IC-CNR, Institute of Crystallography, National Research Council, Via Salaria km 29.300, 00015 Monterotondo, Rome, Italy.
University of Palermo, Department of Physics and Chemistry, Viale delle Scienze Ed. 17, Italy; Institute of Structure of Matter, National Research Council, Laboratorio Liquidi Ionici, Rome, Italy.
Int J Biol Macromol. 2020 Nov 15;163:817-823. doi: 10.1016/j.ijbiomac.2020.07.010. Epub 2020 Jul 10.
Biomimetic design represents an emerging field for improving knowledge of natural molecules, as well as to project novel artificial tools with specific functions for biosensing. Effective strategies have been exploited to design artificial bioreceptors, taking inspiration from complex supramolecular assemblies. Among them, size-minimization strategy sounds promising to provide bioreceptors with tuned sensitivity, stability, and selectivity, through the ad hoc manipulation of chemical species at the molecular scale. Herein, a novel biomimetic peptide enabling herbicide binding was designed bioinspired to the D1 protein of the Photosystem II of the green alga Chlamydomonas reinhardtii. The D1 protein portion corresponding to the Q plastoquinone binding niche is capable of interacting with photosynthetic herbicides. A 50-mer peptide in the region of D1 protein from the residue 211 to 280 was designed in silico, and molecular dynamic simulations were performed alone and in complex with atrazine. An equilibrated structure was obtained with a stable pocked for atrazine binding by three H-bonds with SER222, ASN247, and HIS272 residues. Computational data were confirmed by fluorescence spectroscopy and circular dichroism on the peptide obtained by automated synthesis. Atrazine binding at nanomolar concentrations was followed by fluorescence spectroscopy, highlighting peptide suitability for optical sensing of herbicides at safety limits.
仿生设计代表了一个新兴领域，旨在增进对天然分子的认识，并为生物传感设计具有特定功能的新型人工工具。人们已经利用了有效的策略来设计人工生物受体，从复杂的超分子组装中汲取灵感。其中，通过在分子尺度上专门操纵化学物质，最小化尺寸的策略有望为生物受体提供可调的灵敏度、稳定性和选择性。本文受绿藻莱茵衣藻光系统 II 的 D1 蛋白启发，设计了一种新型仿生肽，使其能够与除草剂结合。D1 蛋白与质体醌结合的部分能够与光合作用除草剂相互作用。在 D1 蛋白区域内设计了一个 50 个残基的肽，从残基 211 到 280，单独和与莠去津复合物进行了分子动力学模拟。通过与 SER222、ASN247 和 HIS272 残基的三个氢键，获得了一个稳定的莠去津结合袋的平衡结构。通过自动合成获得的肽的荧光光谱和圆二色性证实了计算数据。通过荧光光谱跟踪纳摩尔浓度的莠去津结合，突出了该肽在安全限制下光学检测除草剂的适用性。
