title: A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein.
abstract: Structure ensemble determination is the basis of understanding the structure-function relationship of a multidomain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to our knowledge) method to describe structure ensembles using a minimal number of conformers. In this method, individual domains are considered rigid; the position of each spin-label conformer and the structure of each protein conformer are defined by three and six orthogonal parameters, respectively. First, the spin-label ensemble is determined by optimizing the positions and populations of spin-label conformers against intradomain paramagnetic relaxation enhancements with a genetic algorithm. Subsequently, the protein structure ensemble is optimized using a more efficient genetic algorithm-based approach and an overfitting indicator, both of which were established in this work. The method was validated using a reference ensemble with a set of conformers whose populations and structures are known. This method was also applied to study the structure ensemble of the tandem di-domain of a poly (U) binding protein. The determined ensemble was supported by small-angle x-ray scattering and nuclear magnetic resonance relaxation data. The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by the protein.
authors.affiliation: Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.affiliation: Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
authors.forename: Jingfeng
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
authors.forename: Jing-Song
authors.initials: JS
authors.lastname: Fan
authors.affiliation: Nanyang Technological University, School of Biological Sciences, Singapore, Singapore.
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Tria
authors.affiliation: Nanyang Technological University, School of Biological Sciences, Singapore, Singapore.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Grüber
authors.affiliation: Department of Biological Sciences, National University of Singapore, Singapore, Singapore. Electronic address: dbsydw@nus.edu.sg.
authors.forename: Daiwen
authors.initials: D
authors.lastname: Yang
mesh_terms: D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D000072417:Protein Domains; D012313:RNA / Q000378:metabolism*; D000071377:RNA Recognition Motif; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D013113:Spin Labels
chemical_list: D016601:RNA-Binding Proteins; D013113:Spin Labels; D012313:RNA