The RNA E-loop Motif: Folding and Evolution at Atomic Resolution
Date Issued
2016
Date
2016
Author(s)
Yu, Ming-Ying
Abstract
RNA is amazing. Its pliable backbone deviates the RNA local structure plays important roles in many biological functions and enzymatic catalysis. The repetitive RNA structures, called RNA motifs such as Tetraloop, Kink-turn, E-loop, etc., are considered to be essential intrinsic elements that stabilize the RNA conformations and confer the RNA catalytic functions. Among many unique RNA motifs, the RNA E-loop motif is in a helix form with one stand in an A-form conformation, and the other in an S-shape. The RNA E-loop motif is observed in the core of the 23S rRNA, in the three-way junctions of the 23S rRNA, in the catalytic RNA of group II introns, and is critical for anchoring the elongation factor G (EF-G) of the ribosome. Here we iteratively structural mine the E-loop motif within the bacterial and archaeal ribosomes. We focus on analyzing and classifying the three dimensional structures of the RNA E-loop motif. We statistically compute the phylogenic covariations, conformationally inspect the RNA local structural deviations, and systematically analyze the intra-molecular interactions of the E-loop motifs. We also perform the directed MD (molecular dynamics) simulations on the folding of the E-loop motif. Here we show that (i) more than 60% of the E-loops are uncovered, (ii) RNA E-loop motif accommodates the local structural deviations, (iii) we postulate the reaction coordinates of the E-loop motif folding at atomic resolution, (iv) the evolution of the RNA E-loop motif involves with three periods, which we define, are mature, intermediate, and primitive period, and (v) in each period of the E-loop motif is coped with the evolution of the large subunit of the ribosomes.
Subjects
RNA secondary structure
RNA reaction coordinate
RNA motif evolution
E-loop motif
ribosome evolution
bioinformatics
Type
thesis
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