Solution structure of [d(A-T)5]2 via complete relaxation matrix analysis of two-dimensional nuclear Overhauser effect spectra and molecular mechanics calculations: evidence for a hydration tunnel.
Solution structure of [d(A-T)5]2 via complete relaxation matrix analysis of two-dimensional nuclear Overhauser effect spectra and molecular mechanics calculations: evidence for a hydration tunnel.
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通过二维核欧沃豪塞效应谱的完全弛豫矩阵分析和分子力学计算得出 [d(A-T)5]2 的溶液结构：水合隧道的证据。
DOI：
10.1021/bi00370a019
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发表时间：
1986
期刊：
影响因子：
2.9
通讯作者：
James,TL
中科院分区：
文献类型：
--
作者：
Suzuki,E;Pattabiraman,N;Zon,G;James,TL
修订稿于 1986 年 6 月 12 日收到摘要：已在氧化氘溶液中多次混合获得 [d (5'ATATATAT3')] 2 在 500 MHz 下的纯吸收相质子二维核欧沃豪塞效应 (2D NOE) 光谱。 100 个不可交换质子共振已被指定。将实验二维 NOE 光谱与使用完全弛豫矩阵分析方法计算的理论光谱进行比较 [Keepers, J. W., & James, T. L.(1984) J. Magn.共振。 57, 404-426] 和 X 射线衍射确定了 DNA 的 A、B、交替 B、左手 B、C、D 和皱纹 D 形式的分子坐标，以及通过使用分子力学程序 amber 从最有希望的 X 射线晶体结构计算出的能量最小化结构的分子坐标，其中包括所有氢、反离子和水合水分子。对 2D NOE 谱的所有特征的分析在提取有希望的结构方面发挥了重要作用，并且得出的结论是，褶皱的 D 形式最适合 AT 十聚体的 2D NOE 数据。分子力学计算表明，这种小沟较深且较窄的模型结构可能比交替d(AT)DNA的B型结构在能量上更加稳定。该结构的有趣特征包括可能的链内和链间糖磷酸吸引力以及小沟内的水合通道，该水合通道能够容纳三种类型的水分子，通过氢键帮助螺旋稳定。抗衡离子（钠）用于减少链间磷酸盐-磷酸盐排斥效应。多年来的主要目标是确定非晶环境中的分子结构。
Revised Manuscript Received June 12, 1986 abstract: Pure absorption phase proton two-dimensional nuclear Overhauser effect (2D NOE) spectra at 500 MHz have been obtained for [d (5'ATATATATAT3')] 2 in deuterium oxide solution at several mixing times. The 100 nonexchangeable proton resonances have been assigned. Theexperimental 2D NOE spectra were compared with theoretical spectra calculated by using the complete relaxationmatrix analysis method [Keepers, J. W., & James, T. L.(1984) J. Magn. Reson. 57, 404-426] and X-ray diffraction determined molecular coordinates of A, B, alternating B, left-handed B, C, D, and wrinkled D forms of DNA and of energy-minimized structures calculated from themost promising X-ray crystal structures by using the molecular mechanics program amber, in which all hydrogens, counterions, and hydration water molecules were included. The analysis of all features of the 2D NOE spectra played an important role in extracting the promising structures, and it was concluded that the wrinkled D form yields the best fit for the 2D NOE data of the AT decamer. The molecular mechanics calculation indicated that thismodel structure, whose minor groove is comparatively deep and narrow, may be energetically more stable than the B form for alternating d (AT) DNA. Interesting features of thestructure include possible intra-and interchain sugar-phosphate attractions and a hydration tunnel inside the minor groove capable of accommodating three types of water molecules that aidin helixstabilization via hydrogen bonding. Counterions (sodium) serve to reduce interchain phosphate-phosphate repulsiveeffects. major goal for many years has been the determination of molecular structures innoncrystalline environments.