Experimental supporting data on DIS3L2 over nonsense-mediated mRNA decay targets in human cells.

In this article, we present supportive data related to the research article "A role for DIS3L2 over natural nonsense-mediated mRNA decay targets in human cells" [1], where interpretation of the data presented here is available. Indeed, here we analyze the impact of the DIS3L2 exoribonuclease over nonsense-mediated mRNA decay (NMD)-targets. Specifically, we present data on: a) the expression of various reporter human β-globin mRNAs, monitored by Northern blot and RT-qPCR, before and after altering DIS3L2 levels in HeLa cells, and b) the gene expression levels of deregulated transcripts generated by re-analyzing publicly available data from UPF1-depleted HeLa cells that were further cross-referenced with a dataset of transcripts upregulated in DIS3L2-depleted cells.

Constant-pH MD Simulations of DMPA/DMPC Lipid Bilayers.

Current constant-pH molecular dynamics (CpHMD) simulations provide a proper treatment of pH effects on the structure and dynamics of soluble biomolecules like peptides and proteins. However, addressing such effects on lipid membrane assemblies has remained problematic until now, despite the important role played by lipid ionization at physiological pH in a plethora of biological processes. Modeling (de)protonation events in these systems requires a proper consideration of the physicochemical features of the membrane environment, including a sound treatment of solution ions.

Treatment of Ionic Strength in Biomolecular Simulations of Charged Lipid Bilayers.

Biological membranes are complex systems that have recently attracted a significant scientific interest. Due to the presence of many different anionic lipids, these membranes are usually negatively charged and sensitive to pH. The protonation states of lipids and the ion distribution close to the bilayer are two of the main challenges in biomolecular simulations of these systems.

Conformational study of GSH and GSSG using constant-pH molecular dynamics simulations.

Glutathione is a small peptide with a crucial role in living organisms. This molecule is found in Nature in both reduced (GSH) and oxidized (GSSG) forms and a high GSH/GSSG ratio is essential to the cell. Glutathione is also present in several enzymatic reactions and can be found in many protein structures.