title: Rigid-body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape-dependent manner.
abstract: To understand the dynamic aspects of multispecificity of ubiquitin, we studied nine ubiquitin-ligand (partner protein) complexes by normal mode analysis based on an elastic network model. The coupling between ubiquitin and ligand motions was analyzed by decomposing it into rigid-body (external) and vibrational (internal) motions of each subunit. We observed that in total the external motions in one of the subunits largely dominated the coupling. The combination of external motions of ubiquitin and the ligands showed general trends of rotations and translations. Moreover, we observed that the rotational motions of ubiquitin were correlated to the ligand orientations. We also identified ubiquitin atomic vibrations that differentiated the orientation of the ligand molecule. We observed that the extents of coupling were correlated to the shapes of the ligands, and this trend was more pronounced when the coupling involved vibrational motions of the ligand. In conclusion, an intricate interplay between internal and external motions of ubiquitin and the ligands help understand the dynamics of multispecificity, which is mostly guided by the shapes of the ligands and the complex.
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Bhaskar
authors.initials: B
authors.lastname: Dasgupta
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura
authors.forename: Akira R
authors.initials: AR
authors.lastname: Kinjo
mesh_terms: D030562:Databases, Protein; D019281:Dimerization; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D025801:Ubiquitin / Q000737:chemistry* / Q000378:metabolism
chemical_list: D008024:Ligands; D046912:Multiprotein Complexes; D025801:Ubiquitin
keywords: date hub protein; ligand multispecificity; ligand shape; ligand-coupled motion; normal mode analysis; rigid-body motion; ubiquitin