Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University , Manhattan, Kansas 66506-5802, United States.
Universidad Nacional de Colombia , sede Bogotá, Facultad de Ciencias, Departamento de Química, Carrera 30 No. 45-03, Bogotá, 111321, Colombia.
J Phys Chem B. 2017 Apr 20;121(15):3895-3907. doi: 10.1021/acs.jpcb.7b01130. Epub 2017 Mar 24.
Understanding the interaction of carbon nanomaterials with proteins is essential for determining the potential effects of these materials on health and in the design of biotechnology based on them. Here we leverage explicit-solvent molecular simulation and multidimensional free-energy calculations to investigate how adsorption to carbon nanomaterial surfaces affects the conformational equilibrium of alanine dipeptide, a widely used model of protein backbone structure. We find that the two most favorable structures of alanine dipeptide on graphene (or large carbon nanotubes) correspond to the two amide linkages lying in the same plane, flat against the surface, rather than the nonplanar α-helix-like and β-sheet-like conformations that predominate in aqueous solution. On graphenic surfaces, the latter conformations are metastable and most often correspond to amide-π stacking of the N-terminal amide. The calculations highlight the key role of amide-π interactions in determining the conformational equilibrium. Lesser but significant contributions from hydrogen bonding to the high density interfacial water layer or to the hydroxy groups of hydroxylated graphene also define the most favorable conformations. This work should yield insight on the influence of carbon nanotubes, graphene, and their functionalized derivatives on protein structure.
了解碳纳米材料与蛋白质的相互作用对于确定这些材料对健康的潜在影响以及基于它们的生物技术设计至关重要。在这里，我们利用显溶剂分子模拟和多维自由能计算来研究吸附到碳纳米材料表面如何影响丙氨酸二肽的构象平衡，丙氨酸二肽是蛋白质骨架结构的广泛使用模型。我们发现，在石墨烯（或大碳纳米管）上丙氨酸二肽的两种最有利结构对应于两个酰胺键位于同一平面上，与表面平行，而不是在水溶液中占主导地位的非平面α-螺旋样和β-折叠样构象。在石墨烯表面上，后一种构象是亚稳态的，并且通常对应于 N 端酰胺的酰胺-π 堆积。这些计算突出了酰胺-π 相互作用在确定构象平衡中的关键作用。氢键对高密度界面水分子层或羟基化石墨烯的羟基的较小但重要的贡献也定义了最有利的构象。这项工作应该能够深入了解碳纳米管、石墨烯及其功能化衍生物对蛋白质结构的影响。
