Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Go simulations.

ABSTRACT: Assembly of the bacterial ribosomal small subunit (SSU) begins with the folding of the five-way junction upon interaction with the primary binding protein S4. This complex contains the largest contiguous molecular signature, which is a conserved feature in all bacterial 16S rRNAs. In a previous study, we used all-atom molecular dynamics simulations to demonstrate that the co-evolving signature in the N-terminus of S4 is intrinsically disordered and capable of accelerating the binding process through a fly casting mechanism. In this paper, comparisons between the all-atom MD simulations and FRET experiments identify multiple metastable conformations of the naked five-way junction without the presence of S4. Furthermore, we capture the simultaneous folding and binding of the five-way junctio

SUBMITTER: Chen K 

PROVIDER: S-EPMC3422213 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature