Cecchini M, Curcio R, Pappalardo M, Melki R, Caflisch A
Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
J Mol Biol. 2006 Apr 7;357(4):1306-21. doi: 10.1016/j.jmb.2006.01.009. Epub 2006 Jan 26.
A novel computational approach to the structural analysis of ordered beta-aggregation is presented and validated on three known amyloidogenic polypeptides. The strategy is based on the decomposition of the sequence into overlapping stretches and equilibrium implicit solvent molecular dynamics (MD) simulations of an oligomeric system for each stretch. The structural stability of the in-register parallel aggregates sampled in the implicit solvent runs is further evaluated using explicit water simulations for a subset of the stretches. The beta-aggregation propensity along the sequence of the Alzheimer's amyloid-beta peptide (Abeta(42)) is found to be highly heterogeneous with a maximum in the segment V(12)HHQKLVFFAE(22) and minima at S(8)G(9), G(25)S(26), G(29)A(30), and G(38)V(39), which are turn-like segments. The simulation results suggest that these sites may play a crucial role in determining the aggregation tendency and the fibrillar structure of Abeta(42). Similar findings are obtained for the human amylin, a 37-residue peptide that displays a maximal beta-aggregation propensity at Q(10)RLANFLVHSSNN(22) and two turn-like sites at G(24)A(25) and G(33)S(34). In the third application, the MD approach is used to identify beta-aggregation "hot-spots" within the N-terminal domain of the yeast prion Ure2p (Ure2p(1-94)) and to design a double-point mutant (Ure2p-N4748S(1-94)) with lower beta-aggregation propensity. The change in the aggregation propensity of Ure2p-N4748S(1-94) is verified in vitro using the thioflavin T binding assay.
本文提出了一种用于有序β-聚集结构分析的新型计算方法，并在三种已知的淀粉样生成多肽上进行了验证。该策略基于将序列分解为重叠片段，并对每个片段的寡聚体系统进行平衡隐式溶剂分子动力学（MD）模拟。对于一部分片段，使用显式水模拟进一步评估在隐式溶剂模拟中采样的同向平行聚集体的结构稳定性。发现阿尔茨海默病淀粉样β肽（Abeta(42)）序列中的β-聚集倾向高度不均一，在V(12)HHQKLVFFAE(22)片段中最高，而在S(8)G(9)、G(25)S(26)、G(29)A(30)和G(38)V(39)这些呈转角样的片段处最低。模拟结果表明，这些位点可能在决定Abeta(42)的聚集倾向和纤维状结构中起关键作用。对于人胰岛淀粉样多肽也有类似发现，该37个残基的肽在Q(10)RLANFLVHSSNN(22)处显示出最大的β-聚集倾向，在G(24)A(25)和G(33)S(34)处有两个呈转角样的位点。在第三个应用中，MD方法用于鉴定酵母朊病毒Ure2p（Ure2p(1 - 94)）N端结构域内的β-聚集“热点”，并设计了一种β-聚集倾向较低的双点突变体（Ure2p-N4748S(1 - 94)）。使用硫黄素T结合试验在体外验证了Ure2p-N4748S(1 - 94)聚集倾向的变化。
