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Geometrical analysis of cytochrome c unfolding

Urie, Kristopher G. and Pletneva, Ekaterina and Gray, Harry B. and Winkler, Jay R. and Kozak, John J. (2011) Geometrical analysis of cytochrome c unfolding. Molecular Physics, 109 (2). pp. 301-313. ISSN 0026-8976. PMCID PMC3046399. doi:10.1080/00268976.2010.521202.

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A geometrical model has been developed to study the unfolding of iso-1 cytochrome c. The model draws on the crystallographic data reported for this protein. These data were used to calculate the distance between specific residues in the folded state, and in a sequence of extended states defined by n = 3, 5, 7, 9, 11, 13, and 15 residue units. Exact calculations carried out for each of the 103 residues in the polypeptide chain demonstrate that different regions of the chain have different unfolding histories. Regions where there is a persistence of compact structures can be identified, and this geometrical characterization is fully consistent with analyses of time-resolved fluorescence energy-transfer (TrFET) data using dansyl-derivatized cysteine side-chain probes at positions 39, 50, 66, 85, and 99. The calculations were carried out assuming that different regions of the polypeptide chain unfold synchronously. To test this assumption, lattice Monte Carlo simulations were performed to study systematically the possible importance of asynchronicity. Calculations show that small departures from synchronous dynamics can arise if displacements of residues in the main body of the chain are much more sluggish than near-terminal residues.

Item Type:Article
Related URLs:
URLURL TypeDescription CentralArticle
Gray, Harry B.0000-0002-7937-7876
Winkler, Jay R.0000-0002-4453-9716
Additional Information:© 2011 Taylor & Francis. Received 14 July 2010; final version received 31 August 2010. First Published on: 22 December 2010. Research at Caltech is supported by the National Institutes of Health (DKOI9038, GM068461), the National Science Foundation (CHE-0802907), and the Arnold and Mabel Beckman Foundation.
Group:CCI Solar Fuels
Funding AgencyGrant Number
Arnold and Mabel Beckman FoundationUNSPECIFIED
Subject Keywords:protein folding; cytochrome c; Monte Carlo simulations
Issue or Number:2
PubMed Central ID:PMC3046399
Record Number:CaltechAUTHORS:20110321-142051991
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:23014
Deposited By: Tony Diaz
Deposited On:21 Mar 2011 21:33
Last Modified:09 Nov 2021 16:10

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