Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling.
Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling.
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DOI：
10.1038/s41467-021-27342-0
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发表时间：
2021-12-08
影响因子：
16.6
通讯作者：
Schmidt D
中科院分区：
文献类型：
--
作者：
Coyote-Maestas W;Nedrud D;Suma A;He Y;Matreyek KA;Fowler DM;Carnevale V;Myers CL;Schmidt D
蛋白质结构域是蛋白质结构和功能的基本单位。基因组和蛋白质组学的比较分析表明，结构域重组是多结构域蛋白功能多样化的主要驱动因素，并且已知一些限制性基因组机制。关于决定蛋白质结构域是否可以组合成可行的蛋白质折叠的生物物理机制，我们知之甚少。在这里，我们使用大规模平行插入诱变来确定300,000多个内向整流器K+通道Kir2.1的结构域重组变体与通道表面表达的兼容性。我们的数据表明，在离子通道进化过程中，基因组和生物物理机制协同作用，有利于在蛋白质末端获得大的结构域。我们使用机器学习在Kir2.1中构建域兼容性的定量生物物理模型，使我们能够推导出设计域插入变体的基本规则，这些变体可以折叠并传输到细胞表面。定位Kir2.1对基序插入簇的不同组的响应，对应于通道的连续结构区域，具有不同的生物物理特性，可提供折叠稳定性或门控转换。这表明插入分析是一种高通量的离子通道结构区域功能注释方法。在这里，作者进行了大规模，高通量的生化分析，以确定超过300,000个结构域重组变异的相容性内向整流器K+通道Kir2.1。他们推导出设计结构域插入变异的规则，这些变异可以折叠并传输到细胞表面，并得出结论，在蛋白质末端插入结构域在进化上是有利的。
Protein domains are the basic units of protein structure and function. Comparative analysis of genomes and proteomes showed that domain recombination is a main driver of multidomain protein functional diversification and some of the constraining genomic mechanisms are known. Much less is known about biophysical mechanisms that determine whether protein domains can be combined into viable protein folds. Here, we use massively parallel insertional mutagenesis to determine compatibility of over 300,000 domain recombination variants of the Inward Rectifier K+ channel Kir2.1 with channel surface expression. Our data suggest that genomic and biophysical mechanisms acted in concert to favor gain of large, structured domain at protein termini during ion channel evolution. We use machine learning to build a quantitative biophysical model of domain compatibility in Kir2.1 that allows us to derive rudimentary rules for designing domain insertion variants that fold and traffic to the cell surface. Positional Kir2.1 responses to motif insertion clusters into distinct groups that correspond to contiguous structural regions of the channel with distinct biophysical properties tuned towards providing either folding stability or gating transitions. This suggests that insertional profiling is a high-throughput method to annotate function of ion channel structural regions. Here, the authors perform a large-scale, high-throughput biochemical assay to determine the compatibility of over 300,000 domain recombination variants of the inward rectifier K+ channel Kir2.1. They derive rules for designing domain insertion variants that fold and traffic to the cell surface and conclude that the insertion of domains at protein termini is evolutionary favoured.
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影响因子：
7
作者：
Basu, Malay Kumar;Carmel, Liran;Koonin, Eugene V.
通讯作者：
Koonin, Eugene V.
影响因子：
48
作者：
Fowler, Douglas M.;Fields, Stanley
通讯作者：
Fields, Stanley
影响因子：
56.9
作者：
Dahiyat, BI;Mayo, SL
通讯作者：
Mayo, SL
影响因子：
48
作者：
Alberio, Laura;Locarno, Andrea;Moroni, Anna
通讯作者：
Moroni, Anna
DOI：
10.1073/pnas.0604580103
发表时间：
2006-11-28
影响因子：
11.1
作者：
Batey, Sarah;Clarke, Jane
通讯作者：
Clarke, Jane