title: Analysis of riboswitch structure and function by an energy landscape framework.
abstract: The thiamine pyrophosphate (TPP) riboswitch employs modular domains for binding TPP to form a platform for gene expression regulation. Specifically, TPP binding triggers a conformational switch in the RNA from a transcriptionally active "on" state to an inactive "off" state that concomitantly causes the formation of a terminator hairpin and halting of transcription. Here, clustering analysis of energy landscapes at different nucleotide lengths suggests a novel computational tool for analysis of the mechanics of transcription elongation in the presence or absence of the ligand. Namely, we suggest that the riboswitch's kinetics are tightly governed by a length-dependent switch, whereby the energy landscape has two clusters available during transcription elongation and where TPP's binding shifts the preference to one form. Significantly, the biologically active and inactive structures determined experimentally matched well the structures predominant in each computational set. These clustering/structural analyses combined with modular computational design suggest design principles that exploit the above features to analyze as well as create new functions and structures of RNA systems.
authors.affiliation: Department of Chemistry, New York University, 251 Mercer Street, New York, NY 10012, USA.
authors.forename: Giulio
authors.initials: G
authors.lastname: Quarta
authors.forename: Namhee
authors.initials: N
authors.lastname: Kim
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Izzo
authors.forename: Tamar
authors.initials: T
authors.lastname: Schlick
mesh_terms: D000465:Algorithms; D001412:Bacillus subtilis / Q000201:enzymology / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D015964:Gene Expression Regulation, Bacterial; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013835:Thiamine Pyrophosphate / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D012313:RNA; D013835:Thiamine Pyrophosphate