Structural predictions for curli amyloid fibril subunits CsgA and CsgB

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.