Bamdad Kourosh, Naderi-Manesh Hossein, Baumgaertner Artur
Department of Biology, Faculty of Science, Payame Noor University, Iran.
Department of Biophysics, Faculty of Science, Tarbiat Modares University, Iran.
EXCLI J. 2014 Mar 3;13:212-22. eCollection 2014.
Technical strategies like amino acid substitution and residue modification have been widely used to characterize the importance of key amino acids and the role that each residue plays in the structural and functional properties of protein molecules. However, there is no systematic approach to assess the impact of the substituted/modified amino acids on the conformational dynamics of proteins. In this investigation to clarify the effects of residue modifications on the structural dynamics of human prion protein (PrP), a comparative molecular dynamics simulation study on the native and the amino acid-substituted analog at position 208 of PrP has been performed. It is believed that Arginine to Histidine mutation at position 208 is responsible for the structural transition of the native form of human prion protein to the pathogenic isoform causing Creutzfeldt-Jakob disease (CJD). So, three 10 ns molecular dynamics simulations on three model constructs have been performed. Simulation results indicated considerable differences of conformational fluctuations for Alanine substituted construct (PrPALA) and the analog form (PrPSB) comprising the neutralized state of the Arginine residue at position 208 of the human prion protein. According to our data, substitution of the Arginine residue by the uncharged state of this residue induces some reversible structural alterations in the intrinsically flexible loop area including residues 167-171 of PrP. Thus, deprotonation of Arg(208) is a weak perturbation to the structural fluctuations of the protein backbone and the resulting construct behaves almost identical as its native form. Otherwise, Alanine substitution at position 208 imposed an irreversible impact on the secondary and tertiary structure of the protein, which leads to conformational instabilities in the remote hot region comprising residues 190-195 of the C-terminal part of helix 2. Based on the results, it could be deduced that the observed conformational transitions upon Arg(208) to His point mutation, which is the main reason for CJD, may be mainly related to the structural instabilities due to the induced-conformational changes that caused alterations in local/spatial arrangements of the force distributions in the backbone of the human prion protein.
诸如氨基酸取代和残基修饰等技术策略已被广泛用于确定关键氨基酸的重要性以及每个残基在蛋白质分子结构和功能特性中所起的作用。然而，目前尚无系统的方法来评估取代/修饰氨基酸对蛋白质构象动力学的影响。在这项旨在阐明残基修饰对人朊病毒蛋白（PrP）结构动力学影响的研究中，我们对PrP第208位氨基酸的天然形式和取代类似物进行了比较分子动力学模拟研究。据信，第208位的精氨酸突变为组氨酸是导致人朊病毒蛋白天然形式向引起克雅氏病（CJD）的致病异构体发生结构转变的原因。因此，我们对三种模型构建体进行了三次10纳秒的分子动力学模拟。模拟结果表明，丙氨酸取代构建体（PrPALA）和包含人朊病毒蛋白第208位精氨酸残基中和状态的类似物形式（PrPSB）在构象波动方面存在显著差异。根据我们的数据，用该残基的不带电状态取代精氨酸残基会在包括PrP第167 - 171位残基的内在柔性环区域诱导一些可逆的结构改变。因此，Arg(208)的去质子化对蛋白质主链的结构波动是一种微弱的扰动，所得构建体的行为与其天然形式几乎相同。否则，第208位的丙氨酸取代对蛋白质的二级和三级结构产生了不可逆的影响，这导致了螺旋2 C端部分包含第190 - 195位残基的远程热点区域的构象不稳定。基于这些结果，可以推断出观察到的由Arg(208)突变为His导致的构象转变（这是CJD的主要原因）可能主要与由于诱导的构象变化导致的结构不稳定性有关，这些变化引起了人朊病毒蛋白主链中力分布的局部/空间排列改变。
