 and −160 °C, the 33S splitting became small and the CH3 splitting was higher. However, the group kept rotating; therefore, only the isotropic splitting values were measured, and the g-values were anisotropic. When the temperature decreased below −180 °C, the CH3 group stopped rotating, and the hydrogen splitting values became nonequivalent due to an inhomogeneous electron distribution. The observed structures can be explained by referring to both the experimental and theoretically calculated values reported

Assessing Computational Methods of Cis-Regulatory Module Prediction

Computational methods attempting to identify instances of cis-regulatory modules (CRMs) in the genome face a challenging problem of searching for potentially interacting transcription factor binding sites while knowledge of the specific interactions involved remains limited. Without a comprehensive comparison of their performance, the reliability and accuracy of these tools remains unclear. Faced with a large number of different tools that address this problem, we summarized and categorized them based on search strategy and input data requirements. Twelve representative methods were chosen and applied to predict CRMs from the Drosophila CRM database REDfly, and across the human ENCODE regions. Our results show that the optimal choice of method varies depending on species and composition of the sequences in question. When discriminating CRMs from non-coding regions, those methods considering evolutionary conservation have a stronger predictive power than methods designed to be run on a single genome. Different CRM representations and search strategies rely on different CRM properties, and different methods can complement one another. For example, some favour homotypical clusters of binding sites, while others perform best on short CRMs. Furthermore, most methods appear to be sensitive to the composition and structure of the genome to which they are applied. We analyze the principal features that distinguish the methods that performed well, identify weaknesses leading to poor performance, and provide a guide for users. We also propose key considerations for the development and evaluation of future CRM-prediction methods

A lipoprotein lipase --GPI-anchored high density lipoprotein binding protein 1 fusion lowers triglycerides in mice: implications for managing familial chylomicronemia syndrome

Lipoprotein lipase (LPL) is central to triglyceride metabolism. Severely compromised LPL activity causes familial chylomicronemia syndrome (FCS), which is associated with very high plasma triglyceride levels and increased risk of life-threatening pancreatitis. Currently, no approved pharmacological intervention can acutely lower plasma triglycerides in FCS. Low yield, high aggregation, and poor stability of recombinant LPL have thus far prevented development of enzyme replacement therapy. Recently, we showed that LPL monomers form 1:1 complexes with the LPL transporter glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 (GPIHBP1) and solved the structure of the complex. In the present work, we further characterized the monomeric LPL/GPIHBP1 complex, and its derivative, the LPL-GPIHBP1 fusion protein, with the goal of contributing to the development of an LPL enzyme replacement therapy. Fusion of LPL to GPIHBP1 increased yields of recombinant LPL, prevented LPL aggregation, stabilized LPL against spontaneous inactivation, and made it resistant to inactivation by the LPL antagonists angiopoietin-like protein 3(ANGPTL3) or ANGPTL4. The high stability of the fusion protein enabled us to identify LPL amino acids that interact with ANGPTL4. Additionally, the LPL-GPIHBP1 fusion protein exibited high enzyme activity in in vitro assays. Importantly, both intravenous and subcutaneous administrations of the fusion protein lowered triglycerides in several mouse strains without causing adverse effects. These results indicate that the LPL-GPIHBP1 fusion protein has potential for use as a therapeutic for managing FC