A Euclidean perspective on the unfolding of azurin: chain motion.

ABSTRACT: We present a new approach to visualizing and quantifying the displacement of segments of Pseudomonas aeruginosa azurin in the early stages of denaturation. Our method is based on a geometrical method developed previously by the authors, and elaborated extensively for azurin. In this study, we quantify directional changes in three ?-helical regions, two regions having ?-strand residues, and three unstructured regions of azurin. Snapshots of these changes as the protein unfolds are displayed and described quantitatively by introducing a scaling diagnostic. In accord with molecular dynamics simulations, we show that the long ?-helix in azurin (residues 54-67) is displaced from the polypeptide scaffolding and then pivots first in one direction, and then in the opposite direction as the protein continues to unfold. The two ?-strand chains remain essentially intact and, except in the earliest stages, move in tandem. We show that unstructured regions 72-81 and 84-91, hinged by ?-strand residues 82-83, pivot oppositely. The region comprising residues 72-91 (40 % hydrophobic and 16 % of the 128 total residues) forms an effectively stationary region that persists as the protein unfolds. This static behavior is a consequence of a dynamic balance between the competing motion of two segments, residues 72-81 and 84-91.

SUBMITTER: Gray HB 

PROVIDER: S-EPMC4031266 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature