Life Sciences

Principal Investigator: Christine Peter , Computational and Theoretical Chemistry, University of Konstanz

HPC Platform used: JUWELS of JSC

Local Project ID: chkn01

The conformations of ubiquitin chains are crucial for the so-called ubiquitin code, i.e. the selective signaling of ubiquitylated proteins for different fates in the eukaryotic cellular system. Extensive molecular dynamics simulations at two resolution levels were carried out for ubiquitin di-, tri- and tetramers of all possible linkage types. Analyzing the resulting, exceedingly large high-dimensional data sets was made possible by combining highly efficient neural network based dimensionality reduction with density based clustering and a metric to compare conformational spaces. The so obtained conformational characteristics of ubiquitin chains could be correlated with linkage-type and chain-length dependent experimental observations.