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化学学报
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化学学报 ›› 1998, Vol. 56 ›› Issue (8): 799-806. 上一篇    下一篇

研究论文

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

阎江丽;王黎明;张晓东;张友杰;毛希安;沈联芳   

  1. 中国科学院武汉物理与数学研究所;波谱与原子分子物理国家重点实验室;华中师范大学分析测试中心
  • 发布日期:1998-08-15

Three-dimensional structure of oligodeoxyribonucleotide d(GGTATACC)~2 in solution simulated by distance restrained molecular dynamic calculations

YAN JIANGLI;WANG LIMING;ZHANG XIAODONG;ZHANG YOUJIE;MAO XIAN;SHEN LIANFANG   

  • Published:1998-08-15

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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。

关键词: 约束, 三维结构, 核磁共振, 氢键, 立体结构, 构象, 低聚物, 核苷酸, 分子动力学

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 100ms 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±5kJ/mol were obtained. The root mean square deviations (rmsd) between different structures were all less than 0.06nm and the average rmsd was 0.043nm. The calculated result was illustrated to be reliable also by the back-calculated NOESY which was in good agreement with that from experiment.

Key words: CONSTRAINTS, THREE DIMENSIONAL STRUCTURE, NUCLEAR MAGNETIC RESONANCE, HYDROGEN BONDS, SPATIAL STRUCTURE, CONFORMATION, LOW POLYMER, NUCLEOTIDES, MOLECULAR DYNAMICS

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