Modeling Amyloid Aggregation Kinetics: A Case Study with Sup35NM
Modeling Amyloid Aggregation Kinetics: A Case Study with Sup35NM
复制标题
淀粉样蛋白聚集动力学建模：Sup35NM 案例研究
DOI：
10.1021/acs.jpcb.0c11250
复制
发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Bommarius, Andreas S.
中科院分区：
文献类型：
--
作者：
Sharma, Aditi;McDonald, Matthew A.;Rose, Harrison B.;Chernoff, Yury O.;Behrens, Sven H.;Bommarius, Andreas S.
了解淀粉样蛋白的聚集机制，如Sup35NM，对了解淀粉样疾病至关重要。最近的重要工作集中在利用硫黄素T （ThT）的荧光来监测淀粉样蛋白纤维的形成，ThT在与淀粉样蛋白聚集体结合时发生红移。在本研究中，在原纤维形成过程中，为了推断相关的聚集机制，监测了初始单体浓度的聚集物总质量的进展。该工作流程使用淀粉样蛋白形成片段Sup35NM在不同搅拌条件下实现，初始单体浓度跨越2个数量级。分析表明，原生成核、单体延伸、次生成核和破碎可能都是相关的，但它们的相对重要性无法明确确定，尽管有大量高质量的数据。鉴别原纤维产生过程需要额外的信息，如原纤维长度分布。以Sup35NM为例，基于种群平衡模型（PBM）建立了一个拟合任意淀粉样蛋白聚集动力学参数的框架，该模型不仅解决了总聚集质量（通过ThT荧光实验监测），而且解决了整个纤维长度随时间的分布。除了丰富的新ThT荧光数据集外，我们还使用这种方法重新分析了以前发表的聚集体尺寸分布。根据尺寸分布，在体外再分析实验中，二次成核产生的新Sup35NM原纤维明显少于断裂产生的新Sup35NM原纤维。提出的策略是将相同的PBM应用于荧光监测和实验纤维长度分布的动力学数据的组合，这将比单独的荧光研究更有信心地推断聚集机制。
Understanding the aggregation mechanism of amyloid proteins, such as Sup35NM, is essential to understanding amyloid diseases. Significant recent work has focused on using the fluorescence of thioflavin T (ThT), which undergoes a red shift when bound to amyloid aggregates, to monitor amyloid fibril formation. In the present study, the progression of the total mass of aggregates during fibril formation is monitored for initial monomer concentrations in order to infer the relevant aggregation mechanisms. This workflow was implemented using the amyloid-forming fragment Sup35NM under different agitation conditions and for initial monomer concentrations spanning 2 orders of magnitude. The analysis suggests that primary nucleation, monomeric elongation, secondary nucleation, and fragmentation might all be relevant, but their relative importance could not be determined unambiguously, despite the large set of high-quality data. Discriminating between the fibril-generating processes is shown to require additional information, such as a fibril length distribution. Using Sup35NM as a case study, a framework for fitting the parameters of arbitrary amyloid aggregation kinetics is developed based on a population balance model (PBM), which resolves not only the total aggregate mass (monitored experimentally via ThT fluorescence) but the entire fibril length distribution over time. In addition to the rich new set of ThT fluorescence data, we have reanalyzed a previously published aggregate size distribution using this method. With the size distribution, it was determined that in the reanalyzedin vitroexperiment, secondary nucleation generated significantly fewer new Sup35NM fibrils than fragmentation. The proposed strategy of applying the same PBM to a combination of kinetic data from fluorescence monitoring and experimental fibril length distributions will allow the inference of aggregation mechanisms with far greater confidence than fluorescence studies alone.