title: Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling.
abstract: In bacteriophage λ, interactions between a 22-amino acid peptide (called the N-peptide) and a stem-loop RNA element (called boxB) play a critical role in transcription anti-termination. The N-peptide/boxB complex has been extensively studied, and serves as a paradigm for understanding mechanisms of protein/RNA recognition. Particularly, ultrafast spectroscopy techniques have been applied to monitor picosecond fluorescence decay behaviors of 2-aminopurines embedded at various positions of the boxB RNA. The studies have led to a model in which the bound N-peptide exists in dynamic equilibrium between two states, with peptide C-terminal fragment either stacking on (i.e., the stacked state) or peeling away from (i.e., the unstacked state) the RNA loop. The function of the N-peptide/boxB complex seems to correlate with the fraction of the stacked state. Here, the N-peptide/boxB system is studied using the site-directed spin labeling technique, in which X-band electron paramagnetic resonance spectroscopy is applied to monitor nanosecond rotational behaviors of stable nitroxide radicals covalently attached to different positions of the N-peptide. The data reveal that in the nanosecond regime the C-terminal fragment of bound N-peptide adopts multiple discrete conformations within the complex. The characteristics of these conformations are consistent with the proposed stacked and unstacked states, and their distributions vary upon mutations within the N-peptide. These results suggest that the dynamic two-state model remains valid in the nanosecond regime, and represents a unique mode of function in the N-peptide/boxB RNA complex. It also demonstrates a connection between picosecond and nanosecond dynamics in a biological complex.
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, USA.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Zhang
authors.forename: Sang Won
authors.initials: SW
authors.lastname: Lee
authors.forename: Liang
authors.initials: L
authors.lastname: Zhao
authors.forename: Tianbing
authors.initials: T
authors.lastname: Xia
authors.forename: Peter Z
authors.initials: PZ
authors.lastname: Qin
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D010582:Bacteriophage lambda / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods; D008954:Models, Biological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017433:Protein Structure, Secondary; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013113:Spin Labels
chemical_list: D010446:Peptide Fragments; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D013113:Spin Labels