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通过模拟和实验得到的一种内在无序肽的反向自由能景观。

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

作者信息

Granata Daniele, Baftizadeh Fahimeh, Habchi Johnny, Galvagnion Celine, De Simone Alfonso, Camilloni Carlo, Laio Alessandro, Vendruscolo Michele

机构信息

International School for Advanced Studies (SISSA), 34136 Trieste, Italy.

Institute of Computational and Molecular Science (ICMS), Temple University, Philadelphia, PA 19122, USA.

出版信息

Sci Rep. 2015 Oct 26;5:15449. doi: 10.1038/srep15449.

Abstract

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

摘要

自由能景观理论在解释球状蛋白质的折叠行为方面非常成功,因为这种表示方式提供了有关折叠过程中涉及的状态数量、它们的丰度以及相互转化途径的直观信息。我们在此将这种形式主义扩展到Aβ40肽的情况,Aβ40肽是一种与阿尔茨海默病相关的由40个残基组成的内在无序蛋白质片段。通过使用一种先进的采样技术,即使在蛋白质高度无序状态下也能使自由能计算达到收敛,我们对该肽的自由能景观进行了精确的结构表征。我们发现,这种景观与典型的折叠蛋白质的景观具有相反的特征。虽然全局自由能最小值由高度无序的结构组成,但较高自由能区域对应于多种具有二级结构元件以几种不同方式排列的瞬态结构化构象,并且它们之间没有被可观的自由能垒隔开。基于自由能景观的这种特殊结构,我们预测随着温度升高,该肽不仅会变得更紧凑,还会变得更结构化,并且我们通过一系列生物物理测量表明情况确实如此。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9e0d/4620491/046426f87a1a/srep15449-f1.jpg

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