Berlin 2018 – wissenschaftliches Programm

Bereiche | Tage | Auswahl | Suche | Aktualisierungen | Downloads | Hilfe

BP: Fachverband Biologische Physik

BP 15: Postersession III

BP 15.70: Poster

Dienstag, 13. März 2018, 14:00–16:00, Poster B

Molecular Dynamics Simulation of SIM-SUMO complexes — •Alexander Kötter and Andreas Heuer — Institut für physikalische Chemie, Universität Münster

The small ubiquitin related modifier (SUMO) plays an important role in many cellular processes [1]. In these processes SUMO forms non covalent bonds to target proteins via interactions with the sumo interacting motif (SIM). Complexes may be formed by a single SUMO interaction with a SIM of the target protein, but also by oligomers of SUMO proteins each interacting with one SIM of the target protein. Atomistic molecular dynamics simulations of a complex formed by a single SUMO (monoSUMO) and a single SIM (monoSIM) show the transient nature of these complexes, irrespective of the type of the SIM or its orientation towards the SUMO. To investigate further the nature of these monoSUMO-monoSIM complexes we calculate their standard binding free energies. To do so we employ a sophisticated scheme [2], that involves calculating the contribution of several degrees of freedom orthogonal to the distance of SUMO and SIM in order to get an accurate estimate of the binding free energy. Furthermore we investigate the structure of complexes of a SUMO dimer (diSUMO) and a peptide chain containing two SIMs (diSIM). We find that the complexation of the diSUMO with the diSIM has limited influence on the dynamics of the diSUMO as characterized by its root mean squared displacement (rmsd). [1] Xu et al. Nat. Comm. 5, 4217 (2014) [2] Gumbart et al. JCTC 9, 794 (2012)