Westhof E
Laboratoire de Cristallographie Biologique, Centre National de la Recherche Scientifique, Strasbourg, France.
J Biomol Struct Dyn. 1987 Dec;5(3):581-600. doi: 10.1080/07391102.1987.10506414.
The effects of X-ray refinement algorithm on parameters characterising nucleic acid structure are analysed following the re-refinement of the B-dodecamer d(CGCGAATTCGCG). The main conclusions are the following. Mean deviations of main chain torsion angles between the two refinements average 12.6 degrees. Phase angle of pseudorotation for sugar puckers vary between 100 degrees and 180 degrees in the present refinement with amplitude of pucker around 30 degrees. On the other hand, the helical parameters have mean deviations less than 2 degrees. At most half of the assigned solvent positions are within 2 A in both refinements. In the second part of the work, plots of temperature factors (B's) versus occupancies (Q's) for solvent peaks have been analysed in the B-dodecamer and in the Z-hexamer d(5BrCG5BrCG5BrCG). Owing to the poor statistics, some of those conclusions should be regarded as tentative. Occupancy appears to depend on the number of contacts made by the solvent peak with the nucleic acid while temperature factor does not. Except when engaged in particular interaction sites, solvent molecules bound to phosphates have a tendency for high B's and variable Q's. Water molecules bound to polar atoms of the bases occupy various positions in the B-Q diagram. Particularly striking is the behavior of the water molecules belonging to the B-spine and to the Z-spine: the spread in occupancy of water molecules in the hydration spine of the Z-oligomer is larger than in the hydration spine of the B-oligomer. An opposite tendency is observed for the temperature factors. The first observation might reflect the special mobility of the water molecules building up the spine hydration in the Z-form where it continues without interruption from one hexamer to the next. In the B-form, on the contrary, the spine is restricted to the center part of the dodecamer. The second observation might reflect the sharpness of the local attractive potential in the Z-form and its broadness in the B-form. In both cases, dipole reorientations would occur, leading to a high local dielectric constant: in the Z-form, through water molecules hopping from one site to another and, in the B-form, because of rotational freedom.
在对B型十二聚体d（CGCGAATTCGCG）进行重新精修之后，分析了X射线精修算法对表征核酸结构的参数的影响。主要结论如下。两次精修之间主链扭转角的平均偏差为12.6度。在当前精修中，糖环假旋转的相角在100度至180度之间变化，环化幅度约为30度。另一方面，螺旋参数的平均偏差小于2度。在两次精修中，最多一半的指定溶剂位置在2埃以内。在工作的第二部分，分析了B型十二聚体和Z型六聚体d（5BrCG5BrCG5BrCG）中溶剂峰的温度因子（B值）与占有率（Q值）的关系图。由于统计数据不佳，其中一些结论应被视为初步的。占有率似乎取决于溶剂峰与核酸形成的接触数量，而温度因子则不然。除了处于特定相互作用位点时，与磷酸基团结合的溶剂分子往往具有较高的B值和可变的Q值。与碱基极性原子结合的水分子在B-Q图中占据不同位置。特别引人注目的是属于B型骨架和Z型骨架的水分子的行为：Z型寡聚体水合骨架中水分子占有率的分布比B型寡聚体水合骨架中的更大。温度因子则呈现相反的趋势。第一个观察结果可能反映了构成Z型骨架水合的水分子的特殊流动性，在Z型中这种流动性从一个六聚体到下一个六聚体持续不间断。相反，在B型中，骨架局限于十二聚体的中心部分。第二个观察结果可能反映了Z型中局部吸引势的尖锐程度及其在B型中的宽泛程度。在这两种情况下，都会发生偶极子重新定向，导致局部介电常数较高：在Z型中，通过水分子从一个位点跳到另一个位点；在B型中，是由于旋转自由度。
