Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems, Palacký University at Olomouc tr. 17. listopadub 12, 771 46 Olomouc Czech Republic.
J Biomol Struct Dyn. 2010 Feb;27(4):521-40. doi: 10.1080/07391102.2010.10507336.
Ankyrin repeat proteins (ARPs) are ubiquitous proteins that play critical regulatory roles in organisms and consist of repeating motifs (ankyrin repeats) stacked in non-globular, almost linear, "quasi one-dimensional" configurations. They also have highly unusual mechanical properties, notably ARPs can behave as nano-springs. Both their essential cellular functions and distinctive nano-mechanical properties have aroused interest in ARPs for potential applications in medicine and nanotechnology. Further, the modular architecture of ARPs, which lack the long-range contacts that typically stabilize globular proteins, provides a new paradigm for understanding protein stability and folding mechanisms of proteins. In the present study, the stability of ARP p18INK4c (p18) and fifty p18 fragments was investigated by all- atomic molecular dynamics (MD) simulations in explicit water on a ~3.3 micro- seconds timescale. The fragment simulations indicate that p18 alpha-helices are significantly stabilized by tertiary interactions, because in the absence of their native context they readily melt. All single p18 ARs and their structural elements are also unstable outside their native context. The minimal stable motifs are pairs of ARs, implying that inter-repeat contacts are essential for AR stability. Further, pairs of internal ARs are less stable than pairs that include a native capping AR. The MD simulations also provide indications of the functional roles of p18 turns and loops; the turns appear to be essential for the stability of the protein, while the loops both help to stabilize the p18 structure and are involved in recognition processes. Temperature-induced unfolding analysis shows that the p18 melts from the N-terminus to the C- terminus.
锚蛋白重复蛋白（ARPs）是普遍存在的蛋白质，在生物体中发挥着关键的调节作用，由重复基序（锚蛋白重复）堆叠而成，呈非球形、几乎线性的“准一维”构象。它们还具有非常特殊的机械性能，特别是 ARPs 可以表现为纳米弹簧。它们的基本细胞功能和独特的纳米机械性能引起了人们对 ARP 的兴趣，认为它们有可能在医学和纳米技术领域得到应用。此外，ARPs 的模块化结构缺乏通常稳定球形蛋白质的长程接触，为理解蛋白质稳定性和折叠机制提供了新的范例。在本研究中，通过在 ~3.3 微秒的时间尺度上在明水环境中进行全原子分子动力学（MD）模拟，研究了 ARP p18INK4c（p18）和 50 个 p18 片段的稳定性。片段模拟表明，p18 螺旋通过三级相互作用得到显著稳定，因为在没有其天然环境的情况下，它们很容易熔化。所有的单个 p18 AR 及其结构元件在其天然环境之外也不稳定。最小稳定的基序是 AR 对，这意味着重复之间的相互作用对于 AR 的稳定性至关重要。此外，内部 AR 对比包含天然帽状 AR 的 AR 对更不稳定。MD 模拟还提供了 p18 转角和环的功能作用的迹象；转角似乎对蛋白质的稳定性至关重要，而环既有助于稳定 p18 结构，又参与识别过程。温度诱导的解折叠分析表明，p18 从 N 端到 C 端熔化。
