Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins.pdf

a r X i v : q - b i o / 0 6 1 1 0 5 0 v 1 [ q - b i o .B M ] 1 6 N o v 2 0 0 6 Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins Changbong Hyeon1, Ruxandra I Dima3 D. Thirumalai1,2? 1Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742 2Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742 3Department of Chemistry University of Cincinnati Cincinnati, Ohio 45221 1 Abstract Using self-organized polymer models, we predict mechanical unfolding and refolding pathways of ribo-zymes, and the green fluorescent protein. In agreement with experiments, there are between six and eight unfolding transitions in the Tetrahymena ribozyme. Depending on the loading rate, the number of rips in the force-ramp unfolding of the Azoarcus ribozymes is between two and four. Force- quench refolding of the P4-P6 subdomain of the Tetrahymena ribozyme occurs through a compact intermediate. Subsequent formation of tertiary contacts between helices P5b-P6a and P5a/P5c-P4 leads to the native state. The force-quench refolding pathways agree with ensemble experiments. In the dominant unfolding route, the N-terminal a helix of GFP unravels first, followed by disruption of the N terminus b strand. There is a third intermediate that involves disruption of three other strands. In accord with experiments, the force-quench refolding pathway of GFP is hierarchic, with the rate-limiting step being the closure of the barrel. ?Corresponding author phone: 301-405-4803; fax: 301-314-9404; thirum@ 2 I. INTRODUCTION Despite significant advances (Onuchic and Wolynes, 2004; Thirumalai and Hyeon, 2005), major unsolved problems remain in our understanding of how monomeric RNA and protein molecules navigate the rough energy landscape to reach their folded states. Single-molecule experiments, which use mechanical force to manipulate the initial conformations, have begun to provi