Enabling QTY Server for Designing Water-Soluble α-Helical Transmembrane Proteins.
Enabling QTY Server for Designing Water-Soluble α-Helical Transmembrane Proteins.
复制标题
启用 QTY 服务器来设计水溶性 α 螺旋跨膜蛋白
作者：
Tao F;Tang H;Zhang S;Li M;Xu P
膜蛋白，特别是那些α-螺旋，如转运蛋白和G-蛋白偶联受体（GPCR），具有重要的生物相关性。然而，它们的表达和纯化由于它们差的水溶性而造成困难，这阻碍了该领域的进展。QTY方法是一种基于编码的蛋白质工程方法，最近被开发用于生产可溶性跨膜蛋白。在这里，我们描述了一个全面的Web服务器建立的QTY设计和它的相关性，在硅片分析。通常，简单设计模型预计仅需要2至4分钟的计算机时间，文库设计模型需要2至5小时，这取决于靶蛋白的大小和跨膜螺旋的数量。提供了将服务器与简单设计和库设计模块一起使用的详细协议。实验方法的QTY设计后，也包括促进这种方法的实施。使用微生物跨膜蛋白和设计的蛋白质与其来源之间的结构比对，通过采用AlphaFold 2，进一步评估了设计管道。结果表明，由开发的管道产生的突变体在三维（3D）结构方面与它们的起源高度相同。总之，我们的Web服务器和相关协议的利用将使基于QTY的蛋白质工程以方便，快速，准确和合理的方式实现。蛋白质溶解服务器（PSS）可在http://pss.sjtu.edu.cn公开获得。
Membrane proteins, particularly those that are α-helical, such as transporters and G-protein-coupled receptors (GPCRs), have significant biological relevance. However, their expression and purification pose difficulties because of their poor water solubilities, which impedes progress in this field. The QTY method, a code-based protein-engineering approach, was recently developed to produce soluble transmembrane proteins. Here, we describe a comprehensive Web server built for QTY design and its relevance for in silico analyses. Typically, the simple design model is expected to require only 2 to 4 min of computer time, and the library design model requires 2 to 5 h, depending on the target protein size and the number of transmembrane helices. Detailed protocols for using the server with both the simple design and library design modules are provided. Methods for experiments following the QTY design are also included to facilitate the implementation of this approach. The design pipeline was further evaluated using microbial transmembrane proteins and structural alignment between the designed proteins and their origins by employing AlphaFold2. The results reveal that mutants generated by the developed pipeline were highly identical to their origins in terms of three-dimensional (3D) structures. In summary, the utilization of our Web server and associated protocols will enable QTY-based protein engineering to be implemented in a convenient, fast, accurate, and rational manner. The Protein Solubilizing Server (PSS) is publicly available at http://pss.sjtu.edu.cn.
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影响因子：
64.8
作者：
Jumper J;Evans R;Pritzel A;Green T;Figurnov M;Ronneberger O;Tunyasuvunakool K;Bates R;Žídek A;Potapenko A;Bridgland A;Meyer C;Kohl SAA;Ballard AJ;Cowie A;Romera-Paredes B;Nikolov S;Jain R;Adler J;Back T;Petersen S;Reiman D;Clancy E;Zielinski M;Steinegger M;Pacholska M;Berghammer T;Bodenstein S;Silver D;Vinyals O;Senior AW;Kavukcuoglu K;Kohli P;Hassabis D
通讯作者：
Hassabis D
影响因子：
14.9
作者：
Schymkowitz J;Borg J;Stricher F;Nys R;Rousseau F;Serrano L
通讯作者：
Serrano L
影响因子：
2.9
作者：
Li, Yunqi;Zhang, Jian;Tai, David;Middaugh, C. Russell;Zhang, Yang;Fang, Jianwen
通讯作者：
Fang, Jianwen
影响因子：
6
作者：
Buß O;Rudat J;Ochsenreither K
通讯作者：
Ochsenreither K
影响因子：
5.8
作者：
Möller, S;Croning, MDR;Apweiler, R
通讯作者：
Apweiler, R