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首页> 外文期刊>Physical chemistry chemical physics: PCCP >Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 proteasef
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Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 proteasef

机译：共识模式，对来自多个最小值正常模式分析的蛋白质集体运动的有力描述，适用于HIV-1蛋白酶f

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摘要

Protein flexibility is essential for enzymatic function, ligand binding, and protein-protein or protein-nucleic acid interactions. Normal mode analysis has increasingly been shown to be well suited for studying such flexibility, as it can be used to identify favorable structural deformations that correspond to functional motions. However, normal modes are strictly relevant to a single structure, reflecting a particular minimum on a complex energy surface, and are thus susceptible to artifacts. We describe a new theoretical framework for determining "consensus" normal modes from a set of related structures, such as those issuing from a short molecular dynamics simulation. This approach is more robust than standard normal mode analysis, and provides higher collectivity and symmetry properties. In an application to HIV-1 protease, the low-frequency consensus modes describe biologically relevant motions including flap opening and closing that can be used in interpreting structural changes accompanying the binding of widely differing inhibitors.
机译：蛋白质柔韧性对于酶功能，配体结合以及蛋白质-蛋白质或蛋白质-核酸相互作用至关重要。正常模式分析已越来越显示出非常适合研究这种灵活性，因为它可用于识别与功能运动相对应的有利结构变形。但是，正常模式与单个结构严格相关，在复杂的能量表面上反映出特定的最小值，因此容易受到伪影的影响。我们描述了一种新的理论框架，用于从一组相关结构中确定“共识”正常模式，例如从短分子动力学模拟中得出的那些结构。这种方法比标准的正常模式分析更健壮，并提供更高的集合性和对称性。在对HIV-1蛋白酶的一种应用中，低频共有模式描述了包括襟翼打开和闭合在内的生物学相关运动，可用于解释伴随着广泛不同的抑制剂结合而发生的结构变化。

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