Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.

ABSTRACT:

Introduction

Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating its conformational changes upon ligand binding mostly remains to be elucidated. In this open framework it has been suggested that the ligand stabilizes the interaction of the distal "kissing loop" complex. Using accurate full-atom molecular dynamics with explicit solvent in combination with enhanced sampling techniques and advanced analysis methods it could be possible to provide a more detailed perspective on the formation of these tertiary contacts.

Methods

In this work, we used umbrella sampling simulations to stu

SUBMITTER: Di Palma F 

PROVIDER: S-EPMC4464220 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature