Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation
Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation
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DOI：
10.1021/ja028383j
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发表时间：
2003-02-12
影响因子：
15
通讯作者：
Kuszewski, J
中科院分区：
文献类型：
--
作者：
Clore, GM;Kuszewski, J
模拟退火精炼中使用的非键接触项的描述可能对 NMR 数据生成的核酸结构产生重大影响。通过完整的偶极耦合交叉验证，我们证明了通过利用平均力的两个构象数据库势可以显着提高RNA NMR结构的坐标精度：由各种多维扭转角相关性组成的核酸扭转角数据库势； RNA特异性碱基-碱基定位势能提供对顺序和非顺序碱基-碱基相互作用的简单几何、基于统计的描述。前者基于416个核酸晶体结构，分辨率小于或等于2埃，R因子小于或等于25%；后者基于 131 个 RNA 晶体结构，分辨率小于或等于 3 埃，R 因子小于或等于 25%，并且包括核糖体的大亚基和小亚基。这两个数据库势的应用说明了 RNA 适体/茶碱复合物的结构精炼，已在溶液中测量了广泛的 NOE 和残余偶极耦合数据。
The description of the nonbonded contact terms used in simulated annealing refinement can have a major impact on nucleic acid structures generated from NMR data. Using complete dipolar coupling cross-validation, we demonstrate that substantial improvements in coordinate accuracy of NMR structures of RNA can be obtained by making use of two conformational database potentials of mean force: a nucleic acid torsion angle database potential consisting of various multidimensional torsion angle correlations; and an RNA specific base-base positioning potential that provides a simple geometric, statistically based, description of sequential and nonsequential base-base interactions. The former is based on 416 nucleic acid crystal structures solved at a resolution of less than or equal to2 Angstrom and an R-factor less than or equal to25%; the latter is based on 131 RNA crystal structures solved at a resolution of less than or equal to3 Angstrom and an R-factor of less than or equal to25%, and includes both the large and small subunits of the ribosome. The application of these two database potentials is illustrated for the structure refinement of an RNA aptamer/theophylline complex for which extensive NOE and residual dipolar coupling data have been measured in solution.