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Issue 42, 2013
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Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

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Abstract

The kink-turn sRNA motif in archaea, whose combination with protein L7Ae initializes the assembly of small ribonucleoprotein particles (sRNPs), plays a key role in ribosome maturation and the translation process. Although many studies have been reported on this motif, the mechanism of sRNA folding coupled with protein binding is still poorly understood. Here, room and high temperature molecular dynamics (MD) simulations were performed on the complex of 25-nt kink-turn sRNA and L7Ae. The average RMSD values between the bound and corresponding apo structures and Kolmogorov–Smirnov P test analysis indicate that sRNA may follow an induced fit mechanism upon binding with L7Ae, both locally and globally. These conclusions are further supported by high-temperature unfolding kinetic analysis. Principal component analysis (PCA) found both closing and opening motions of the kink-turn sRNA. This might play a key role in the sRNP assembly and methylation catalysis. These combined computational methods can be used to study the specific recognition of other sRNAs and proteins.

Graphical abstract: Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

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Supplementary files

Article information


Submitted
26 Jul 2013
Accepted
10 Sep 2013
First published
11 Sep 2013

Phys. Chem. Chem. Phys., 2013,15, 18510-18522
Article type
Paper

Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

W. Ye, J. Yang, Q. Yu, W. Wang, J. Hancy, R. Luo and H. Chen, Phys. Chem. Chem. Phys., 2013, 15, 18510
DOI: 10.1039/C3CP53145G

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