Although the fast association between DNA-binding proteins (DBPs) and DNA is explained by a facilitated diffusion mechanism, in which DBPs adopt a weighted combination of three-dimensional diffusion and one-dimensional (1D) sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large-scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA-bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through, to our knowledge, novel 1D scanning mechanisms. In this one-dimensional scanning mode, the protein can float along the DNA under the influence of nonspecific interactions of bulk crowder molecules. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics in which protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedites the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowder-concentration-dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu.

中文翻译：

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在拥挤的细胞环境中促进 DNA 结合蛋白扩散的结构基础

尽管 DNA 结合蛋白 (DBP) 和 DNA 之间的快速关联可以通过促进扩散机制来解释，其中 DBP 采用三维扩散和一维 (1D) 滑动和跳跃运输方式的加权组合，但作用是包含许多非特异性相互作用的蛋白质和其他生物分子的细胞环境的变化大多被忽视。通过在存在非特异性相互作用的大量和 DNA 结合拥挤物（基因组拥挤物）的情况下使用适当调整的蛋白质和 DNA 模型进行大规模计算模拟，我们证明了 DBP 在拥挤的细胞环境中促进扩散的结构基础据我们所知，通过新颖的一维扫描机制。在这种一维扫描模式下，在大量拥挤分子的非特异性相互作用的影响下，蛋白质可以沿着 DNA 漂浮。与通常的 1D 滑动和跳跃动力学相比，搜索模式明显不同，其中蛋白质扩散受 DNA 静电调节。相比之下，基因组拥挤物的存在通过形成瞬时蛋白质-拥挤物桥接复合物将蛋白质运输到 DNA 片段上，从而加快了目标搜索过程。通过分析相关势能格局的坚固性，我们支持了这些搜索模式动力学优势的分子起源，并表明它们成功地解释了实验观察到的分子拥挤剂和拥挤浓度依赖性酶促 DBP 促进扩散的加速。转录因子的活性。