The Zero-Order Loop in Apoazurin Modulates Folding Mechanism In Silico

Pseudomonas aeruginosa apoazurin (apo, without the copper cofactor) has a single disulfide bond between residues 3 and 26 and unfolds in a two-state reaction in vitro. The disulfide bond covalently connects the N-termini of β-strands 1 and 3; thereby, it creates a zero-order loop or a "cinch" that restricts conformational space. Covalent loops and threaded topologies are emerging as important structural elements in folded proteins and may be important for function. In order to understand the role of a zero-order loop in the folding process of a protein, here we used coarse-grained molecular dynamics (CGMD) simulations in silico to compare two variants of apoazurin: one named "loop" which contained the disulfide, and another named "open" in which the disulfide bond between residues 3 and 26 was removed. CGMD simulations were performed to probe the stability and unfolding pathway of the two apoazurin variants at different urea concentrations and temperatures. Our results show that the covalent loop plays a prominent role in the unfolding mechanism of apoazurin; its removal alters both the folding-transition state and the unfolded-state ensemble of conformations. We propose that modulation of azurin's folding landscape by the disulfide bridge may be related to both copper capturing and redox sensing.