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首页> 外文期刊>Journal of Molecular Biology >STRUCTURE REFINEMENT OF THE GLUCOCORTICOID RECEPTOR-DNA BINDING DOMAIN FROM NMR DATA BY RELAXATION MATRIX CALCULATIONS
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STRUCTURE REFINEMENT OF THE GLUCOCORTICOID RECEPTOR-DNA BINDING DOMAIN FROM NMR DATA BY RELAXATION MATRIX CALCULATIONS

机译：弛豫矩阵计算从NMR数据细化糖皮质激素受体-DNA结合域

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The solution structure of the glucocorticoid receptor (GR) DNA-binding domain (DBD), consisting of 93 residues, has been refined from two and three-dimensional NMR data using an ensemble iterative relaxation matrix approach followed by direct NOE refinement with DINOSAUR. A set of 47 structures of the rat GR fragment Cys440-Arg510 was generated with distance geometry and further refined with a combination of restrained energy minimization and restrained molecular dynamics in a parallel refinement protocol. Distance constraints were obtained from an extensive set of NOE build-up curves in H2O and (H2O)-H-2 via relaxation matrix calculations (1186 distance constraints from NOE intensities, 10 phi and 22 chi(1) dihedral angle constraints from J- coupling data were used for the calculations). The root-mean-square deviation values of the 11 best structures on the well-determined part of the protein (Cys440 to Ser448, His451 to Glu469 and Pro493 to Glu508) are 0.60 Angstrom and 1.20 Angstrom from the average for backbone and all heavy atoms, respectively. The final structures have X-factors around 0.40 and good stereochemical qualities. The first zinc-coordinating domain of the GR DBD is very similar to the crystal structure with a root-mean-square difference of 1.4 Angstrom. The second zinc-coordinating domain is still disordered in solution. No secondary structure element is found in this domain in the free state. As suggested by crystallographic studies on the estrogen receptor DBD-DNA and GR DBD-DNA complexes, part of this region will form a distorted helix and the D-box will undergo a conformational change upon cooperative binding to DNA. [References: 43]
机译：糖皮质激素受体（GR）DNA结合结构域（DBD）的溶液结构，由93个残基组成，已使用整体迭代弛豫矩阵方法从二维和三维NMR数据中精制，然后使用DINOSAUR直接进行NOE精制。大鼠GR片段Cys440-Arg510的47个结构的集合具有一定的距离几何形状，并在并行精炼方案中结合了约束能量最小化和约束分子动力学进行了进一步精炼。距离约束是通过弛豫矩阵计算从H2O和（H2O）-H-2中的大量NOE累积曲线获得的（NOE强度的1186距离约束，J-面的10 phi和22 chi（1）二面角约束）耦合数据用于计算）。在蛋白质确定的部分（Cys440至Ser448，His451至Glu469和Pro493至Glu508）的11个最佳结构的均方根偏离值分别是主链和所有重原子的平均值的0.60埃和1.20埃， 分别。最终结构的X因子约为0.40，并且具有良好的立体化学性质。 GR DBD的第一个锌配位域与晶体结构非常相似，其均方根差为1.4埃。第二个锌配位域在溶液中仍然是无序的。在自由状态下在此域中找不到二级结构元素。正如对雌激素受体DBD-DNA和GR DBD-DNA复合物的晶体学研究所暗示的那样，该区域的一部分将形成扭曲的螺旋，并且D-box在与DNA协同结合后将发生构象变化。 [参考：43]

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