首页> 外文学位 >Practical treatment of nuclear magnetic resonance relaxation in carbon-13/nitrogen-15-labeled nucleic acids: Application to d(CGCGAATTCGCG).
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Practical treatment of nuclear magnetic resonance relaxation in carbon-13/nitrogen-15-labeled nucleic acids: Application to d(CGCGAATTCGCG).

机译:碳13 /氮15标记核酸中核磁共振弛豫的实际处理:在d(CGCGAATTCGCG)中的应用。

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摘要

A computational approach to the modeling of heteronuclear NMR data is outlined in the relaxation matrix formalism convenient for application to macromolecules. Given a model structure, the principal axis system of the diffusion tensor is computed or taken as that of the moment of inertia tensor. All pair-wise heteronuclear and homonuclear dipolar interaction tensors are then computed in this frame, and the chemical shift anisotropy (CSA) tensors are placed on each nucleus of interest. The latter may be taken from experimental data, or provided by electronic structure calculation at the desired level of theory. Using these data as input, the relaxation rates, R 1 and R2, and the ssNOE enhancement are systematically computed. The computed rates are compared to experimental data for the determination of rotational hydrodynamics and/or intramolecular dynamics parameters. No assumptions are made as to the relative orientations of any of the interaction tensors, and fully anisotropic rigid body diffusion is accommodated. The method is useful for testing the validity of a wide range of assumptions often made in the analysis of NMR relaxation data for macromolecular systems. The software package, Y&barbelow;et A&barbelow;nother R&barbelow;elaxation M&barbelow;atrix (YARM) program, was enhanced to perform these calculations. As a model system, a nucleic acid helix, d(CGCGAATTCGCG), D12, was chosen, for which several models exist in the literature. The dynamics of DNA are complex, and the rotational hydrodynamics are deemed indeterminate for data collected at a single field; however, the fast motion parameters of the “model-free” formalism are determined and discussed with respect to the “worm-like” chain model of DNA.
机译:在弛豫矩阵形式学中概述了一种用于异核NMR数据建模的计算方法,可方便地应用于大分子。给定模型结构,计算扩散张量的主轴系统或将其用作惯性矩张量的主轴系统。然后在该框架中计算所有成对的异核和同核偶极相互作用张量,并将化学位移各向异性(CSA)张量放置在每个感兴趣的核上。后者可以从实验数据中获取,也可以通过电子结构计算以所需的理论水平提供。使用这些数据作为输入,弛豫率 R 1 R 2 ,以及 ssNOE 增强是系统地计算的。将计算出的速率与实验数据进行比较,以确定旋转流体动力学和/或分子内动力学参数。没有任何相互作用张量的相对取向的假设,并且完全各向异性的刚体扩散被容纳。该方法可用于测试大分子系统NMR弛豫数据分析中经常做出的各种假设的有效性。增强了软件包Y和A,其他R和Elaxation M&atrix(YARM)程序,以执行这些计算。作为模型系统,选择了核酸螺旋d(CGCGAATTCGCG)D12,文献中存在几种模型。 DNA的动力学很复杂,对于单个场中收集的数据,旋转流体动力学被认为是不确定的。然而,相对于DNA的“蠕虫状”链模型,确定并讨论了“无模型”形式主义的快速运动参数。

著录项

  • 作者

    Coker, George Sansing, II.;

  • 作者单位

    Yale University.;

  • 授予单位 Yale University.;
  • 学科 Biophysics General.; Chemistry Biochemistry.
  • 学位 Ph.D.
  • 年度 2001
  • 页码 457 p.
  • 总页数 457
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 生物物理学;生物化学;
  • 关键词

  • 入库时间 2022-08-17 11:47:06

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