Understanding how signaling proteins like G proteins are allosterically activated is a long-standing challenge with significant biological and medical implications. Because it is difficult to directly observe such dynamic processes, much of our understanding is based on inferences from a limited number of static snapshots of relevant protein structures, mutagenesis data, and patterns of sequence conservation. Here, we use computer simulations to directly interrogate allosteric coupling in six G protein α-subunit isoforms covering all four G protein families. To analyze this data, we introduce automated methods for inferring allosteric networks from simulation data and assessing how allostery is conserved or diverged among related protein isoforms. We find that the allosteric networks in these six G protein α subunits are largely conserved and consist of two pathways, which we call pathway-I and pathway-II. This analysis predicts that pathway-I is generally dominant over pathway-II, which we experimentally corroborate by showing that mutations to pathway-I perturb nucleotide exchange more than mutations to pathway-II. In the future, insights into unique elements of each G protein family could inform the design of isoform-specific drugs. More broadly, our tools should also be useful for studying allostery in other proteins and assessing the extent to which this allostery is conserved in related proteins.

中文翻译：

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G 蛋白激活是通过一种基本通用的机制发生的

了解 G 蛋白等信号蛋白如何变构激活是一个长期存在的挑战，具有重大的生物学和医学意义。由于很难直接观察这样的动态过程，因此我们的大部分理解都是基于相关蛋白质结构、诱变数据和序列保守模式的有限数量的静态快照的推论。在这里，我们使用计算机模拟来直接询问涵盖所有四个 G 蛋白家族的六种 G 蛋白 α 亚基亚型中的变构偶联。为了分析这些数据，我们引入了自动化方法，用于从模拟数据推断变构网络，并评估相关蛋白质亚型之间变构如何保守或发散。我们发现这六个 G 蛋白 α 亚基中的变构网络在很大程度上是保守的，并且由两条途径组成，我们称之为途径 I 和途径 II。该分析预测途径 I 通常比途径 II 占主导地位，我们通过实验证明途径 I 的突变比途径 II 的突变对核苷酸交换的干扰更大，从而证实了这一点。未来，对每个 G 蛋白家族独特元素的深入了解可以为异构体特异性药物的设计提供信息。更广泛地说，我们的工具还应该可用于研究其他蛋白质的变构并评估这种变构在相关蛋白质中的保守程度。