title: 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 α-helical regions, two regions having β-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 α-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 β-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 β-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.
authors.affiliation: Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA.
authors.forename: Harry B
authors.initials: HB
authors.lastname: Gray
authors.forename: Jeffery J
authors.initials: JJ
authors.lastname: Warren
authors.forename: Jay R
authors.initials: JR
authors.lastname: Winkler
authors.forename: John J
authors.initials: JJ
authors.lastname: Kozak
mesh_terms: D001400:Azurin / Q000737:chemistry* / Q000378:metabolism*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011550:Pseudomonas aeruginosa / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D001400:Azurin