Fig. 5: Molecular Dynamics (MD) simulations of nitrocefin binding to PSMα3 amyloid fibrils’ surface.
From: Staphylococcus aureus functional amyloids catalyze degradation of β-lactam antibiotics
a The cross-α amyloid fibrils of PSMα3, composed of bilayer made of amphiphilic α-helices, display arrays of lysine residues (marked in purple, based on PDB structure 5I5523). b MD simulations reveal two distinct binding conformations of nitrocefin to the fibril surface (conformation (i) and (ii)). In both conformations, the β-lactam ring binds the primary amines of PSMα3 (β-lactam carbonyl marked with a black arrow). c The fraction of contacts between the β-lactam carbonyl and the peptide residues, calculated with a 0.45 nm contact cutoff. d Three-state Bayesian Markov State Model between the unbound state and the bound states M1|K6 (b, right) and K9|K12 (b, left). The free energy for each state at 20 oC and transition rates between the states were calculated from the MSM transition matrix. The sample standard deviation is shown in parentheses.
