The graphite–water interface provides a unique environment for polypeptides that generally favors ordered structures more than in solution. Therefore, systems consisting of designed peptides and graphitic carbon might serve as a convenient medium for controlled self-assembly of functional materials. Here, we computationally designed cyclic peptides that spontaneously fold into a β-sheet-like conformation at the graphite–water interface and self-assemble, and we subsequently observed evidence of such assembly by atomic force microscopy. Using a novel protocol, we screened nearly 2000 sequences, optimizing for formation of a unique folded conformation while discouraging unfolded or misfolded conformations. A head-to-tail cyclic peptide with the sequence GTGSGTGGPGGGCGTGTGSGPG showed the greatest apparent propensity to fold spontaneously, and this optimized sequence was selected for larger scale molecular dynamics simulations, rigorous free-energy calculations, and experimental validation. In simulations ranging from hundreds of nanoseconds to a few microseconds, we observed spontaneous folding of this peptide at the graphite–water interface under many different conditions, including multiple temperatures (295 and 370 K), with different initial orientations relative to the graphite surface, and using different molecular dynamics force fields (CHARMM and Amber). The thermodynamic stability of the folded conformation on graphite over a range of temperatures was verified by replica-exchange simulations and free-energy calculations. On the other hand, in free solution, the folded conformation was found to be unstable, unfolding in tens of picoseconds. Intermolecular hydrogen bonds promoted self-assembly of the folded peptides into linear arrangements where the peptide backbone exhibited a tendency to align along one of the six zigzag directions of the graphite basal plane. For the optimized peptide, atomic force microscopy revealed growth of single-molecule-thick linear patterns of 6-fold symmetry, consistent with the simulations, while no such patterns were observed for a control peptide with the same amino acid composition but a scrambled sequence.

中文翻译：

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石墨上折叠和自组装肽的设计


石墨-水界面为多肽提供了一个独特的环境，通常比在溶液中更有利于有序结构。因此，由设计的肽和石墨碳组成的系统可以作为功能材料受控自组装的便利介质。在这里，我们通过计算设计了环肽，它们在石墨-水界面自发折叠成β-片状构象并自组装，随后我们通过原子力显微镜观察了这种组装的证据。使用一种新颖的方案，我们筛选了近 2000 个序列，优化了独特折叠构象的形成，同时阻止未折叠或错误折叠构象。序列为 GTGSGTGGPGGGCGTGTGSGPG 的头尾环肽显示出最明显的自发折叠倾向，并且选择该优化序列用于更大规模的分子动力学模拟、严格的自由能计算和实验验证。在从数百纳秒到几微秒的模拟中，我们观察到这种肽在许多不同条件下在石墨-水界面处自发折叠，包括多个温度（295 和 370 K），相对于石墨表面具有不同的初始方向，并使用不同的分子动力学力场（CHARMM 和 Amber）。通过复制交换模拟和自由能计算验证了石墨折叠构象在一定温度范围内的热力学稳定性。另一方面，在自由溶液中，折叠构象被发现不稳定，在数十皮秒内展开。 分子间氢键促进折叠肽自组装成线性排列，其中肽主链表现出沿着石墨基面的六个锯齿形方向之一排列的趋势。对于优化的肽，原子力显微镜显示出 6 重对称的单分子厚度线性模式的生长，与模拟一致，而对于具有相同氨基酸组成但序列混乱的对照肽，没有观察到这种模式。