title: DEAD-box-protein-assisted RNA structure conversion towards and against thermodynamic equilibrium values.
abstract: RNAs in biological processes often interconvert between defined structures. These RNA structure conversions are assisted by proteins and are frequently coupled to ATP hydrolysis. It is not well understood how proteins coordinate RNA structure conversions and which role ATP hydrolysis has in these processes. Here, we have investigated in vitro how the DEAD-box ATPase Ded1 facilitates RNA structure conversions in a simple model system. We find that Ded1 assists RNA structure conversions via two distinct pathways. One pathway requires ATP hydrolysis and involves the complete disassembly of the RNA strands. This pathway represents a kinetically controlled steady state between the RNA structures, which allows formation of less stable from more stable RNA conformations and thus RNA structure conversion against thermodynamic equilibrium values. The other pathway is ATP-independent and proceeds via multipartite intermediates that are stabilized by Ded1. Our results provide a basic mechanistic framework for protein-assisted RNA structure conversions that illuminates the role of ATP hydrolysis and reveal an unexpected diversity of pathways.
authors: Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
authors: Quansheng
authors: Q
authors: Yang
authors: Margaret E
authors: ME
authors: Fairman
authors: Eckhard
authors: E
authors: Jankowsky
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D053487:DEAD-box RNA Helicases / Q000737:chemistry* / Q000378:metabolism; D006868:Hydrolysis; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012313:RNA; D000255:Adenosine Triphosphate; D053487:DEAD-box RNA Helicases