Receptor–ligand interactions are involved in various biological processes, therefore understanding the binding mechanism and ability to predict the binding mode are essential for many biological investigations. While many computational methods exist to predict the 3D structure of the corresponding complex provided the knowledge of the monomers, here we use the newly developed DelPhiForce steered Molecular Dynamics (DFMD) approach to model the binding of barstar to barnase to demonstrate that first-principles methods are also capable of modeling the binding. Essential component of DFMD approach is enhancing the role of long-range electrostatic interactions to provide guiding force of the monomers toward their correct binding orientation and position. Thus, it is demonstrated that the DFMD can successfully dock barstar to barnase even if the initial positions and orientations of both are completely different from the correct ones. Thus, the electrostatics provides orientational guidance along with pulling force to deliver the ligand in close proximity to the receptor.

中文翻译：

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使用 DelPhiForce 引导分子动力学 (DFMD) 方法从头算结合 barnase-barstar

受体 - 配体相互作用涉及各种生物过程，因此了解结合机制和预测结合模式的能力对于许多生物学研究至关重要。虽然存在许多计算方法来预测相应复合物的 3D 结构，但提供了单体知识，这里我们使用新开发的 DelPhiForce 引导分子动力学 (DFMD) 方法来模拟 barstar 与 barnase 的结合，以证明第一性原理方法也能够对绑定进行建模。DFMD 方法的基本组成部分是增强长程静电相互作用的作用，以提供单体朝向其正确结合方向和位置的引导力。因此，事实证明，即使两者的初始位置和方向与正确的完全不同，DFMD 也可以成功地将 barstar 停靠到 barnase。因此，静电提供方向引导以及拉力以将配体递送到接近受体的位置。