In Silico Structural and Functional Analysis of Fragments of the Ankyrin Repeat Protein p18INK4c
In Silico Structural and Functional Analysis of Fragments of the Ankyrin Repeat Protein p18INK4c
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DOI：
10.1080/07391102.2010.10507336
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发表时间：
2010-02
影响因子：
4.4
通讯作者：
Petr Sklenovský;M. Otyepka
中科院分区：
文献类型：
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作者：
Petr Sklenovský;M. Otyepka
锚蛋白重复序列蛋白（Ankyrin repeat proteins，ARPs）是生物体中普遍存在的一种蛋白质，它是由一系列非球状、几乎呈线性的“准一维”结构的重复序列（Ankyrin repeats）组成。它们还具有非常不寻常的机械性能，特别是ARP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ARPs在医学和纳米技术中潜在应用的兴趣。此外，ARPs的模块化结构缺乏通常稳定球状蛋白的长距离接触，为理解蛋白质稳定性和蛋白质折叠机制提供了新的范例。在本研究中，阿普p18 INK 4c（p18）和50 p18片段的稳定性进行了研究，在明确的水在一个3.3微秒的时间尺度上的全原子分子动力学（MD）模拟。片段模拟表明，p18 α-螺旋是显着稳定的三级相互作用，因为在其天然的背景下，他们很容易融化。所有单个p18 AR及其结构元件在其天然背景之外也是不稳定的。最小稳定基序是成对的AR，这意味着重复序列间的接触对AR稳定性至关重要。此外，内部AR对比包括天然加帽AR的对更不稳定。MD模拟还提供了p18转角和环的功能作用的指示;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-末端到C-末端熔化。
Abstract 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 microseconds timescale. The fragment simulations indicate that p18 a-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.