Lei Hongxing, Wu Chun, Wang Zhixiang, Duan Yong
UC Davis Genome Center and Department of Applied Science, One Shields Avenue, Davis, CA 95616, USA.
J Mol Biol. 2006 Mar 3;356(4):1049-63. doi: 10.1016/j.jmb.2005.11.087. Epub 2005 Dec 15.
Amyloid formation is associated with many neurodegenerative diseases. Recent findings suggest that early oligomeric aggregates could be major sources of toxicity. We present a computational investigation of the first step of amyloid initiation-dimer formation of a seven residue peptide (NHVTLSQ) from human beta2-microglobulin at pH 2.0, which renders +2.0 units charges to each peptide. A total of over 1.2 micros of simulations with explicit solvent and 1.0 micros of simulations with implicit solvent were conducted. Main-chain conformational restraint was applied to facilitate the formation of ordered dimers. An antiparallel beta-sheet with six main-chain hydrogen bonds was dominant in the implicit solvent simulations. In contrast, no stable dimers were observed in the two negative controls, the mouse heptapeptide (KHDSMAE, +3.0 units charges) and the scrambled human heptapeptide (QVLHTSN). Explicit solvent simulations presented a more complex scenario. The wild-type human heptapeptide formed predominantly antiparallel beta-sheets ( approximately 38%) although parallel ones ( approximately 12%) were also observed. Hydrophobic contacts preceded hydrogen bond saturation in the majority of the association events in the explicit solvent simulations, highlighting the important role of hydrophobic interaction in amyloid initiation. The fact that the mouse dimer dissociated immediately after the removal of conformational restraint suggests that the higher conformational entropy barrier, along with the stronger charge repulsion and weaker hydrophobic interaction, contributed to its inability to form amyloid fibril. The closeness of positive charge pairs in the dimers of the scrambled human heptapeptide may prohibit further beta-sheet extension and fibril growth. Combining the results from simulations and free energy analyses, we propose that the building block for this amyloid fibril is an antiparallel dimer with a two-residue register shift and six main-chain hydrogen bonds. A double-layer protofibril structure is also proposed in which two antiparallel beta-sheets face each other and are held together by hydrophobic staples and hydrogen bonds of the polar side-chains.
淀粉样蛋白的形成与许多神经退行性疾病相关。最近的研究结果表明，早期寡聚聚集体可能是毒性的主要来源。我们对人β2-微球蛋白的七肽（NHVTLSQ）在pH 2.0时淀粉样蛋白起始的第一步——二聚体形成进行了计算研究，该条件下每个肽带有 +2.0 个单位电荷。进行了总共超过1.2微秒的显式溶剂模拟和1.0微秒的隐式溶剂模拟。应用主链构象限制以促进有序二聚体的形成。在隐式溶剂模拟中，具有六个主链氢键的反平行β-折叠占主导。相比之下，在两个阴性对照——小鼠七肽（KHDSMAE，+3.0个单位电荷）和人七肽乱序序列（QVLHTSN）中未观察到稳定的二聚体。显式溶剂模拟呈现出更复杂的情况。野生型人七肽主要形成反平行β-折叠（约38%），尽管也观察到了平行β-折叠（约12%）。在显式溶剂模拟的大多数缔合事件中，疏水接触先于氢键饱和，突出了疏水相互作用在淀粉样蛋白起始中的重要作用。小鼠二聚体在去除构象限制后立即解离这一事实表明，较高的构象熵垒，连同较强的电荷排斥和较弱的疏水相互作用，导致其无法形成淀粉样纤维。人七肽乱序序列二聚体中正电荷对的紧密程度可能会阻止进一步的β-折叠延伸和纤维生长。结合模拟结果和自由能分析，我们提出这种淀粉样纤维的构建单元是具有两个残基错位和六个主链氢键的反平行二聚体。还提出了一种双层原纤维结构，其中两个反平行β-折叠相互面对，并通过疏水钉和极性侧链的氢键结合在一起。
