Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
J Biomol Struct Dyn. 2010 Jun;27(6):843-59. doi: 10.1080/07391102.2010.10508586.
In addition to bending and twisting deformabilities, the lateral displacements of the DNA axis (Kink-and-Slide) play an important role in DNA wrapping around the histone core (M. Y. Tolstorukov, A. V. Colasanti, D. M. McCandlish, W. K. Olson, V. B. Zhurkin, J. Mol. Biol. 371, 725-738 (2007)). Here, we show that these Kink-and-Slide deformations are likely to be stabilized by the arginine residues of histones interacting with the minor groove of DNA. The arginines are positioned asymmetrically in the minor groove, being closer to one strand. The asymmetric arginine-DNA interactions facilitate lateral displacement of base pairs across the DNA grooves, thus leading to a stepwise accumulation of the superhelical pitch of nucleosomal DNA. To understand the sequence dependence of such Kink-and-Slide deformations, we performed all-atom calculations of DNA hexamers with the YR and RY steps in the center. We found that when the unrestrained DNA deformations are allowed, the YR steps tend to bend into the major groove, and RY steps bend into the minor groove. However, when the nucleosomal Kink-and-Slide deformation is considered, the YR steps prove to be more favorable for bending into the minor groove. Overall, the Kink-and-Slide deformation energy of DNA increases in the order TA < CA < CG < GC < AC < AT. We propose a simple stereochemical model accounting for this sequence dependence. Our results agree with experimental data indicating that the TA step most frequently occurs in the minor-groove kink positions in the most stable nucleosomes. Our computations demonstrate that the Kink-and-Slide distortion is accompanied by the BI to BII transition. This fact, together with irregularities in the two-dimensional (Roll, Slide) energy contour maps, suggest that the Kink-and-Slide deformations represent a nonharmonic behavior of the duplex. This explains the difference between the two estimates of the DNA deformation energy in nucleosome - the earlier one made using knowledge-based elastic energy functions, and the current one based on all-atom calculations. Our findings are useful for refining the score functions for the prediction of nucleosome positioning. In addition, the reverse bending behavior of the YR and RY steps revealed under the Kink-and-Slide constraint is important for understanding the molecular mechanisms of binding transcription factors (such as p53) to DNA exposed on the surface of nucleosome.
除了弯曲和扭曲变形,DNA 轴的侧向位移(扭结-滑动)在 DNA 缠绕组蛋白核心(M. Y. Tolstorukov、A. V. Colasanti、D. M. McCandlish、W. K. Olson、V. B. Zhurkin、J. Mol. Biol. 371,725-738(2007))中起着重要作用。在这里,我们表明这些扭结-滑动变形可能由与 DNA 小沟相互作用的组蛋白的精氨酸残基稳定。精氨酸在小沟中不对称地定位,更接近一条链。不对称的精氨酸-DNA 相互作用促进碱基对在 DNA 沟槽中的侧向位移,从而导致核小体 DNA 的超螺旋螺距逐步积累。为了了解这种扭结-滑动变形的序列依赖性,我们对中心具有 YR 和 RY 步的 DNA 六聚体进行了全原子计算。我们发现,当允许不受限制的 DNA 变形时,YR 步倾向于弯曲到大沟中,而 RY 步弯曲到小沟中。然而,当考虑核小体的扭结-滑动变形时,YR 步被证明更有利于弯曲到小沟中。总体而言,DNA 的扭结-滑动变形能按 TA<CA<CG<GC<AC<AT 的顺序增加。我们提出了一个简单的立体化学模型来解释这种序列依赖性。我们的结果与实验数据一致,表明 TA 步最常出现在最稳定核小体的小沟扭结位置。我们的计算表明,扭结-滑动变形伴随着 BI 到 BII 的转变。这一事实,以及二维(Roll、Slide)能量等高线图中的不规则性,表明扭结-滑动变形代表了双螺旋的非谐行为。这解释了核小体中 DNA 变形能的两种估计之间的差异-较早的一种使用基于知识的弹性能量函数,而当前的一种基于全原子计算。我们的发现对于改进核小体定位预测的评分函数很有用。此外,在扭结-滑动约束下揭示的 YR 和 RY 步的反向弯曲行为对于理解结合转录因子(如 p53)到核小体表面暴露的 DNA 的分子机制很重要。