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Unfolding cytochromes c-b₅₆₂ and Rd apo b₅₆₂

Kozak, John J. and Gray, Harry B. and Garza-López, Roberto A. (2020) Unfolding cytochromes c-b₅₆₂ and Rd apo b₅₆₂. Journal of Inorganic Biochemistry, 211 . Art. No. 111209. ISSN 0162-0134.

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We have analyzed the early stages of unfolding of cytochromes c-b₅₆₂ (PDB ID: 2BC5) and Rd apo b₅₆₂ (PDB ID: 1YYJ). Our geometrical approach proceeds from an analysis of the crystal structure reported for each protein. We quantify, residue-by-residue and region-by-region, the spatial and angular changes in the structure as the protein denatures, and quantify differences that result from the seven residues that differ in the two proteins. Using two independent analyses, one based on spatial metrics and the second on angular metrics, we establish the order of unfolding of the five helices in cyt c-b₅₆₂ and the four helices in the apo protein. For the two helices nearest the N-terminal end of both proteins, the ones in the apo protein unfold first. For the two helices nearest the C-terminal end, the interior helix of the apo protein unfolds first, whereas the terminal helix of the holo protein unfolds first. Excluded-volume effects (repulsive interactions) are minimized in turning regions; the overall range in Δ values is Δ = 36.3 ų for cyt c-b₅₆₂ and Δ = 36.6 ų for the apo protein, whereas the span for all 20 amino acids is Δ = 167.7 ų. As our work indicates that the interior helix of cytochrome c-b₅₆₂ is the first to fold, we suggest that this helix protects the heme from misligation, consistent with ultrafast folding over a minimally frustrated funneled landscape.

Item Type:Article
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Gray, Harry B.0000-0002-7937-7876
Additional Information:© 2020 Elsevier Inc. Received 30 April 2020, Revised 26 July 2020, Accepted 28 July 2020, Available online 10 August 2020. We thank Devarajan (Dave) Thirumalai for very helpful comments. Work at Caltech was supported by the NIH (DK019038) and the Arnold and Mabel Beckman Foundation. Support at Pomona College was provided by the Howard Hughes Medical Institute Research Program and a Sontag Research Fellowship Award. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Funding AgencyGrant Number
Arnold and Mabel Beckman FoundationUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Sontag FoundationUNSPECIFIED
Subject Keywords:Cytochromes; Unfolding; Misligation; Apoprotein; Holoprotein; Angular
Record Number:CaltechAUTHORS:20200810-134213212
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Official Citation:John J. Kozak, Harry B. Gray, Roberto A. Garza-López, Unfolding cytochromes c-b562 and Rd apo b562, Journal of Inorganic Biochemistry, Volume 211, 2020, 111209, ISSN 0162-0134, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:104882
Deposited By: Tony Diaz
Deposited On:10 Aug 2020 20:51
Last Modified:24 Aug 2020 22:30

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