title: An artificial PPR scaffold for programmable RNA recognition.
abstract: Pentatricopeptide repeat (PPR) proteins control diverse aspects of RNA metabolism in eukaryotic cells. Although recent computational and structural studies have provided insights into RNA recognition by PPR proteins, their highly insoluble nature and inconsistencies between predicted and observed modes of RNA binding have restricted our understanding of their biological functions and their use as tools. Here we use a consensus design strategy to create artificial PPR domains that are structurally robust and can be programmed for sequence-specific RNA binding. The atomic structures of these artificial PPR domains elucidate the structural basis for their stability and modelling of RNA-protein interactions provides mechanistic insights into the importance of RNA-binding residues and suggests modes of PPR-RNA association. The modular mode of RNA binding by PPR proteins holds great promise for the engineering of new tools to target RNA and to understand the mechanisms of gene regulation by natural PPR proteins.
authors.affiliation: Department of Molecular Biology, University of Geneva, Science III, 30, Quai Ernest-Ansermet, Geneva 4 1211, Switzerland.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Coquille
authors.affiliation: 1] Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia [2] School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Filipovska
authors.affiliation: Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia.
authors.forename: Tiongsun
authors.initials: T
authors.lastname: Chia
authors.affiliation: Department of Molecular Biology, University of Geneva, Science III, 30, Quai Ernest-Ansermet, Geneva 4 1211, Switzerland.
authors.forename: Lional
authors.initials: L
authors.lastname: Rajappa
authors.affiliation: Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia.
authors.forename: James P
authors.initials: JP
authors.lastname: Lingford
authors.affiliation: Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia.
authors.forename: Muhammad F M
authors.initials: MF
authors.lastname: Razif
authors.affiliation: Department of Molecular Biology, University of Geneva, Science III, 30, Quai Ernest-Ansermet, Geneva 4 1211, Switzerland.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Thore
authors.affiliation: 1] Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia [2] School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.
authors.forename: Oliver
authors.initials: O
authors.lastname: Rackham
mesh_terms: D020816:Amino Acid Motifs; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D005786:Gene Expression Regulation; D006801:Humans; D024101:Mitochondrial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D015202:Protein Engineering; D055550:Protein Stability; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D024101:Mitochondrial Proteins; D016601:RNA-Binding Proteins; D011994:Recombinant Proteins; D012313:RNA