Department of Chemistry, University of Copenhagen, Frederiksberg, Denmark.
PLoS One. 2024 May 8;19(5):e0293786. doi: 10.1371/journal.pone.0293786. eCollection 2024.
α-zeins are amphiphilic maize seed storage proteins with material properties suitable for a multitude of applications e.g., in renewable plastics, foods, therapeutics and additive manufacturing (3D-printing). To exploit their full potential, molecular-level insights are essential. The difficulties in experimental atomic-resolution characterization of α-zeins have resulted in a diversity of published molecular models. However, deep-learning α-zein models are largely unexplored. Therefore, this work studies an AlphaFold2 (AF2) model of a highly expressed α-zein using molecular dynamics (MD) simulations. The sequence of the α-zein cZ19C2 gave a loosely packed AF2 model with 7 α-helical segments connected by turns/loops. Compact tertiary structure was limited to a C-terminal bundle of three α-helices, each showing notable agreement with a published consensus sequence. Aiming to chart possible α-zein conformations in practically relevant solvents, rather than the native solid-state, the AF2 model was subjected to MD simulations in water/ethanol mixtures with varying ethanol concentrations. Despite giving structurally diverse endpoints, the simulations showed several patterns: In water and low ethanol concentrations, the model rapidly formed compact globular structures, largely preserving the C-terminal bundle. At ≥ 50 mol% ethanol, extended conformations prevailed, consistent with previous SAXS studies. Tertiary structure was partially stabilized in water and low ethanol concentrations, but was disrupted in ≥ 50 mol% ethanol. Aggregated results indicated minor increases in helicity with ethanol concentration. β-sheet content was consistently low (∼1%) across all conditions. Beyond structural dynamics, the rapid formation of branched α-zein aggregates in aqueous environments was highlighted. Furthermore, aqueous simulations revealed favorable interactions between the protein and the crosslinking agent glycidyl methacrylate (GMA). The proximity of GMA epoxide carbons and side chain hydroxyl oxygens simultaneously suggested accessible reactive sites in compact α-zein conformations and pre-reaction geometries for methacrylation. The findings may assist in expanding the applications of these technologically significant proteins, e.g., by guiding chemical modifications.
α-zeins 是一种具有两亲性的玉米种子贮藏蛋白，具有适用于多种应用的物质特性，例如可再生塑料、食品、治疗和添加剂制造（3D 打印）。为了充分发挥其潜力，需要从分子水平进行深入了解。由于实验原子分辨率表征α-zein 存在困难，导致已发表的分子模型多种多样。然而，深度学习的α-zein 模型在很大程度上尚未得到探索。因此，这项工作使用分子动力学（MD）模拟研究了高度表达的α-zein 的 AlphaFold2（AF2）模型。α-zein cZ19C2 的序列给出了一个松散堆积的 AF2 模型，其中包含 7 个α-螺旋片段，通过转角/环连接。紧凑的三级结构仅限于三个α-螺旋的 C 端束，每个螺旋都与已发表的共识序列表现出显著的一致性。为了在实际相关的溶剂中而不是在天然固态中描绘可能的α-zein 构象，该 AF2 模型在具有不同乙醇浓度的水/乙醇混合物中进行了 MD 模拟。尽管模拟得到的结构终点具有多样性，但仍表现出几种模式：在水和低乙醇浓度下，模型迅速形成紧凑的球形结构，很大程度上保留了 C 端束。在≥50mol%乙醇时，扩展构象占主导地位，与之前的小角 X 射线散射（SAXS）研究一致。在水和低乙醇浓度下，三级结构部分稳定，但在≥50mol%乙醇时被破坏。聚合结果表明，随着乙醇浓度的增加，螺旋度略有增加。所有条件下β-折叠含量均保持在较低水平（约 1%）。除了结构动力学之外，还强调了在水相环境中快速形成支化的α-zein 聚集体。此外，水相模拟还揭示了蛋白质与交联剂甲基丙烯酸缩水甘油酯（GMA）之间的有利相互作用。GMA 环氧化物碳原子和侧链羟基氧原子的接近性同时表明，在紧凑的α-zein 构象中存在可及的反应性位点，并为甲丙烯酰化提供了预反应几何形状。这些发现可能有助于扩展这些具有技术意义的蛋白质的应用，例如通过指导化学修饰。
