Supramolecular Organization of Heptapyrenotide Oligomers鈥擜n in Depth Investigation by Molecular Dynamics Simulations

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• 作者：Fabio Simona ; Alina L. Nussbaumer ; Robert H盲ner ; Michele Cascella
• 刊名：The Journal of Physical Chemistry B
• 出版年：2013
• 出版时间：February 28, 2013
• 年：2013
• 卷：117
• 期：8
• 页码：2576-2585
• 全文大小：466K
• 年卷期：v.117,no.8(February 28, 2013)
• ISSN：1520-5207

文摘

We present a molecular modeling study based on ab initio and classical molecular dynamics calculations, for the investigation of the tridimensional structure and supramolecular assembly formation of heptapyrenotide oligomers in water solution. Our calculations show that free oligomers self-assemble in helical structures characterized by an inner core formed by 蟺-stacked pyrene units, and external grooves formed by the linker moieties. The coiling of the linkers has high ordering, dominated by hydrogen-bond interactions among the phosphate and amide groups. Our models support a mechanism of longitudinal supramolecular oligomerization based on interstrand pyrene intercalation. Only a minimal number of pyrene units intercalate at one end, favoring formation of very extended longitudinal chains, as also detected by AFM experiment. Our results provide a structural explanation of the mechanism of chirality amplification in 1:1 mixtures of standard heptapyrenotides and modified oligomers with covalently linked deoxycytidine, based on selective molecular recognition and binding of the nucleotide to the groove of the left-wound helix.