caa a22 4500 605511950 CHVBK 20210128100653.0 cr unu---uuuuu 210128e20150301xx s 000 0 eng 10.1007/s00894-015-2597-1 doi (NATIONALLICENCE)springer-10.1007/s00894-015-2597-1 Binding properties of SUMO-interacting motifs (SIMs) in yeast [Elektronische Daten] [Christophe Jardin, Anselm Horn, Heinrich Sticht] Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome. Springer-Verlag Berlin Heidelberg, 2015 Linear motif nationallicence Molecular dynamics (MD) simulations nationallicence Protein-protein interaction nationallicence SUMO-binding motif (SBM) nationallicence SUMO-interacting motif (SIM) nationallicence SUMO-SIM complexes nationallicence Jardin Christophe Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstr. 17, 91054, Erlangen, Germany aut Horn Anselm Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstr. 17, 91054, Erlangen, Germany aut Sticht Heinrich Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstr. 17, 91054, Erlangen, Germany aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/3(2015-03-01), 1-12 1610-2940 21:3<1 2015 21 894 https://doi.org/10.1007/s00894-015-2597-1 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-015-2597-1 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Jardin Christophe Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstr. 17, 91054, Erlangen, Germany aut NATIONALLICENCE 700 1- Horn Anselm Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstr. 17, 91054, Erlangen, Germany aut NATIONALLICENCE 700 1- Sticht Heinrich Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstr. 17, 91054, Erlangen, Germany aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/3(2015-03-01), 1-12 1610-2940 21:3<1 2015 21 894