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号外 | 王初课题组与陈鹏课题组合作开发通用活体蛋白激活技术

作者: 王初课题组 发布: 2019-05-12 353阅读 386评论

近日，本课题组与北京大学化学与分子工程学院陈鹏课题组合作，在Nature杂志上发表题为“Time-resolved protein activation by proximal decaging in living systems”的研究文章，报道了一种基于基因编码的非天然氨基酸“邻近脱笼”策略（CAGE-Prox），利用计算机辅助筛选，在一系列不同蛋白质上实现了高时间分辨率的原位激活，为在活体环境下研究蛋白质的瞬时功能动态变化提供了一种通用的技术手段。

“化学脱笼”策略是一类适用性广、干扰度低的蛋白质激活方法，通过对酶的关键催化残基进行保护与脱保护，实现蛋白功能“关”和“开”的操控。陈鹏课题组先后在赖氨酸、酪氨酸等活性氨基酸上实现了生物正交的断键反应和“脱笼”，在活细胞及动物活体实现了蛋白激酶，荧光素酶等蛋白质家族的特异性激活。然而对于很多没有“脱笼”反应的氨基酸或者活性位点不明确的酶，尚缺乏一种通用易行的原位激活手段。

王初课题组一直致力于在蛋白质组学的各种维度海量数据中，使用计算机辅助手段进行数据的理解和信息挖掘。例如对于质谱数据（0维）中Se同位素特征谱的识别（Gao, Yang, et. al., 2018）；对蛋白序列（1维）中活性半胱氨酸酸的预测（Wang, Chen, Li, et. al., 2017）；利用同源蛋白的多序列比对（2维）对氨基酸相互作用网络的预测（work in preparation）；以及利用Rosetta软件对蛋白质进行结构（3维）建模和设计。

两个课题组一拍即合，希望能够共同开发一种不受氨基酸种类限制的通用“脱笼策略”。我们猜测，在蛋白质催化中心附近的其他氨基酸，都可能对稳定蛋白结构或支持底物结合起到重要贡献，如果可以找到某种氨基酸，在口袋中合适位置引入它的突变体，使其在被保护的状态下通过位阻效应阻止底物结合，而脱保护后却不影响蛋白活性，就可以用相同的“脱笼”反应操控任意蛋白的活性。于是，我们首先分析了一个含有一百多个蛋白与小分子复合物结构的数据库，统计其中口袋附近每种氨基酸出现的概率，并计算把它突变成其它种类氨基酸时对蛋白质稳定性的影响。结果发现，酪氨酸具有较高的天然丰度，且引入酪氨酸突变不易影响蛋白稳定性。同时，针对酪氨酸已经有了理想的脱笼反应以及非天然氨基酸（ONBY）插入手段（见下图）。

解决了what和how的问题，我们接着要问where。以萤火虫-荧光素酶（Fluc）为模型，我们随机选择了60个位点插入ONBY，实验发现有四个位点在脱保护后具有较高的激活能力，而保护时的抑制倍数很高。其他位置或者不能被保护基团抑制，或者不能在脱保护后被重新激活。

经过对每个位点进行几何参数和突变能量的分析，我们找到了一组合适的参数阈值，可以在保留期望的成功位点同时，筛掉大部分无效的位点。

基于这些信息，我们设计了一整套计算机虚拟位点筛选流程，可以发现合适的邻近位点插入非天然氨基酸ONBY，推荐给实验进行验证。完整计算流程见下图。

由此我们得到了一套通用的蛋白原位激活的解决方案。首先对感兴趣的目标蛋白进行计算机筛选，找到合适的ONBY插入位点。接着用非天然氨基酸插入技术在该位点引入带保护的酪氨酸，此时要求蛋白的活性被抑制。在需要的时间点通过UV照射使其脱保护，得到一个天然的酪氨酸或酪氨酸突变体，此时要求蛋白活性被重新激活。通过实验验证得到符合我们预期的突变体。我们在七种不同的蛋白酶上测试这套方案，均可以通过计算筛选得到不多于10个的建议位点，并通过实验找到符合要求的突变体。值得一提的是纳米荧光素酶（NFluc），这个酶并没有已知的活性位点和底物结合结构，我们利用分子对接方法得到多个可能的底物结合构象，再进行筛选计算，最后的15个推荐位点中，有3个获得成功。

接下来，我们对其中三种重要蛋白进行高时间分辨率的体内原位特异性激活，进一步建立了“激酶正交激活系统”，实现了“时间分辨的蛋白质组分析”，发展了“抗肿瘤蛋白质前药”。这些实例进一步展示了CAGE-Prox作为一种通用的前沿化学生物学技术，在活细胞及活体内进行蛋白质功能动态调控与研究的广阔前景。限于篇幅，对于这三个应用的介绍我们会在后续的报道中详细介绍，敬请关注。

北京大学前沿交叉学科研究院博士毕业生王杰、化学与分子工程学院博士后刘源、研究生刘衍军为该论文共同第一作者，陈鹏教授和王初研究员为本文的共同通讯作者。该项工作得到了国家自然科学基金委、科技部、教育部、北京分子科学国家研究中心和北大—清华生命科学联合中心的资助。王初研究员特别感谢中组部“青年千人计划”的支持。

本文作者：LY
原文链接：https://www.nature.com/articles/s41586-019-1188-1
原文引用：doi:10.1038/s41586-019-1188-1

衷心感谢BioArt公众号对本工作的报道以及各位资深专家的点评：专家点评Nature长文 | 突破！北大陈鹏/王初合开发作活体内蛋白质瞬时原位激活新技术
Nature杂志News and Views专栏评论：
https://www.nature.com/articles/d41586-019-01394-1

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作者: 王初课题组

Our research programs focus on the development and application of multi-disciplinary tools in chemoproteomics, biochemistry, bioinformatics and computational structure biology to 1) globally uncover novel funtional sites in enzymes that are post-translationally regulated by endogenous reactive metabolites or targeted by drug compounds; 2) interrogate the underlying molecular mechanisms by which these modifications regulate protein function to perturb key cellular signaling pathways and 3) develop computational tools to predict, model and design such protein-small molecule interactions. These studies have the great potential to provide penetrating mechanistic insights into the molecular basis for numerous diseases functionally linked to metabolic disorder as well as to integrate and streamline efforts in inhibitor discovery, drug design and the functional annotation of uncharacterized enzymes in the post-genomic era.



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