Investigation of Protein-DNA recognition using Molecular Dynamics and advanced sampling simulations

蛋白质-DNA相互作用对于DNA的复制和转录以及所有的基因调控和DNA修复过程都是至关重要的。该项目的目的是使用计算机模拟来实现对间接DNA识别的更精确的理解，间接DNA识别是由序列相关的DNA变形能力决定的。此外，我们还想了解蛋白质与DNA在分子细节上沿DNA滑动结合的过程，从而分析DNA变形性的作用。在第一个项目资助阶段，我们设法开发了一个序列依赖的DNA灵活性的近乎定量的模型。这个多峰伊辛模型既包括DNA可能的半稳定构象分布，也包括每个半稳定构象的构象分布。该方法允许给定的DNA序列和给定的变形结构来计算与变形相关的自由能。除了这一发展，还有可能在原子分辨率下模拟结合在DNA小槽中的配体的滑动过程，并使用先进的采样方法研究蛋白质-DNA系统的滑动过程。在第二个资助阶段，我们计划改进和应用多模式伊辛模型来系统地计算已知蛋白质-DNA复合体的间接DNA识别。此外，蛋白质-DNA结合的变构效应将通过蛋白质与DNA结合来研究，这是近年来实验研究的热点。在这里，我们预计会有很大范围的影响，特别是对于末端流动性有限的DNA片段，因为整体曲率和整体扭曲在这里是恒定的。也就是说，局部曲率或扭曲(或其他螺旋变量)的变化必然会导致其他地方的曲率或扭曲的耦合(反向)变化，这可能会影响第二个蛋白质结合。具有受限迁移率的DNA片段经常出现在包装的DNA中(例如在真核生物中)，并可以实现变构效应。在第二个项目阶段，我们还将使用先进的采样方法来研究DNA沟槽中配体滑动过程的动力学，以及DNA变形是如何调制这一过程的。

Protein-DNA interactions are of fundamental importance for the replication and transcription of DNA as well as for all gene regulation and DNA repair processes. The aim of the project is to use computer simulations to achieve a more precise understanding of indirect DNA recognition, which is determined by the sequence-dependent DNA deformability. In addition, we also want to understand the process of protein-DNA binding by “sliding” along the DNA in molecular detail and thereby analyze the role of DNA deformability. In the first project funding phase, we managed to develop a near quantitative model of sequence-dependent DNA flexibility. This multimodal Ising model includes both the distribution of possible semi-stable conformational states of DNA and the distribution of conformations in each of these semi-stable states. The method allows for a given DNA sequence and given deformed structure to calculate the associated free energy of the deformation. In addition to this development, it was also possible to simulate at atomic resolution the sliding process for a ligand that binds in the DNA minor groove and to investigate the sliding process for a protein-DNA system using advanced sampling methods. In the second funding phase, we plan to improve and apply the multimodal Ising model to systematically calculate indirect DNA recognition for known protein-DNA complexes. Furthermore, allosteric effects of protein-DNA binding will be investigated through protein binding to DNA near a neighboring DNA site with a bound protein, which have increasingly been the focus of experimental studies in recent years. Here we expect effects with a significant range, especially for DNA segments that are subject to limited mobility at their ends, since the overall curvature and the overall twist are constant here. That is, a local change in curvature or twist (or other helical variables) necessarily causes a coupled (reverse) change in curvature or twist elsewhere, which can influence a second protein binding. DNA segments with restricted mobility occur frequently in packaged DNA (e.g. in eukaryotes) and can enable allosteric effects. In the second project phase we will also use advanced sampling methods to investigate the kinetics of the sliding processes of Ligands in DNA grooves and how it is modulated by DNA deformation.