Molecular Mechanism of preQ1 Riboswitch Action: A Molecular Dynamics Study
نویسندگان
چکیده
منابع مشابه
Insights into Ligand Binding to PreQ1 Riboswitch Aptamer from Molecular Dynamics Simulations
Riboswitches play roles in transcriptional or translational regulation through specific ligand binding of their aptamer domains. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, preQ1 riboswitch aptamer domain from Ba...
متن کاملDynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch
Riboswitches are a class of metabolism control elements mostly found in bacteria. Due to their fundamental importance in bacteria gene regulation, riboswitches have been proposed as antibacterial drug targets. Prequeuosine (preQ1) is the last free precursor in the biosynthetic pathway of queuosine that is crucial for translation efficiency and fidelity. However, the regulation mechanism for the...
متن کاملFolding of a transcriptionally acting preQ1 riboswitch.
7-Aminomethyl-7-deazaguanine (preQ(1)) sensitive mRNA domains belong to the smallest riboswitches known to date. Although recent efforts have revealed the three-dimensional architecture of the ligand-aptamer complex less is known about the molecular details of the ligand-induced response mechanism that modulates gene expression. We present an in vitro investigation on the ligand-induced folding...
متن کاملA DFT and Molecular Dynamics Study on Inhibitory Action of Three Amine Derivatives on Corrosion of Carbon Steel
Inhibition efficiencies of three amine derivatives (Diethylenetriamine (I), Triethylenetetramine (II), and Pentaethylenehexamine (III)) have been studied on corrosion of carbon steel using density functional theory (DFT) method in gas phase. Quantum chemical parameters such as EHOMO (highest occupied molecular orbital energy), ELUMO (lowest unoccupied molecular orbital energy), hardness (η), po...
متن کاملUrea-induced denaturation of preQ1-riboswitch.
Urea, a polar molecule with a large dipole moment, not only destabilizes folded RNA structures but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well understood, the action of urea on RNA has barely been explored. We performed extensive all-atom molecular dynamics simulations to determine the molecular underpinnings o...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: The Journal of Physical Chemistry B
سال: 2012
ISSN: 1520-6106,1520-5207
DOI: 10.1021/jp309230v