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首页> 外文期刊>Physical chemistry chemical physics: PCCP >Molecular simulation of conformational transitions in biomolecules using a combination of structure-based potential and empirical valence bond theory
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Molecular simulation of conformational transitions in biomolecules using a combination of structure-based potential and empirical valence bond theory

机译：基于结构的电势和经验价键理论相结合的生物分子构象转变的分子模拟

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摘要

The functions of biological macromolecules are inherently linked to their complex conformational behaviour. As a consequence of this complexity, the corresponding potential energy landscapes encompass multiple minima. Some of the intermediate structures between initial and final states can be characterized by experimental techniques. Computer simulations can explore the dynamics of individual states and bring these together to rationalize the overall process. Here, we show that the experimental structures can be exploited to define simple yet accurate atomistic structure-based potentials (SBP) that describe individual conformational states. These individual states can then be coupled by using the empirical valence bond (EVB) model. The overall energy landscape can easily be parameterised to reproduce available kinetic and thermodynamic data. We illustrate the procedure by applying the EVB-SBP method to study base flipping in B-DNA. Simple SBP is shown to reproduce structural ensembles obtained by using more refined force field simulations. Umbrella sampling in conjunction with the general energy gap reaction coordinate enables us to study alternative molecular pathways efficiently. We find that base rotation takes place via both grooves of the B-DNA with a marked preference for the major groove pathway. We also identify an unusual high-energy off-pathway intermediate that may appear if the base closing process is initiated from a syn base.
机译：生物大分子的功能固有地与它们复杂的构象行为有关。由于这种复杂性，相应的势能范围包含多个极小值。初始状态和最终状态之间的某些中间结构可以通过实验技术来表征。计算机模拟可以探索各个状态的动态并将这些动态组合在一起以合理化整个过程。在这里，我们表明可以利用实验结构来定义描述单个构象状态的简单而准确的基于原子结构的电势（SBP）。然后可以使用经验价键（EVB）模型耦合这些单独的状态。可以轻松地对总能量分布进行参数化，以重现可用的动力学和热力学数据。我们通过应用EVB-SBP方法研究B-DNA中的碱基翻转来说明该过程。显示了简单的SBP可以复制通过使用更精细的力场模拟获得的结构体。伞采样结合一般的能隙反应坐标使我们能够有效地研究替代分子途径。我们发现碱基旋转是通过B-DNA的两个凹槽发生的，对主要的凹槽路径有明显的偏爱。我们还确定了一种异常的高能偏路中间体，如果该碱基关闭过程是从syn碱基开始的，则可能会出现。

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