Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Nature. 2024 Aug;632(8026):911-920. doi: 10.1038/s41586-024-07813-2. Epub 2024 Aug 14.
Allosteric modulation of protein function, wherein the binding of an effector to a protein triggers conformational changes at distant functional sites, plays a central part in the control of metabolism and cell signalling. There has been considerable interest in designing allosteric systems, both to gain insight into the mechanisms underlying such 'action at a distance' modulation and to create synthetic proteins whose functions can be regulated by effectors. However, emulating the subtle conformational changes distributed across many residues, characteristic of natural allosteric proteins, is a significant challenge. Here, inspired by the classic Monod-Wyman-Changeux model of cooperativity, we investigate the de novo design of allostery through rigid-body coupling of peptide-switchable hinge modules to protein interfaces that direct the formation of alternative oligomeric states. We find that this approach can be used to generate a wide variety of allosterically switchable systems, including cyclic rings that incorporate or eject subunits in response to peptide binding and dihedral cages that undergo effector-induced disassembly. Size-exclusion chromatography, mass photometry and electron microscopy reveal that these designed allosteric protein assemblies closely resemble the design models in both the presence and absence of peptide effectors and can have ligand-binding cooperativity comparable to classic natural systems such as haemoglobin. Our results indicate that allostery can arise from global coupling of the energetics of protein substructures without optimized side-chain-side-chain allosteric communication pathways and provide a roadmap for generating allosterically triggerable delivery systems, protein nanomachines and cellular feedback control circuitry.
蛋白质功能的变构调节,其中效应物与蛋白质的结合触发功能位点的远距离构象变化,在代谢和细胞信号转导的控制中起着核心作用。人们对设计变构系统产生了浓厚的兴趣,既为了深入了解这种“远距离作用”调节的机制,也为了创造其功能可以被效应物调节的合成蛋白质。然而,模拟自然变构蛋白中特征性的、分布在许多残基上的微妙构象变化是一个重大挑战。在这里,受经典的 Monod-Wyman-Changeux 变构协同模型的启发,我们通过将肽可切换铰链模块刚性耦合到指导形成替代寡聚状态的蛋白质界面,来研究从头设计变构。我们发现,这种方法可用于产生各种变构开关系统,包括响应肽结合而包含或排出亚基的环状分子,以及经历效应物诱导的拆卸的二面角笼。尺寸排阻色谱、质量光度法和电子显微镜显示,这些设计的变构蛋白组装体在存在和不存在肽效应物的情况下都非常类似于设计模型,并且可以具有与经典天然系统(如血红蛋白)相当的配体结合协同性。我们的结果表明,变构作用可以源自蛋白质亚结构的能量的全局耦合,而不需要优化的侧链-侧链变构通讯途径,并为产生变构触发的递药系统、蛋白质纳米机器和细胞反馈控制电路提供了路线图。