Molecular dynamics simulation of the induced-fit binding process of DNA aptamer and L-argininamide

Po Hsun Lin, Ching Wei Tsai, Josephine W. Wu, Ruoh Chyu Ruaan, Wen Yih Chen

研究成果: 雜誌貢獻期刊論文同行評審

24 引文 斯高帕斯(Scopus)

摘要

Aptamers are rare functional nucleic acids with binding affinity to and specificity for target ligands. Recent experiments have lead to the proposal of an induced-fit binding mechanism for L-argininamide (Arm) and its binding aptamer. However, at the molecular level, this mechanism between the aptamer and its coupled ligand is still poorly understood. The present study used explicit solvent molecular dynamics (MD) simulations to examine the critical bases involved in aptamer-Arm binding and the induced-fit binding process at atomic resolution. The simulation results revealed that the Watson-Crick pair (G10-C16), C9, A12, and C17 bases play important roles in aptamer-Arm binding, and that binding of Arm results in an aptamer conformation optimized through a general induced-fit process. In an aqueous solution, the mechanism has the following characteristic stages: (a) adsorption stage, the Arm anchors to the binding site of aptamer with strong electrostatic interaction; (b) binding stage, the Arm fits into the binding site of aptamer by hydrogen-bond formation; and (c) complex stabilization stage, the hydrogen bonding and electrostatic interactions cooperatively stabilize the complex structure. This study provides dynamics information on the aptamer-ligand induced-fit binding mechanism. The critical bases in aptamer-ligand binding may provide a guideline in aptamer design for molecular recognition engineering. Aptamer-ligand induced-fit binding mechanism provides a guideline in aptamer design for molecular recognition engineering.

原文???core.languages.en_GB???
頁(從 - 到)1367-1375
頁數9
期刊Biotechnology Journal
7
發行號11
DOIs
出版狀態已出版 - 11月 2012

指紋

深入研究「Molecular dynamics simulation of the induced-fit binding process of DNA aptamer and L-argininamide」主題。共同形成了獨特的指紋。

引用此