Abstract

Amino acid substitutions at nonconserved protein positions can have noncanonical and “long-distance” outcomes on protein function. Such outcomes might arise from changes in the internal protein communication network, which is often accompanied by changes in structural flexibility. To test this, we calculated flexibilities and dynamic coupling for positions in the linker region of the lactose repressor protein. This region contains nonconserved positions for which substitutions alter DNA-binding affinity. We first chose to study 11 substitutions at position 52. In computations, substitutions showed long-range effects on flexibilities of DNA-binding positions, and the degree of flexibility change correlated with experimentally measured changes in DNA binding. Substitutions also altered dynamic coupling to DNA-binding positions in a manner that captured other experimentally determined functional changes. Next, we broadened calculations to consider the dynamic coupling between 17 linker positions and the DNA-binding domain. Experimentally, these linker positions exhibited a wide range of substitution outcomes: Four conserved positions tolerated hardly any substitutions (“toggle”), ten nonconserved positions showed progressive changes from a range of substitutions (“rheostat”), and three nonconserved positions tolerated almost all substitutions (“neutral”). In computations with wild-type lactose repressor protein, the dynamic couplings between the DNA-binding domain and these linker positions showed varied degrees of asymmetry that correlated with the observed toggle/rheostat/neutral substitution outcomes. Thus, we propose that long-range and noncanonical substitutions outcomes at nonconserved positions arise from rewiring long-range communication among functionally important positions. Such calculations might enable predictions for substitution outcomes at a range of nonconserved positions.

中文翻译：

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非保守变阻器位置的取代通过重新连接长距离动态相互作用来调节功能。

摘要

非保守蛋白质位置的氨基酸取代可能对蛋白质功能产生非规范和“远距离”的结果。这种结果可能是由于内部蛋白质通讯网络的变化而引起的，这种变化通常伴随着结构灵活性的变化。为了测试这一点，我们计算了乳糖阻遏蛋白的接头区域中位置的柔性和动态偶联。该区域包含非保守位置，其取代会改变DNA结合亲和力。我们首先选择研究在位置52处的11个取代。在计算中，取代对DNA结合位置的柔韧性表现出远距离影响，并且柔韧性变化的程度与DNA结合的实验测量值相关。替代还以捕获其他实验确定的功能变化的方式改变了与DNA结合位置的动态偶联。接下来，我们扩大了计算范围，以考虑17个接头位置与DNA结合域之间的动态偶联。从实验上讲，这些接头位置表现出广泛的取代结果：四个保守位置几乎不容许任何取代（“切换”），十个非保守位置显示出一系列取代的渐进变化（“变阻器”），三个非保守位置几乎可以耐受替代（“中立”）。在使用野生型乳糖阻遏蛋白进行计算时，DNA结合结构域与这些接头位置之间的动态偶联显示出不同程度的不对称性，与观察到的肘节/变阻器/中性取代结果相关。因此，我们建议在非保守位置进行远程和非规范性替换的结果是由于重排功能重要位置之间的远程通信而引起的。这样的计算可以预测一系列非保守位置的替代结果。