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A Euclidean perspective on the unfolding of azurin: chain motion

Gray, Harry B. and Warren, Jeffery J. and Winkler, Jay R. and Kozak, John J. (2014) A Euclidean perspective on the unfolding of azurin: chain motion. Journal of Biological Inorganic Chemistry, 19 (4-5). pp. 555-563. ISSN 0949-8257. PMCID PMC4031266. https://resolver.caltech.edu/CaltechAUTHORS:20140106-090740745

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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.


Item Type:Article
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URLURL TypeDescription
http://dx.doi.org/10.1007/s00775-013-1077-2DOIArticle
http://link.springer.com/article/10.1007%2Fs00775-013-1077-2PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031266/PubMed CentralArticle
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ORCID:
AuthorORCID
Winkler, Jay R.0000-0002-4453-9716
Additional Information:© 2013 SBIC. Received: 23 September 2013; Accepted: 6 December 2013. Published online 31 December 2013. Topical Issue in honor of Ivano Bertini. 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.).
Funders:
Funding AgencyGrant Number
NIHGM095037
NIHDK019038
Subject Keywords:Protein folding; Azurin; Modeling
Issue or Number:4-5
PubMed Central ID:PMC4031266
Record Number:CaltechAUTHORS:20140106-090740745
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20140106-090740745
Official Citation:Gray, H.B., Warren, J.J., Winkler, J.R. et al. J Biol Inorg Chem (2014) 19: 555. doi:10.1007/s00775-013-1077-2
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:43215
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:09 Jan 2014 16:26
Last Modified:03 Oct 2019 06:05

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