Project description:Analysis of genes and biological processes influenced by Neuronal calcium sensor 1 (NCS1) based on whole transcriptome analyiss of Ncs1+/+ (wildtype) and Ncs1-/- (knockout) mouse brain tissues, i.d. the frontal cortex and the hippocampus.
Project description:This project investigates the conformational dynamics of the ASK1(269-658) protein fragment and the structural changes induced by its interaction with the small molecule H43. Using hydrogen-deuterium exchange mass spectrometry (HDX-MS), we compared the deuterium uptake profiles of apo ASK1(269-658) and its complex with H43. Samples were prepared with different exchange times (30, 90, 600, and 1800 seconds) in D₂O buffer, quenched, enzymatically digested with immobilized pepsin, and analyzed by LC-MS on a Thermo Orbitrap QE mass spectrometer. Peptide identification was performed using PEAKS Online, and HDX data analysis was conducted with HDExaminer software. The results provide insights into dynamic regions within ASK1(269-658) and reveal ligand-induced conformational changes.
Project description:Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful protein footprinting technique to study protein dynamics and binding; however, HDX-MS data analysis is often challenging and time consuming. Moreover, the HDX community is expanding to investigate multi-protein and highly complex protein systems such as cell lysates which further complicates data analysis. Thus, a simple and easy-to-use open source software package designed to analyze large and highly complex protein systems is needed. In this vein, we have developed The Deuterium Calculator, a Python-based software package for HDX-MS data analysis. The Deuterium Calculator is capable of differential and nondifferential HDX-MS analysis, produces standardized data files according to the recommendations put forth by the International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX) to increase transparency in data analysis, and generates Woods’ plots for statistical analysis and data visualization. This standard output can be used to perform further analysis on HDX such as determination of labeling time dependent deuteration and for the study of protein folding kinetics or differential uptake. Moreover, the Deuterium Calculator is capable of analyzing large HDX-MS datasets (e.g., LC-HDX-MS from complex samples such as cell lysates) to determine the extent of deuteration on individual peptides from numerous proteins, perform differential analysis under varying experimental conditions, and time-dependent deuterium exchange. The Deuterium Calculator is freely available for download at https://github.com/OUWuLab/TheDeuteriumCalculator.git.