title: Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement.
abstract: Paramagnetic NMR is a useful technique to study proteins and protein complexes and the use of paramagnetic relaxation enhancement (PRE) for this purpose has become wide-spread. PREs are commonly generated using paramagnetic spin labels (SLs) that contain an unpaired electron in the form of a nitroxide radical, with 1-oxyl-2,2,5,5-tetramethyl-2,5-dihydropyrrol-3-ylmethyl methane thiosulfonate (MTSL) being the most popular tag. The inherent flexibility of the SL causes sampling of several conformations in solution, which can be problematic as over- or underestimation of the spatial distribution of the unpaired electron in structural calculations will lead to errors in the distance restraints. We investigated the effect of this mobility on the accuracy of protein-protein docking calculations using intermolecular PRE data by comparing MTSL and the less mobile 3-methanesulfonilthiomethyl-4-(pyridin-3-yl)-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-1-yloxyl (pyMTSL) on the dynamic complex of cytochrome c and cytochrome c peroxidase. No significant differences were found between the two SLs. Docking was performed using either single or multiple conformers and either fixed or flexible SLs. It was found that mobility of the SLs is the limiting factor for obtaining accurate solutions. Optimization of SL conformer orientations using intra-molecular PRE improves the accuracy of docking.
authors.affiliation: Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands. m.ubbink@chem.leidenuniv.nl.
authors.forename: Jesika
authors.initials: J
authors.lastname: Schilder
authors.affiliation: Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands. m.ubbink@chem.leidenuniv.nl.
authors.forename: Wei-Min
authors.initials: WM
authors.lastname: Liu
authors.affiliation: Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands.
authors.forename: Pravin
authors.initials: P
authors.lastname: Kumar
authors.affiliation: Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands. m.ubbink@chem.leidenuniv.nl.
authors.forename: Mark
authors.initials: M
authors.lastname: Overhand
authors.affiliation: Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands.
authors.forename: Martina
authors.initials: M
authors.lastname: Huber
authors.affiliation: Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands. m.ubbink@chem.leidenuniv.nl.
authors.forename: Marcellus
authors.initials: M
authors.lastname: Ubbink
mesh_terms: D004578:Electron Spin Resonance Spectroscopy; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D015394:Molecular Structure; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D013113:Spin Labels
chemical_list: D011506:Proteins; D013113:Spin Labels