Biophysical Society Thematic Meeting - June 28-July 1, 2015

New Biological Frontiers Illuminated by Molecular Sensors and Actuators

Poster Abstracts

2-POS Board 2 Structural Dynamic Model of Programmed Ribosomal Frameshifting Kai-Chun Chang 1 , Emmanuel Salawu 2,3 , Lee-Wei Yang 2,3 , Jin-Der Wen 1 .

1 Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan, 2 Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, 3 Bioinformatics Program, Institute of Information Sciences, Academia Sinica, Taipei, Taiwan. Programmed ribosomal frameshifting (PRF) is promoted by a slippery sequence and a road- blocking downstream RNA secondary structure, such as a hairpin or pseudoknot (PK). Despite extensive biophysical and biochemical studies of － 1 PRF for the past few decades, how the ribosome changes its conformation during PRF and how the RNA structures are unwound remain largely unknown. Recent single-molecule Förster resonance energy transfer (smFRET) experiments indicated that the ribosome may engage in a hyper-rotated state upon encountering an RNA structure. To model the intrinsic dynamics of the ribosome, we build a full-atom ribosome model devoid of any missing subunits and residues, and then apply anisotropic network model (ANM) combined with a novel technique that removes the “tip effect” by preserving bond lengths during large conformational changes. The ANM model with full modes solved (63,768 modes) not only agrees well with experimental B-factor (correlation coefficient r = 0.63), but also captures the ratcheting motion of the ribosome (orientation correlation C = 0.68). The pairwise distance changes between multiple labeling sites from previous smFRET experiments are also examined, and all quantitatively comparable with our predicted values. The PK bound to the ribosome is modeled by fitting a solution structure of PK to the cryo-EM map and then refined by steered molecular dynamics simulations. The global conformational change of the ribosome in response to the external force exerted by PK is modeled by linear response theory. We found that PK may force the 30S subunit to “roll” in a direction perpendicular to ratcheting, and thereby prolonging the ratcheted state and inducing tRNA distortion that disrupts tRNA-mRNA interaction, as previously observed. We propose that the “rolled” state may contribute to PRF by storing the potential energy for a later power stroke that unwinds the downstream RNA structure.

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