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Published February 2018 | Supplemental Material + Accepted Version
Journal Article Open

Relaxation of structural constraints during Amicyanin unfolding

Abstract

We study the thermal unfolding of amicyanin by quantifying the resiliency of the native state to structural perturbations. Three signatures characterizing stages of unfolding are identified. The first signature, lateral extension of the polypeptide chain, is calculated directly from the reported crystallographic data. Two other signatures, the radial displacement of each residue from Cu(II) and the angular spread in the chain as the protein unfolds, are calculated using crystallographic data in concert with a geometrical model we introduced previously (J.J. Kozak, H. B. Gray, R. A. Garza-López, J. Inorg. Biochem. 155(2016) 44–55). Particular attention is paid to the resiliency of the two beta sheets in amicyanin. The resiliency of residues in the near neighborhood of the Cu center to destabilization provides information on the persistence of the entatic state. Similarly, examining the resiliency of residues intercalated between structured regions (beta sheets, the alpha helix) provides a basis for identifying a "hydrophobic core." A principal focus of our study is to compare results obtained using our geometrical model with the experimental results (C. La Rosa, D. Milardi, D. M. Grasso, M. P. Verbeet, G. W. Canters, L. Sportelli, R. Guzzi, Eur. Biophy. J.30(8),(2002) 559–570) on the denaturation of amicyanin, and we show that our results support a classical model proposed by these authors.

Additional Information

© 2017 Elsevier Inc. Received 5 July 2017, Revised 28 September 2017, Accepted 17 November 2017, Available online 22 November 2017. We thank NIH (R01 DK019038 to HBG) for support of work performed at the California Institute of Technology. Financial support for R.A.G.-L. was provided in part by grant # 52007555 to Pomona College from the Howard Hughes Medical Institute through the Precollege and Undergraduate Science Education Program. Molecular graphics images were produced using the Chimera package from the Computer Graphics Laboratory, University of California, San Francisco (supported by NIH P41RR-01081).

Attached Files

Accepted Version - nihms-926215.pdf

Supplemental Material - mmc1.pdf

Supplemental Material - table.csv

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Additional details

Created:
August 19, 2023
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October 17, 2023