Bouvier Benjamin, Grubmüller Helmut
Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Biophys J. 2007 Aug 1;93(3):770-86. doi: 10.1529/biophysj.106.091751. Epub 2007 May 11.
Individual DNA bases are known to be able to flip out of the helical stack, providing enzymes with access to the genetic information otherwise hidden inside the helix. Consequently, base flipping is a necessary first step to many more complex biological processes such as DNA transcription or replication. Much remains unknown about this elementary step, despite a wealth of experimental and theoretical studies. From the theoretical point of view, the involved timescale of milliseconds or longer requires the use of enhanced sampling techniques. In contrast to previous theoretical studies employing umbrella sampling along a predefined flipping coordinate, this study attempts to induce flipping without prior knowledge of the pathway, using information from a molecular dynamics simulation of a B-DNA fragment and the conformational flooding method. The relevance to base flipping of the principal components of the simulation is assayed, and a combination of modes optimally related to the flipping of the base through either helical groove is derived for each of the two bases of the central guanine-cytosine basepair. By applying an artificial flooding potential along these collective coordinates, the flipping mechanism is accelerated to within the scope of molecular dynamics simulations. The associated free energy surface is found to feature local minima corresponding to partially flipped states, particularly relevant to flipping in isolated DNA; further transitions from these minima to the fully flipped conformation are accelerated by additional flooding potentials. The associated free energy profiles feature similar barrier heights for both bases and pathways; the flipped state beyond is a broad and rugged attraction basin, only a few kcal/mol higher in energy than the closed conformation. This result diverges from previous works but echoes some aspects of recent experimental findings, justifying the need for novel approaches to this difficult problem: this contribution represents a first step in this direction. Important structural factors involved in flipping, both local (sugar-phosphate backbone dihedral angles) and global (helical axis bend), are also identified.
已知单个DNA碱基能够从螺旋堆叠中翻转出来，从而使酶能够获取原本隐藏在螺旋内部的遗传信息。因此，碱基翻转是许多更复杂生物过程（如DNA转录或复制）的必要第一步。尽管有大量的实验和理论研究，但关于这一基本步骤仍有许多未知之处。从理论角度来看，涉及的毫秒级或更长时间尺度需要使用增强采样技术。与之前沿预定义翻转坐标采用伞形采样的理论研究不同，本研究试图在不预先了解路径的情况下诱导翻转，利用来自B-DNA片段分子动力学模拟的信息和构象泛洪方法。分析了模拟主成分与碱基翻转的相关性，并为中心鸟嘌呤-胞嘧啶碱基对的两个碱基中的每一个推导了通过螺旋沟与碱基翻转最佳相关的模式组合。通过沿着这些集体坐标施加人工泛洪势，翻转机制被加速到分子动力学模拟的范围内。发现相关的自由能表面具有对应于部分翻转状态的局部最小值，这与孤立DNA中的翻转特别相关；从这些最小值到完全翻转构象的进一步转变通过额外的泛洪势加速。相关的自由能分布对于两个碱基和路径具有相似的势垒高度；超出的翻转状态是一个宽广且崎岖的吸引盆地，其能量仅比封闭构象高几千卡/摩尔。这一结果与之前的研究不同，但呼应了近期实验结果的某些方面，证明了针对这个难题需要新方法的必要性：本研究是朝着这个方向迈出的第一步。还确定了参与翻转的重要结构因素，包括局部（糖-磷酸主链二面角）和全局（螺旋轴弯曲）因素。
