Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data.
Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data.
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DOI：
10.1007/s10858-008-9267-x
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发表时间：
2008-10
影响因子：
2.7
通讯作者：
Bax A
中科院分区：
文献类型：
--
作者：
Grishaev A;Ying J;Canny MD;Pardi A;Bax A
大肠杆菌tRNAVal的同源性模型，最初基于酵母tRNAPhe的X-射线结构，使用实验残留偶极耦合（RDC）和小角X-射线散射（SAXS）数据的改进程序。描述了一种球形采样算法，用于对SAXS数据进行细化，该算法不需要globbic近似，这对于其中这种近似不太合适的核酸特别重要。该算法的速度大大提高，也使其适用于蛋白质。除了SAXS数据外，结构精修还采用了稀疏的NMR数据集，该数据集由Pf 1噬菌体比对测量的24个亚氨基N-HN RDC和从tRNAVal的磁场依赖性比对获得的20个亚氨基N-HN RDC组成。改进策略旨在通过确保核糖磷酸骨架和保守碱基对的短重叠片段的原子坐标保持接近起始模型的原子坐标，在很大程度上保留58%相同的tRNAPhe的局部几何形状。使用XPLOR-NIH或CNS软件包中的非晶体学对称性（NCS）项强制执行局部坐标约束，同时仍允许相邻节段的适度移动。RDC主要驱动螺旋臂的相对取向，而SAXS限制确保整体分子形状与实验散射数据兼容。得到的结构表现出良好的交叉验证统计（折刀Qfree = 14%的Pf 1 RDC，相比之下，25%的起始模型），并表现出更大的角度之间的两个螺旋臂比观察到的X射线结构的tRNAPhe，与以前的NMR为基础的tRNAVal模型。
A procedure is presented for refinement of a homology model of E.Coli tRNAVal, originally based on the X-ray structure of yeast tRNAPhe, using experimental residual dipolar coupling (RDC) and small angle X-ray scattering (SAXS) data. A spherical sampling algorithm is described for refinement against SAXS data that does not require a globbic approximation, which is particularly important for nucleic acids where such approximations are less appropriate. Substantially higher speed of the algorithm also makes its application favorable for proteins. In addition to the SAXS data, the structure refinement employed a sparse set of NMR data consisting of 24 imino N-HN RDCs measured with Pf1 phage alignment, and 20 imino N-HN RDCs obtained from magnetic field dependent alignment of tRNAVal. The refinement strategy aims to largely retain the local geometry of the 58% identical tRNAPhe by ensuring that the atomic coordinates for short, overlapping segments of the ribose-phosphate backbone and the conserved base pairs remain close to those of the starting model. Local coordinate restraints are enforced using the non-crystallographic symmetry (NCS) term in the XPLOR-NIH or CNS software package, while still permitting modest movements of adjacent segments. The RDCs mainly drive the relative orientation of the helical arms, whereas the SAXS restraints ensure an overall molecular shape compatible with experimental scattering data. The resulting structure exhibits good cross-validation statistics (jack-knifed Qfree = 14% for the Pf1 RDCs, compared to 25% for the starting model) and exhibits a larger angle between the two helical arms than observed in the X-ray structure of tRNAPhe, in agreement with previous NMR-based tRNAVal models.
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影响因子：
4.8
作者：
Cai, ML;Williams, DC;Clore, GM
通讯作者：
Clore, GM
影响因子：
2.2
作者：
Al-Hashimi, HM;Valafar, H;Prestegard, JH
通讯作者：
Prestegard, JH
影响因子：
6.1
作者：
FRASER, RDB;MACRAE, TP;SUZUKI, E
通讯作者：
SUZUKI, E
DOI：
10.1038/nsb1004
发表时间：
2003-12-01
期刊：
NATURE STRUCTURAL BIOLOGY
影响因子：
--
作者：
Lukavsky, PJ;Kim, I;Puglisi, JD
通讯作者：
Puglisi, JD
影响因子：
2.7
作者：
Grishaev, Alexander;Tugarinov, Vitali;Bax, Ad
通讯作者：
Bax, Ad