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A Euclidean perspective on the unfolding of azurin: chain motion

  • Harry B. Gray
  • Jeffery J. Warren
  • Jay R. Winkler
  • John J. KozakEmail author
Original Paper
Part of the following topical collections:
  1. Topical Issue in honor of Ivano Bertini

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.

Keywords

Protein folding Azurin Modeling 

Notes

Acknowledgments

Work at the California Institute of Technology was supported by the National Institutes of Health (grant GM095037 to J.J.W. and grant DK019038 to H.B.G. and J.R.W.).

Supplementary material

775_2013_1077_MOESM1_ESM.pdf (2.9 mb)
Example calculation of S i and β i , expanded version of Fig. 4, and coordinates for all unfolding 12 cases studied. Electronic supplementary material is available online (PDF 3011 kb)

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Copyright information

© SBIC 2013

Authors and Affiliations

  • Harry B. Gray
    • 1
  • Jeffery J. Warren
    • 1
    • 3
  • Jay R. Winkler
    • 1
  • John J. Kozak
    • 2
    Email author
  1. 1.Beckman InstituteCalifornia Institute of TechnologyPasadenaUSA
  2. 2.Department of ChemistryDePaul UniversityChicagoUSA
  3. 3.Department of ChemistrySimon Fraser UniversityBurnabyCanada

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