Singh Reman K, Chamachi Neharika G, Chakrabarty Suman, Mukherjee Arnab
Department of Chemistry, Indian Institute of Science Education and Research , Pune 411008, Maharashtra, India.
Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India.
J Phys Chem B. 2017 Jan 26;121(3):550-564. doi: 10.1021/acs.jpcb.6b11416. Epub 2017 Jan 13.
Misfolding and aggregation of prion proteins are associated with several neurodegenerative diseases. Therefore, understanding the mechanism of the misfolding process is of enormous interest in the scientific community. It has been speculated and widely discussed that the native cellular prion protein (PrP) form needs to undergo substantial unfolding to a more stable PrP state, which may further oligomerize into the toxic scrapie (PrP) form. Here, we have studied the mechanism of the unfolding of the human prion protein (huPrP) using a set of extensive well-tempered metadynamics simulations. Through multiple microsecond-long metadynamics simulations, we find several possible unfolding pathways. We show that each pathway leads to an unfolded state of lower free energy than the native state. Thus, our study may point to the signature of a PrP form that corresponds to a global minimum on the conformational free-energy landscape. Moreover, we find that these global minima states do not involve an increased β-sheet content, as was assumed to be a signature of PrP formation in previous simulation studies. We have further analyzed the origin of metastability of the PrP form through free-energy surfaces of the chopped helical segments to show that the helices, particularly H2 and H3 of the prion protein, have the tendency to form either a random coil or a β-structure. Therefore, the secondary structural elements of the prion protein are only weakly stabilized by tertiary contacts and solvation forces so that relatively weak perturbations induced by temperature, pressure, pH, and so forth can lead to substantial unfolding with characteristics of intrinsically disordered proteins.
朊病毒蛋白的错误折叠和聚集与多种神经退行性疾病相关。因此，了解错误折叠过程的机制在科学界引起了极大的兴趣。人们已经推测并广泛讨论过，天然细胞朊病毒蛋白（PrP）形式需要经历大量展开，转变为更稳定的PrP状态，而这种状态可能会进一步寡聚化为有毒的羊瘙痒病（PrP）形式。在此，我们使用了一系列广泛的加权元动力学模拟来研究人类朊病毒蛋白（huPrP）的展开机制。通过多个长达微秒级的元动力学模拟，我们发现了几种可能的展开途径。我们表明，每条途径都会导致一种自由能低于天然状态的未折叠状态。因此，我们的研究可能指向一种PrP形式的特征，该特征对应于构象自由能景观上的全局最小值。此外，我们发现这些全局最小值状态并不涉及β-折叠含量的增加，而在先前的模拟研究中曾认为β-折叠含量增加是PrP形成的一个特征。我们通过对截断螺旋片段的自由能表面进一步分析了PrP形式亚稳态的起源，以表明螺旋，特别是朊病毒蛋白的H2和H3螺旋，有形成无规卷曲或β-结构的倾向。因此，朊病毒蛋白的二级结构元件仅通过三级相互作用和溶剂化力得到微弱的稳定，以至于温度、压力、pH等引起的相对较弱的扰动就可能导致具有内在无序蛋白特征的大量展开。
