Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK.
Phys Chem Chem Phys. 2021 Sep 7;23(33):18001-18011. doi: 10.1039/d1cp02072b. Epub 2021 Aug 12.
A hydrophobic heptapeptide, with sequence AFILPTG, as part of a phage capsid protein binds effectively to silica particles carrying negative charge. Here, we explore the silica binding activity of the sequence as a short polypeptide with polar N and C terminals. To describe the structural changes that occur on binding, we fit experimental infrared, Raman and circular dichroism data for a number of structures simulated in the full configuration space of the hepta-peptide using replica exchange molecular dynamics. Quantum chemistry was used to compute normal modes of infrared and Raman spectra and establish a relationship to structures from MD data. To interpret the circular dichroism data, instead of empirical factoring of optical activity into helical/sheet/random components, we exploit natural transition orbital theory and specify the contributions of backbone amide units, side chain functional groups, water, sodium ions and silica to the observed transitions. Computed optical responses suggest a less folded backbone and importance of the N-terminal when close to silica. We further discuss the thermodynamics of the interplay of charged and hydrophobic moieties of the polypeptide on association with the silica surface. The outcomes of this study may assist in the engineering of novel artificial bio-silica heterostructures.
一段疏水性七肽，序列为 AFILPTG，作为噬菌体衣壳蛋白的一部分，能有效地与带负电荷的硅颗粒结合。在这里，我们探索了该序列作为具有极性 N 和 C 末端的短多肽的硅结合活性。为了描述结合过程中发生的结构变化，我们使用 replica exchange 分子动力学方法在七肽的全构象空间中模拟了一系列结构，并拟合了实验红外、拉曼和圆二色性数据。量子化学被用于计算红外和拉曼光谱的简正模式，并建立与 MD 数据结构的关系。为了解释圆二色性数据，我们没有将旋光性经验地分解为螺旋/片层/无规构象成分，而是利用自然跃迁轨道理论，并指定了骨架酰胺单元、侧链官能团、水、钠离子和硅对观察到的跃迁的贡献。计算的光学响应表明，当接近硅时，肽的无规构象部分的折叠程度更低，且 N 末端的重要性更高。我们进一步讨论了多肽的带电和疏水性部分与硅表面缔合的热力学。这项研究的结果可能有助于设计新型人工生物硅异质结构。
