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通过二维NOE和双量子滤波COSY实验得到的NMR约束进行受限分子动力学模拟，对d(AC)4.d(GT)4进行溶液结构研究。

Solution structure studies of d(AC)4.d(GT)4 via restrained molecular dynamics simulations with NMR constraints derived from two-dimensional NOE and double-quantum-filtered COSY experiments.

作者信息

Gochin M, James T L

机构信息

Department of Pharmaceutical Chemistry, University of California, San Francisco 94143.

出版信息

Biochemistry. 1990 Dec 25;29(51):11172-80. doi: 10.1021/bi00503a004.

DOI:10.1021/bi00503a004
PMID:2271704
Abstract

The structure of d(AC)4.d(GT)4 is investigated by constrained molecular dynamics simulations. The constraints include proton pair distances derived from 2D NOE intensities by using the iterative relaxation matrix analysis algorithm MARDIGRAS and sugar pucker phases and amplitudes derived from double-quantum-filtered COSY spectra. Molecular dynamics runs on simulated intensity and distance sets as well as the experimental data were carried out to determine the effects of starting structure, distance constraint derivation, energy functions, and experimental errors on the end result. It was found that structural details could not be elucidated within about 1.5-A overall atomic deviation. This limitation is due in part to the accuracy of the experimental data but, more importantly, is attributable to the quantity of experimental constraints available and to imperfections in the force field utilized in the molecular dynamics calculations. Within the limits of the method, some structural characteristics of d(AC)4.d(GT)4 could be elucidated.

摘要

通过约束分子动力学模拟研究了d(AC)4.d(GT)4的结构。这些约束包括使用迭代弛豫矩阵分析算法MARDIGRAS从二维NOE强度得出的质子对距离，以及从双量子滤波COSY光谱得出的糖环构象相位和幅度。对模拟强度和距离集以及实验数据进行分子动力学运行，以确定起始结构、距离约束推导、能量函数和实验误差对最终结果的影响。结果发现，在总体原子偏差约1.5埃的范围内无法阐明结构细节。这种限制部分归因于实验数据的准确性，但更重要的是，归因于可用实验约束的数量以及分子动力学计算中使用的力场的不完善之处。在该方法的限制范围内，可以阐明d(AC)4.d(GT)4的一些结构特征。

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