北京大學理論生物學中心/化學與分子工程學院來魯華教授領(lǐng)導的課題組在功能蛋白質(zhì)設計方面取得可喜進展，其研究成果發(fā)表于3月27日出版的《美國科學院院刊》上（Liu S, Liu SY, Zhu XL, Liang HH, Cao AN, Chang ZJ and Lai LH*. Nonnatural protein-protein interaction-pair design by key residues grafting. PNAS,104:5330-5335,2007）。論文發(fā)表后引起了學界關(guān)注，BioCentury就此成果發(fā)表了專訪。該論文的第一作者劉森同學是理論生物學中心2002年正式招收的第一批跨學科的研究生,。
蛋白質(zhì)在生命活動中占有非常重要的地位，幾乎所有的生命活動都需要蛋白質(zhì)的參與。生命現(xiàn)象紛繁復雜,，所涉及到的蛋白質(zhì)功能各異。在履行生命功能的過程中，蛋白質(zhì)不斷地與其它分子（如蛋白質(zhì),，核酸,，小分子等）發(fā)生相互作用。就如同現(xiàn)實生活中,，我們看到的鑰匙有各種各樣的形狀,，但是只要它們的關(guān)鍵部分“齒紋”一樣，就能夠有同樣的功能,，打開同一把鎖,。相互作用的兩個蛋白質(zhì)，就有如“鎖”和“鑰匙”的關(guān)系,。來魯華教授課題組的研究目的,，就是將一個蛋白質(zhì)行使功能的關(guān)鍵“齒紋”（氨基酸殘基），復制（“嫁接”）到另一個結(jié)構(gòu)完全不同的蛋白質(zhì)上,，使它具有開同一把“鎖”的功能（和同一個蛋白質(zhì)結(jié)合）,。
蛋白質(zhì)和蛋白質(zhì)結(jié)合時，往往存在少數(shù)幾個非常關(guān)鍵的殘基,，對結(jié)合起到主要作用,。基于這種情況,，來魯華教授課題組發(fā)展了一種“蛋白質(zhì)關(guān)鍵殘基嫁接”的算法,，用于將一個蛋白質(zhì)的關(guān)鍵功能性殘基嫁接到另一個不同結(jié)構(gòu)的蛋白質(zhì)上，并將這種方法應用到了實際體系的研究中,，取得了成功,。促紅細胞生成素（EPO）通過和它的受體（EPOR）相互作用，促進紅細胞的分化和成熟,。將EPO上的關(guān)鍵功能性殘基嫁接到一個結(jié)構(gòu)完全不同的PH結(jié)構(gòu)域蛋白上后,，PH蛋白具有了和EPOR結(jié)合的功能，而這種功能在自然界中是不存在的,。這種方法將有可能應用在更為廣泛的例子上,，實現(xiàn)蛋白質(zhì)功能的自由設計。
原始出處:
Published online before print March 19, 2007, 10.1073/pnas.0606198104
PNAS | March 27, 2007 | vol. 104 | no. 13 | 5330-5335
Nonnatural protein–protein interaction-pair design by key residues grafting
Sen Liu*,, Shiyong Liu*,, Xiaolei Zhu*, Huanhuan Liang*, Aoneng Cao*, Zhijie Chang, and Luhua Lai*,,
*Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Center for Theoretical Biology, Peking University, Beijing 100871, China; and Department of Biological Sciences and Biotechnology, School of Medicine, Tsinghua University, Beijing 100084, China
Edited by Stephen L. Mayo, California Institute of Technology, Pasadena, CA, and approved January 22, 2007 (received for review July 21, 2006)
Protein–protein interface design is one of the most exciting fields in protein science; however, designing nonnatural protein–protein interaction pairs remains difficult. In this article we report a de novo design of a nonnatural protein–protein interaction pair by scanning the Protein Data Bank for suitable scaffold proteins that can be used for grafting key interaction residues and can form stable complexes with the target protein after additional mutations. Using our design algorithm, an unrelated protein, rat PLC1-PH (pleckstrin homology domain of phospholipase C-1), was successfully designed to bind the human erythropoietin receptor (EPOR) after grafting the key interaction residues of human erythropoietin binding to EPOR. The designed mutants of rat PLC1-PH were expressed and purified to test their binding affinities with EPOR. A designed triple mutation of PLC1-PH (ERPH1) was found to bind EPOR with high affinity (KD of 24 nM and an IC50 of 5.7 µM) both in vitro and in a cell-based assay, respectively, although the WT PLC1-PH did not show any detectable binding under the assay conditions. The in vitro binding affinities of the PLC1-PH mutants correlate qualitatively to the computational binding affinities, validating the design and the protein–protein interaction model. The successful practice of finding a proper protein scaffold and making it bind with EPOR demonstrates a prospective application in protein engineering targeting protein–protein interfaces.
de novo design of protein–protein interaction pair | erythropoietin | functional site grafting | key residue at interface
