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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