小柯机器人

美国华盛顿大学David Baker等研究人员合作通过超螺旋匹配从头设计模块化的肽结合蛋白。该研究于2023年4月5日在线发表于国际一流学术期刊《自然》。

受自然和重新设计的蛋白质-肽系统的启发，研究人员着手设计出由重复单元组成的蛋白质，这些重复单元能与具有重复序列的肽结合，蛋白质的重复单元与肽的重复单元之间有一对一的对应。研究人员使用几何散列法来确定了蛋白质骨架和肽对接的安排，这些安排与蛋白质侧链和肽骨架之间的双叉氢键兼容。然后，蛋白质序列的其余部分被优化，以利于折叠和肽的结合。设计出的重复蛋白在多肽II构象中与六个不同的三肽-重复序列结合。

这些蛋白质是超稳定的，在体外和活细胞中以纳摩尔到皮摩尔的亲和力与它们的三肽目标的四到六个串联重复序列结合。晶体结构显示了蛋白质和肽之间重复的相互作用，包括从蛋白质侧链到肽骨的氢键梯子。通过重新设计各个重复单元的结合界面，对非重复的肽序列和原生蛋白质无序区域的特异性可以被实现。

据悉，设计序列特异性肽结合蛋白的一般方法将在蛋白质组学和合成生物学中具有广泛的用途。然而，设计肽结合蛋白是具有挑战性的，因为大多数肽没有孤立的定义结构，氢键必须与肽骨架中埋藏的极性基团结合。

附：英文原文

Title: De novo design of modular peptide-binding proteins by superhelical matching

Author: Wu, Kejia, Bai, Hua, Chang, Ya-Ting, Redler, Rachel, McNally, Kerrie E., Sheffler, William, Brunette, T. J., Hicks, Derrick R., Morgan, Tomos E., Stevens, Tim J., Broerman, Adam, Goreshnik, Inna, DeWitt, Michelle, Chow, Cameron M., Shen, Yihang, Stewart, Lance, Derivery, Emmanuel, Silva, Daniel Adriano, Bhabha, Gira, Ekiert, Damian C., Baker, David

Issue&Volume: 2023-04-05

Abstract: General approaches for designing sequence-specific peptide-binding proteins would have wide utility in proteomics and synthetic biology. However, designing peptide-binding proteins is challenging, as most peptides do not have defined structures in isolation, and hydrogen bonds must be made to the buried polar groups in the peptide backbone1,2,3. Here, inspired by natural and re-engineered protein–peptide systems4,5,6,7,8,9,10,11, we set out to design proteins made out of repeating units that bind peptides with repeating sequences, with a one-to-one correspondence between the repeat units of the protein and those of the peptide. We use geometric hashing to identify protein backbones and peptide-docking arrangements that are compatible with bidentate hydrogen bonds between the side chains of the protein and the peptide backbone12. The remainder of the protein sequence is then optimized for folding and peptide binding. We design repeat proteins to bind to six different tripeptide-repeat sequences in polyproline II conformations. The proteins are hyperstable and bind to four to six tandem repeats of their tripeptide targets with nanomolar to picomolar affinities in vitro and in living cells. Crystal structures reveal repeating interactions between protein and peptide interactions as designed, including ladders of hydrogen bonds from protein side chains to peptide backbones. By redesigning the binding interfaces of individual repeat units, specificity can be achieved for non-repeating peptide sequences and for disordered regions of native proteins.

DOI: 10.1038/s41586-023-05909-9

Source: https://www.nature.com/articles/s41586-023-05909-9

Nature：《自然》，创刊于1869年。隶属于施普林格·自然出版集团，最新IF：69.504
官方网址：http://www.nature.com/
投稿链接：http://www.nature.com/authors/submit_manuscript.html