Conjugated Proteins

The ubiquitin system remains elusive as a wide variety of post-translational modifications - including ubiquitylation with longer ubiquitin chains - are possible. Although the ubiquitin building block stays the same, different chain linkage types can result in different cellular processes. To understand the similarities and differences of these chains, a meticulous look at the intricate dynamics is absolutely necessary.

We perform molecular dynamics simulations of a variety of di-/tri- and tetra-ubiquitin chains using different resolution scales and bridge the gap between experimental studies and in silico methods by various cooperations.

Publications

Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers, A. Berg, O. Kukharenko, M. Scheffner, C. Peter, PLOS Comput. Biol., 14(11): e1006589, 2018. [doi]

Simulating and analysing configurational landscapes of protein–protein contact formation, A. Berg, C. Peter, Interface Focus 9 (3), 20180062, 2019. [doi]