西湖大学卢培龙等研究人员合作实现左右异向蛋白质-蛋白质相互作用的精确从头设计。相关论文于2024年8月14日在线发表在《细胞研究》杂志上。

研究人员从头开始设计了由50-65个残基组成的D-蛋白，旨在靶向L-蛋白或L-肽的特定表面区域。研究人员设计的D-蛋白结合剂对人工l-肽以及两种具有治疗意义的天然蛋白：人肌钙蛋白受体激酶A（TrkA）的D5结构域和人白细胞介素-6（IL-6），并具有纳摩尔级的亲和力。

值得注意的是，这些D-蛋白结合剂具有很高的对映体特异性和靶向特异性。在基于细胞的实验中，设计的D-蛋白结合剂以高效力有效抑制了TrkA和IL-6的下游信号传导。这些结合剂还具有显著的热稳定性和抗蛋白酶降解性。所设计的D-蛋白-L-肽左右异向复合物的晶体结构分辨率为2.0埃，与设计模型非常相似，表明所采用的计算方法非常精确。

此外，该晶体结构还提供了有关螺旋L-肽和D-蛋白之间相互作用的宝贵信息，特别是阐明了异螺旋-螺旋相互作用的新模式。利用专门针对L-肽或L-蛋白的D-蛋白设计为系统探索镜像蛋白质宇宙开辟了途径，为各种应用铺平了道路。

据了解，选择性地与天然L-蛋白结合的非生物D-蛋白已引起生物技术的极大兴趣。然而，制约这种左右异向蛋白-蛋白相互作用的基本结构原理在很大程度上仍不为人所知。

附：英文原文

Title: Accurate de novo design of heterochiral protein–protein interactions

Author: Sun, Ke, Li, Sicong, Zheng, Bowen, Zhu, Yanlei, Wang, Tongyue, Liang, Mingfu, Yao, Yue, Zhang, Kairan, Zhang, Jizhong, Li, Hongyong, Han, Dongyang, Zheng, Jishen, Coventry, Brian, Cao, Longxing, Baker, David, Liu, Lei, Lu, Peilong

Issue&Volume: 2024-08-14

Abstract: Abiotic D-proteins that selectively bind to natural L-proteins have gained significant biotechnological interest. However, the underlying structural principles governing such heterochiral protein–protein interactions remain largely unknown. In this study, we present the de novo design of D-proteins consisting of 50–65 residues, aiming to target specific surface regions of L-proteins or L-peptides. Our designer D-protein binders exhibit nanomolar affinity toward an artificial L-peptide, as well as two naturally occurring proteins of therapeutic significance: the D5 domain of human tropomyosin receptor kinase A (TrkA) and human interleukin-6 (IL-6). Notably, these D-protein binders demonstrate high enantiomeric specificity and target specificity. In cell-based experiments, designer D-protein binders effectively inhibited the downstream signaling of TrkA and IL-6 with high potency. Moreover, these binders exhibited remarkable thermal stability and resistance to protease degradation. Crystal structure of the designed heterochiral D-protein–L-peptide complex, obtained at a resolution of 2.0, closely resembled the design model, indicating that the computational method employed is highly accurate. Furthermore, the crystal structure provides valuable information regarding the interactions between helical L-peptides and D-proteins, particularly elucidating a novel mode of heterochiral helix–helix interactions. Leveraging the design of D-proteins specifically targeting L-peptides or L-proteins opens up avenues for systematic exploration of the mirror-image protein universe, paving the way for a diverse range of applications.

DOI: 10.1038/s41422-024-01014-2

Source: https://www.nature.com/articles/s41422-024-01014-2