ENKIE: a package for predicting enzyme kinetic parameter values and their uncertainties.

Motivation: Relating metabolite and enzyme abundances to metabolic fluxes requires reaction kinetics, core elements of dynamic and enzyme cost models. However, kinetic parameters have been measured only for a fraction of all known enzymes, and the reliability of the available values is unknown.

Results: The ENzyme KInetics Estimator (ENKIE) uses Bayesian Multilevel Models to predict value and uncertainty of KM and kcat parameters.

Critical Protein-Protein Interactions Determine the Biological Activity of Elk-1, a Master Regulator of Stimulus-Induced Gene Transcription.

Elk-1 is a transcription factor that binds together with a dimer of the serum response factor (SRF) to the serum-response element (SRE), a genetic element that connects cellular stimulation with gene transcription. Elk-1 plays an important role in the regulation of cellular proliferation and apoptosis, thymocyte development, glucose homeostasis and brain function. The biological function of Elk-1 relies essentially on the interaction with other proteins.

Regulation and function of AP-1 in insulinoma cells and pancreatic β-cells.

Ca1.2 L-type voltage-gated Ca channels play a central role in pancreatic β-cells by integrating extracellular signals with intracellular signaling events leading to insulin secretion and altered gene transcription. Here, we investigated the intracellular signaling pathway following stimulation of Ca1.

Chromatin-embedded reporter genes: Quantification of stimulus-induced gene transcription.

Receptors and ion channels expressed on the cell surface ensure proper communication between the cells and the environment. In multicellular organism, stimulus-regulated gene transcription is the basis for communication with the environment allowing individual cells to respond to stimuli such as nutrients, chemical stressors and signaling molecules released by other cells of the organism. Hormones, cytokines, and mitogens bind to receptors and ion channels and induce intracellular signaling cascades involving second messengers, kinases, phosphatases, and changes in the concentration of particular ions.

Zn ions inhibit gene transcription following stimulation of the Ca channels Ca1.2 and TRPM3.

Zinc, a trace element, is necessary for the correct structure and function of many proteins. Therefore, Zn has to be taken up by the cells, using specific Zn transporters or Ca channels. In this study, we have focused on two Ca channels, the L-type voltage-gated Ca1.