Transient RNA-protein interactions in RNA folding

• Published in: The FEBS journal 2011-05, Vol.278 (10), p.1634-1642
• Main Authors: Doetsch, Martina, Schroeder, Renée, Fürtig, Boris
• Format: Article
• Language: English
• Subjects: adenosine triphosphate; amino acids; DEAD-box RNA Helicases - chemistry; DNA-Binding Proteins - chemistry; electrostatic interactions; energy; Escherichia coli Proteins - chemistry; Gene Products, tat - chemistry; Kinetics; mechanism of action; mode of binding; Models, Chemical; Molecular biology; Molecular Chaperones - chemistry; Nucleic Acid Conformation; Protein folding; Proteins; Proteins - chemistry; proteins that promote RNA folding; Review; Ribonucleic acid; RNA; RNA - chemistry; RNA chaperones; RNA folding; RNA folding problem; RNA-Binding Proteins - chemistry; Thermodynamics; transient interactions
• ISSN: 1742-464X; 1742-4658
• DOI: 10.1111/j.1742-4658.2011.08094.x

The RNA folding trajectory features numerous off-pathway folding traps, which represent conformations that are often equally as stable as the native functional ones. Therefore, the conversion between these off-pathway structures and the native correctly folded ones is the critical step in RNA folding. This process, referred to as RNA refolding, is slow, and is represented by a transition state that has a characteristic high free energy. Because this kinetically limiting process occurs in vivo, proteins (called RNA chaperones) have evolved that facilitate the (re)folding of RNA molecules. Here, we present an overview of how proteins interact with RNA molecules in order to achieve properly folded states. In this respect, the discrimination between static and transient interactions is crucial, as different proteins have evolved a multitude of mechanisms for RNA remodeling. For RNA chaperones that act in a sequence-unspecific manner and without the use of external sources of energy, such as ATP, transient RNA-protein interactions represent the basis of the mode of action. By presenting stretches of positively charged amino acids that are positioned in defined spatial configurations, RNA chaperones enable the RNA backbone, via transient electrostatic interactions, to sample a wider conformational space that opens the route for efficient refolding reactions.