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

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Title:	Molecular dynamics simulation of the induced-fit binding process of DNA aptamer and L-argininamide
Authors:	陳文逸;Lin, Po-Hsun;Tsai, Ching-Wei;Wu, Josephine W.;Ruaan, Ruoh-Chyu;Chen, Wen-Yih
Contributors:	工學院化學工程與材料工程學系
Keywords:	Aptamer;Aptamers, Nucleotide - chemistry;Aptamers, Nucleotide - metabolism;Arginine - analogs & derivatives;Arginine - chemistry;Arginine - metabolism;Binding Sites;Induced-fit binding mechanism;L-Argininamide;Molecular Dynamics Simulation;Molecular recognition engineering;Nucleic Acid Conformation;Static Electricity
Date:	2012-11-01
Issue Date:	2026-04-21 14:02:19 (UTC+8)
Publisher:	Wiley-VCH Verlag;Weinheim: WILEY-VCH Verlag
Abstract:	摘要： AbstractAptamers 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. 其他題名： Biotechnology Journal 出版者： Weinheim: WILEY-VCH Verlag 出版日期： 2012-11 出處： Biotechnology Journal, 2012-11, Vol.7 (11), p.1367-1375 版權： Copyright © 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim 版權： Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. 識別號： ISSN: 1860-6768 識別號： ISSN: 1860-7314 識別號： EISSN: 1860-7314 識別號： DOI: 10.1002/biot.201200003 識別號： PMID: 22678933
Appears in Collections:	[Department of Chemical and Materials Engineering] journal & Dissertation

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