School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.
Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.
Nanoscale. 2021 Dec 2;13(46):19593-19603. doi: 10.1039/d1nr05679d.
Functional amyloids are abundant in living organisms from prokaryotes to eukaryotes playing diverse biological roles. In contrast to the irreversible aggregation of most known pathological amyloids, we postulate that naturally-occurring functional amyloids are reversible under evolutionary pressure to be able to modulate the fibrillization process, reuse the composite peptides, or perform their biological functions. β-Endorphin, an endogenous opioid peptide hormone, forms such kinds of reversible amyloid fibrils in secretory granules for efficient storage and returns to the functional state of monomers upon release into the blood. The environmental change between low pH in secretory granules and neutral pH in extracellular spaces is believed to drive the reversible fibrillization of β-endorphin. Here, we investigate the critical role of a buried glutamate, Glu8, in the pH-responsive disassembly of β-endorphin fibrils using all-atom molecular dynamics simulations along with structure-based p prediction. The fibril was stable at pH 5.5 or lower with all the buried Glu8 residues protonated and neutrally charged. After switching to neutral pH, the Glu8 residues of peptides at the outer layers of the ordered fibrils became deprotonated due to partial solvent exposure, causing sheet-to-coil conformational changes and subsequent exposure of adjacent Glu8 residues in the inner chains. iterative deprotonation of Glu8 and induced structural disruption, all Glu8 residues would be progressively deprotonated. Electrostatic repulsion between deprotonated Glu8 residues along with their high solvation tendency disrupted the hydrogen bonding between the β1 strands and increased the solvent exposure of those otherwise buried residues in the cross-β core. Overall, our computational study reveals that the strategic positioning of ionizable residues into the cross-β core is a potential approach for designing reversible amyloid fibrils as pH-responsive smart bio-nanomaterials.
功能性淀粉样蛋白在原核生物到真核生物的生物体中大量存在，发挥着多样化的生物学作用。与大多数已知病理性淀粉样蛋白的不可逆聚集相反，我们假设天然存在的功能性淀粉样蛋白在进化压力下是可逆的，能够调节纤维形成过程、再利用复合肽或发挥其生物学功能。β-内啡肽是一种内源性阿片肽激素，在分泌颗粒中形成这种可逆的淀粉样纤维，以实现有效的储存，并在释放到血液中时恢复为单体的功能状态。人们认为，在分泌颗粒中的低 pH 和细胞外空间中的中性 pH 之间的环境变化驱动β-内啡肽的可逆纤维形成。在这里，我们使用全原子分子动力学模拟和基于结构的 p 预测，研究了深埋的谷氨酸 Glu8 在β-内啡肽纤维解聚中的关键作用。在 pH5.5 或更低时，纤维是稳定的，所有深埋的 Glu8 残基都质子化和带中性电荷。切换到中性 pH 后，由于部分溶剂暴露，处于有序纤维外层的肽中的 Glu8 残基去质子化，导致片层到螺旋构象变化，随后暴露内层链中的相邻 Glu8 残基。随着 Glu8 的连续去质子化和结构破坏，所有 Glu8 残基将逐渐去质子化。带负电荷的 Glu8 残基之间的静电排斥以及它们高的溶剂化倾向破坏了β1 链之间的氢键，并增加了那些原本在交叉β核心中深埋的残基的溶剂暴露。总的来说，我们的计算研究表明，将可离子化残基定位在交叉β核心中是设计作为 pH 响应型智能生物纳米材料的可逆淀粉样纤维的一种潜在方法。
