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Structural predictions for curli amyloid fibril subunits CsgA and CsgB

机译：卷曲淀粉样蛋白原纤维亚基CsgA和CsgB的结构预测

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Curli are amyloid fibrils that grow from many enteric bacteria and play a structural role in the biofilm extracellular matrix (ECM). Although curli biogenesis is one of the best understood amyloidogenic pathways, the exact atomistic structure of the major subunit CsgA is still unknown. We assess structural models of CsgA and the minor subunit CsgB obtained using the Robetta, Quark, FALCON@home and RaptorX protein structure prediction servers, as well as previously published models. Our objective is to identify or produce models of CsgA and CsgB that exhibit (1) beta-helical structure, (2) sizing in agreement with experiment, (3) alignment among conserved residues, and (4) stability in MD simulations. To this end, an additional CsgA model is created by threading the sequence to the only CsgB model that meets these criteria. Static models are first assessed in terms of structure, sizing, and residue alignment. Additionally, short MD simulations are used to rule out models exhibiting instability. Of the servers used, only Robetta and Raptor produced beta-helical structures. We propose candidate models of CsgA and CsgB that meet all four selection criteria, and remain stable in 150 ns simulations. The development of these subunit structural models will enable molecular-level investigation of curli properties.
机译：Curli是淀粉状蛋白原纤维，由许多肠细菌生长而成，并在生物膜细胞外基质（ECM）中发挥结构作用。虽然curli生物发生是最了解淀粉样蛋白生成途径之一，但主要亚基CsgA的确切原子结构仍是未知的。我们评估使用Robetta，Quark，FALCON @ home和RaptorX蛋白质结构预测服务器获得的CsgA和次要亚基CsgB的结构模型，以及以前发布的模型。我们的目标是识别或产生CsgA和CsgB模型，这些模型具有（1）β-螺旋结构，（2）与实验一致的尺寸，（3）保守残基之间的比对以及（4）MD模拟中的稳定性。为此，通过将序列穿入唯一满足这些条件的CsgB模型，可以创建其他CsgA模型。首先根据结构，大小和残基对齐方式评估静态模型。此外，简短的MD模拟可用来排除表现出不稳定性的模型。在使用的服务器中，只有Robetta和Raptor产生了beta螺旋结构。我们提出了满足所有四个选择标准的CsgA和CsgB候选模型，并在150 ns仿真中保持稳定。这些亚基结构模型的发展将使卷曲度特性的分子水平研究成为可能。

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