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对 Watson-Crick↔wobble 互变异构转化的 2-氨基嘌呤·嘧啶错配的 QM/QTAIM 详细分析。

A QM/QTAIM detailed look at the Watson-Crick↔wobble tautomeric transformations of the 2-aminopurine·pyrimidine mispairs.

机构信息

a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Akademika Zabolotnoho Str., Kyiv 03680 , Ukraine.

b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , 2-h Akademika Hlushkova Ave., Kyiv 03022 , Ukraine.

出版信息

J Biomol Struct Dyn. 2018 May;36(7):1649-1665. doi: 10.1080/07391102.2017.1331864. Epub 2017 Jul 28.

Abstract

This work is devoted to the careful QM/QTAIM analysis of the evolution of the basic physico-chemical parameters along the intrinsic reaction coordinate (IRC) of the biologically important 2AP·T(WC)↔2AP·T*(w) and 2AP·C*(WC)↔2AP·C(w) Watson-Crick(WC)↔wobble(w) tautomeric transformations obtained at each point of the IRC using original authors' methodology. Established profiles reflect the high similarity between the courses of these processes. Basing on the scrupulous analysis of the profiles of their geometric and electron-topological parameters, it was established that the dipole-active WC↔w tautomerizations of the Watson-Crick-like 2AP·T(WC)/2AP·C*(WC) mispairs, stabilized by the two classical N3H⋯N1, N2H⋯O2 and one weak C6H⋯O4/N4 H-bonds, into the wobble 2AP·T*(w)/2AP·C(w) base pairs, respectively, joined by the two classical N2H⋯N3 and O4/N4H⋯N1 H-bonds, proceed via the concerted stepwise mechanism through the sequential intrapair proton transfer and subsequent large-scale shifting of the bases relative each other, through the planar, highly stable, zwitterionic transition states stabilized by the participation of the four H-bonds - N1H⋯O4/N4, N1H⋯N3, N2H⋯N3, and N2H⋯O2. Moreover, it was found out that the 2AP·T(WC)↔2AP·T*(w)/2AP·C*(WC)↔2AP·C(w) tautomerization reactions occur non-dissociatively and are accompanied by the consequent replacement of the 10 unique patterns of the specific intermolecular interactions along the IRC. Obtained data are of paramount importance in view of their possible application for the control and management of the proton transfer, e.g. by external electric or laser fields.

摘要

这项工作致力于仔细的量子力学/量子拓扑分析(QM/QTAIM),以沿生物重要的 2AP·T(WC)↔2AP·T*(w) 和 2AP·C*(WC)↔2AP·C(w) Watson-Crick(WC)↔wobble(w) 互变异构转化的固有反应坐标 (IRC) 上,分析基本物理化学参数的演变。在 IRC 上的每个点,都使用原始作者的方法获得。建立的概况反映了这些过程的高度相似性。基于对其几何和电子拓扑参数概况的细致分析,确定了由两个经典的 N3H⋯N1、N2H⋯O2 和一个弱的 C6H⋯O4/N4 H 键稳定的 Watson-Crick 样 2AP·T(WC)/2AP·C*(WC) 错配物的偶极活性 WC↔w 互变异构,分别转化为 wobble 2AP·T*(w)/2AP·C(w) 碱基对,由两个经典的 N2H⋯N3 和 O4/N4H⋯N1 H 键连接,通过协同逐步机制进行,通过碱基对内的质子转移顺序进行,随后碱基对彼此之间发生大规模移动,通过平面、高度稳定的两性离子过渡态进行,该过渡态由四个氢键 - N1H⋯O4/N4、N1H⋯N3、N2H⋯N3 和 N2H⋯O2 的参与稳定。此外,还发现 2AP·T(WC)↔2AP·T*(w)/2AP·C*(WC)↔2AP·C(w) 互变异构反应非解离发生,并伴随着 IRC 上沿 IRC 取代 10 种独特的特定分子间相互作用模式。考虑到它们在质子转移的控制和管理中的可能应用,获得的数据具有至关重要的意义,例如通过外部电场或激光场。

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