Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Poster Session I

15 – POS Board 15 An Equilibrium-based Model for -1 Programmed Ribosome Frame-shift Stimulator Iren Wang 1 , Ian-Ping Bi 2 , Kung-Yao Chang 2 , Shang-Te Danny Hsu 1,3 . 1 Academia Sinica, Taipei, Taiwan, 2 National Chung Hsin University, Taichung, Taiwan, 3 National Taiwan University, Taipei, Taiwan. The functional determinant of RNA pseudoknot for -1 programmed ribosome frame-shift (PRF) stimulation has been inconclusive. Recently, NMR analysis of the MLV readthrough pseudoknot revealed a pH-dependent conformation change that has been linked to readthrough efficiency. It was proposed that pH-dependent base-triple formation facilitate S1-L2 interaction crucial for read-through competence. This model was further proposed to extend to the pseudoknot stimulator of -1 PRF. We use the human telomerase pseudoknot (hTPK) DU177 as a model system to examine the pH-dependent -1 PRF efficiency. The UAU triples of DU177 can be replaced by isomorphic CGC triples while retaining the -1 PRF stimulation activity. The CGC triple can harbor an extra protonation-mediated tertiary hydrogen-bond to form a C+GC triple. The -1 PRF efficiencies of the CGC variants exhibit strong pH-dependency that correlates very well with their thermal stability. Two distinct thermal transitions were observed for the CGC variants with the first one being more pH-sensitive. Such a systems may serve as a platform for examining the role of S1-L2 interaction (involving conserved AACAA in L2 in several viral -1 PRF pseudoknot stimulators) in -1 PRF stimulation and its coupling to the base-triple formation. Particularly, it will be very informative to analyze the S1-L2 configurations in different pH values that can tune the -1 PRF efficiency to different levels to link a specific pseudoknot configuration to -1 PRF stimulation activity.

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