Mapping the energetic and allosteric landscapes of protein binding domains
Mapping the energetic and allosteric landscapes of protein binding domains
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DOI：
10.1038/s41586-022-04586-4
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发表时间：
2022-04-07
期刊：
影响因子：
64.8
通讯作者：
Lehner, Ben
中科院分区：
文献类型：
--
作者：
Faure, Andre J.;Domingo, Julia;Lehner, Ben
蛋白质中远端位点之间的变构通讯是生物调节的核心，但仍然缺乏表征，限制了理解，工程和药物开发（1-6）。一个重要的原因是缺乏全面量化不同蛋白质变构的方法。在这里，我们解决了这个缺点，并提出了一种方法，使用深度突变扫描全局映射变构。该方法使用了一个有效的实验设计来推断enabeton的因果生物物理效应的突变，通过量化多个分子表型，在这里，我们研究结合和蛋白质丰度，在多个遗传背景和拟合热力学模型，使用神经网络。我们将这种方法应用于人类中发现的两个最常见的蛋白质相互作用结构域，SH 3结构域和PDZ结构域，以产生全面的变构通信图谱。变构突变是丰富的，具有改变网络的“边缘”变体的大的突变靶空间。突变更可能是变构的，更接近结合界面，在甘氨酸残基处和在连接到PDZ结构域内的相对表面的特定残基处。这种量化突变对多种分子表型和多种遗传背景的影响的一般方法应该能够快速而全面地绘制许多蛋白质的能量和变构景观。
Allosteric communication between distant sites in proteins is central to biological regulation but still poorly characterized, limiting understanding, engineering and drug development(1-6). An important reason for this is the lack of methods to comprehensively quantify allostery in diverse proteins. Here we address this shortcoming and present a method that uses deep mutational scanning to globally map allostery. The approach uses an efficient experimental design to infer en masse the causal biophysical effects of mutations by quantifying multiple molecular phenotypes-here we examine binding and protein abundance-in multiple genetic backgrounds and fitting thermodynamic models using neural networks. We apply the approach to two of the most common protein interaction domains found in humans, an SH3 domain and a PDZ domain, to produce comprehensive atlases of allosteric communication. Allosteric mutations are abundant, with a large mutational target space of network-altering 'edgetic' variants. Mutations are more likely to be allosteric closer to binding interfaces, at glycine residues and at specific residues connecting to an opposite surface within the PDZ domain. Thisgeneral approach of quantifying mutational effects for multiple molecular phenotypes and in multiple genetic backgrounds should enable the energetic and allosteric landscapes of many proteins to be rapidly and comprehensively mapped.