结构生物信息学研究实验室(RCSB)中有超过533个核小体结构。总的来说,存在许多变体和物种,核小体家族中的亚核小体和超核小体组件也是如此。组蛋白和DNA的组织在含有145、146或147个碱基对的所有标准八酶体中是高度保守的。此观察结果用于建立核小体参考框架,使我们能够描述和比较所有核小体的总体结构和组织。我们观察到Rise的累积总和,Twist,DNA弧长是碱基对指数的线性函数,几乎所有八酶体结构的R2值都超过0.999。这些关系使我们能够容易地将从晶体结构中提取的DNA指向矢框架的位置和方向与理想的超螺旋值进行比较。这样的比较表明,从X射线结构中提取的DNA超螺旋表现出正弦变化,其振幅约为5,而恒定的超螺旋半径约为42,与早期将核小体组织描述为三方的描述一致。在DNA双螺旋的最外层转弯上,核小体DNA也有明显的拉直。DNA超螺旋的拉直标志着向接头DNA的过渡,并且很容易被认为是超螺旋半径的快速增加,并且伴随着螺距的变化。这提供了从接头DNA分离核小体DNA的严格手段。对于所有X射线结构,我们发现在二元附近,存在一组DNA定向框架,其空间位置和方向高度保守。远离二元,DNA超螺旋表现出“单轨”和“多路径”区域。在单轨区域,所有结构都表现出一条高度保守的途径,所有碱基对都必须沿着该途径追踪,但以不同的速度。在多路径区域,允许碱基对沿着组蛋白八聚体的表面绘制出有限数量的不同途径。为了证明所提出的参考几何形状的实用性,标准和扭曲的八酶体结构,超核小体结构,带有接头DNA的核小体,分析闭合环状DNA中的核小体。
■在线版本包含补充材料,可在10.1007/s12551-024-01206-5获得。
There are over 533
nucleosome structures in the Research Collaboratory for Structural Bioinformatics (RCSB). Collectively, numerous variants and species are present, as are sub-nucleosomal and super-nucleosomal assemblies within the
nucleosome family. The organization of the histones and DNA is highly conserved in all standard octasomes containing 145, 146, or 147 base pairs. This observation is used to establish a
nucleosome reference frame that enables us to describe and compare the gross structure and organization of all nucleosomes. We observe that cumulative sums of Rise, Twist, and DNA arc length are linear functions of the base pair index with R 2 values exceeding 0.999 for almost all octasome structures. These relationships enable us to readily compare the location and orientation of DNA director frames extracted from the crystal structures to ideal superhelix values. Such comparisons reveal that the DNA superhelix extracted from X-ray structures exhibits a sinusoidal variation with an amplitude of approximately 5Å about a constant superhelix radius of ∼ 42 Å, in agreement with early descriptions of
nucleosome organization as tripartite. There is also a distinct straightening of the nucleosomal DNA over the outermost turn of DNA\'s double helix. The straightening of the DNA superhelix marks the transition to linker DNA and is easily recognized as a rapid increase in superhelix radius and is concomitant with a change in pitch. This provides a rigorous means of separating nucleosomal DNA from linker DNA. For all X-ray structures, we find that near the dyad, there exists a set of DNA director frames for which the spatial location and orientation are highly conserved. Away from the dyad, the DNA superhelix exhibits \"singletrack\" and \"multipath\" regions. In the singletrack region, all structures exhibit a single highly conserved pathway along which all base pairs must track, but at varying rates. In the multipath regions, the base pairs are allowed to map out a limited number of different pathways along the surface of the histone octamer. To demonstrate the utility of the proposed reference geometries, standard and distorted octasome structures, super-nucleosomal structures, nucleosomes with linker DNA, and nucleosomes in closed circular DNA are analyzed.
UNASSIGNED: The online version contains supplementary material available at 10.1007/s12551-024-01206-5.