距离约束分子动力学计算低聚核苷酸d(GGTATACC)_2溶液中三维结构

Three - dimensional Structure of Oligodeoxyribonucleotide d(GGTATACC)_2 in Solution Simulated by Distance Restrained Molecular Dynamic Calculations

8聚核苷酸d(GGTATACC)_2溶液中的三维结构通过简单的高温和低温动力学计算以及能量优化的方法获得.计算中以标准B型双螺旋DNA为初始结构,加上螺旋间的20个氢键约束和由核磁共振NOESY谱获得的186个NOE约束,另外还加入二面角约束32个.计算所得的6个低能-302±5kJ/mol)优势构象的均方根偏差(rmsd值)均小于0.06nm,平均均方根偏差为0.043nm,从优化结构反算所得的NOE谱与实验数据相吻合.计算结果表明,所加各约束项合理,优化结构具有较高的可信度.

The solution - structure of oligodeoxyribonucleotide d(GGTATACC)2 was determined by conventional high - temperature and low - temperature distance restrained Molecular Dynamic (rMD) method. One hundred and eighty six NOE constraints from NOESY NMR spectra of 100 ms mixing time and 20 hydrogen bond constraints as well as 32 dihedral angle constraints were added to the initial structure of standard B - type DNA. Six superimposed structures with low energy of - 302±5 kJ/mol were obtained. The root mean square deviations (rmsd) between different structures were all less than 0. 06 nm and the average rmsd was 0. 043 nm. The calculated result was illustrated to be reliable also by the back - calculated NOESY which was in good agreement with that from experiment.