Ubiquitin

The ubiquitin system is involved in a variety of eukariotic cellular processes. It includes ubiquitilation as a post translational modification where substrate proteins are decorated with a single ubiquitin but also with chains containing several of these proteins. Different capabilities of linkage positions between distinct ubiquitin units provide variable chains. Hereinafter, ubiquitilated proteins are recognised by chain type specific antibodies and get processed by regulatory mechanisms like degradation but also by signalling and trafficking. Underlying recognition mechanisms will be elucidated by a combination of molecular modelling experiments facilitating interpretation of experimental investigations on the atomic scale.

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]