Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations.
Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations.
复制标题
DOI：
10.7554/elife.67474
复制
发表时间：
2022-12-06
期刊：
影响因子：
7.7
通讯作者：
Ozkan SB
中科院分区：
文献类型：
--
作者：
Kazan IC;Sharma P;Rahman MI;Bobkov A;Fromme R;Ghirlanda G;Ozkan SB
我们开发了集成的协同进化和动态耦合(ICDC)方法来识别、突变和评估远端位点以调节功能。我们首先通过分析现有的TEM1β-内酰胺酶突变适合度数据来验证该方法，结果表明变构位置与活性部位共同进化并动态耦合显着地调节功能。我们进一步应用ICDC方法来确定选择性与二甘露糖结合的凝集素氰化韦林-N(CV-N)中能够调节结合亲和力的位置及其突变，并通过自适应BP-Dock预测其变体的结合能。计算和实验分析表明，ICDC鉴定的结合增强突变体影响了结合口袋的动力学，并表明结合残基的硬化补偿了结合的熵成本。这项工作提出了一种远端突变通过动态变构来调节功能的机制，并提供了一种确定突变候选者以优化蛋白质功能的蓝图。
We develop integrated co-evolution and dynamic coupling (ICDC) approach to identify, mutate, and assess distal sites to modulate function. We validate the approach first by analyzing the existing mutational fitness data of TEM-1 β-lactamase and show that allosteric positions co-evolved and dynamically coupled with the active site significantly modulate function. We further apply ICDC approach to identify positions and their mutations that can modulate binding affinity in a lectin, cyanovirin-N (CV-N), that selectively binds to dimannose, and predict binding energies of its variants through Adaptive BP-Dock. Computational and experimental analyses reveal that binding enhancing mutants identified by ICDC impact the dynamics of the binding pocket, and show that rigidification of the binding residues compensates for the entropic cost of binding. This work suggests a mechanism by which distal mutations modulate function through dynamic allostery and provides a blueprint to identify candidates for mutagenesis in order to optimize protein function.
影响因子：
2.9
作者：
Patsalo, Vadim;Raleigh, Daniel P.;Green, David F.
通讯作者：
Green, David F.