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Sequence-dependent base-stacking stabilities guide tRNA folding energy landscapes. | LitMetric

Sequence-dependent base-stacking stabilities guide tRNA folding energy landscapes.

J Phys Chem B

Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27106, United States.

Published: October 2013

AI Article Synopsis

Article Abstract

The folding of bacterial tRNAs with disparate sequences has been observed to proceed in distinct folding mechanisms despite their structural similarity. To explore the folding landscapes of tRNA, we performed ion concentration-dependent coarse-grained TIS model MD simulations of several E. coli tRNAs to compare their thermodynamic melting profiles to the classical absorbance spectra of Crothers and co-workers. To independently validate our findings, we also performed atomistic empirical force field MD simulations of tRNAs, and we compared the base-to-base distances from coarse-grained and atomistic MD simulations to empirical base-stacking free energies. We then projected the free energies to the secondary structural elements of tRNA, and we observe distinct, parallel folding mechanisms whose differences can be inferred on the basis of their sequence-dependent base-stacking stabilities. In some cases, a premature, nonproductive folding intermediate corresponding to the Ψ hairpin loop must backtrack to the unfolded state before proceeding to the folded state. This observation suggests a possible explanation for the fast and slow phases observed in tRNA folding kinetics.

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Source
http://dx.doi.org/10.1021/jp402114pDOI Listing

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