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光响应蛋白-蛋白相互作用的从头设计能够实现蛋白质组装体的可逆形成。

De novo design of light-responsive protein-protein interactions enables reversible formation of protein assemblies.

作者信息

Yu Bowen, Liu Jiao, Cui Zhanyuan, Wang Chu, Chen Peipei, Wang Chentong, Zhang Yanzhe, Zhu Xingxing, Zhang Ze, Li Shichao, Pan Jinheng, Xie Mingqi, Shen Huaizong, Cao Longxing

机构信息

School of Life Sciences, Westlake University, Hangzhou, China.

School of Basic Medical Sciences, Shandong Second Medical University, Weifang, China.

出版信息

Nat Chem. 2025 Aug 28. doi: 10.1038/s41557-025-01929-2.


DOI:10.1038/s41557-025-01929-2
PMID:40877575
Abstract

Light-responsive proteins play an essential role in all domains of life by sensing and responding to environmental light signals. However, the de novo design of light-responsive proteins with precisely defined structures and reversible responsive behaviours is an unmet challenge. Here we describe a computational approach to design protein-protein interactions regulated by non-canonical amino acids, focusing on the light-responsive phenylalanine-4'-azobenzene (AzoF). Using this approach, we designed light-responsive cyclic homo-oligomers and heterodimers, which only assemble in AzoF's trans configuration and disassemble when AzoF photoisomerizes to the cis configuration. Biophysical characterization confirms the light-responsive assembly and disassembly of these complexes, and the crystal structures match the design models with atomic accuracy. We demonstrate the applicability of these light-responsive proteins in constructing light-responsive hydrogels and engineering synthetic ligand receptors to optocontrol cell signalling in mammalian cells. Our approach opens avenues for designing environmentally responsive protein structures and broadens the toolkit for optogenetics and optochemistry.

摘要

光响应蛋白通过感知和响应环境光信号,在生命的各个领域发挥着至关重要的作用。然而,从头设计具有精确结构和可逆响应行为的光响应蛋白是一项尚未解决的挑战。在此,我们描述了一种计算方法,用于设计由非天然氨基酸调控的蛋白质-蛋白质相互作用,重点关注光响应性苯丙氨酸-4'-偶氮苯(AzoF)。使用这种方法,我们设计了光响应性环状同聚体和异二聚体,它们仅在AzoF的反式构型中组装,并在AzoF光异构化为顺式构型时解离。生物物理表征证实了这些复合物的光响应性组装和解离,并且晶体结构与设计模型在原子水平上精确匹配。我们展示了这些光响应蛋白在构建光响应水凝胶以及工程化合成配体受体以光控哺乳动物细胞中的细胞信号传导方面的适用性。我们的方法为设计环境响应性蛋白质结构开辟了途径,并拓宽了光遗传学和光化学的工具集。

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本文引用的文献

[1]
Engineering a genomically recoded organism with one stop codon.

Nature. 2025-3

[2]
New Insight Into Phytochromes: Connecting Structure to Function.

Annu Rev Plant Biol. 2024-7

[3]
De novo design of pH-responsive self-assembling helical protein filaments.

Nat Nanotechnol. 2024-7

[4]
Bright and stable monomeric green fluorescent protein derived from StayGold.

Nat Methods. 2024-4

[5]
De novo protein design-From new structures to programmable functions.

Cell. 2024-2-1

[6]
De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity.

Proc Natl Acad Sci U S A. 2024-2-6

[7]
Visualizing the DNA repair process by a photolyase at atomic resolution.

Science. 2023-12

[8]
Light-Oxygen-Voltage (LOV)-sensing Domains: Activation Mechanism and Optogenetic Stimulation.

J Mol Biol. 2024-3-1

[9]
De novo design of protein structure and function with RFdiffusion.

Nature. 2023-8

[10]
Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.

PLoS Comput Biol. 2023-5

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