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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.

SUBMITTER: Kozak JJ

PROVIDER: S-EPMC7222854 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Relaxation of structural constraints during Amicyanin unfolding.

Kozak John J JJ Gray Harry B HB Garza-López Roberto A RA

Journal of inorganic biochemistry 20171122

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 ...[more]

PMID: 29222970

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Project description:BackgroundSelenoproteins are a diverse family of proteins notable for the presence of the 21st amino acid, selenocysteine. Until very recently, all metazoan genomes investigated encoded selenoproteins, and these proteins had therefore been believed to be essential for animal life. Challenging this assumption, recent comparative analyses of insect genomes have revealed that some insect genomes appear to have lost selenoprotein genes.Methodology/principal findingsIn this paper we investigate in detail the fate of selenoproteins, and that of selenoprotein factors, in all available arthropod genomes. We use a variety of in silico comparative genomics approaches to look for known selenoprotein genes and factors involved in selenoprotein biosynthesis. We have found that five insect species have completely lost the ability to encode selenoproteins and that selenoprotein loss in these species, although so far confined to the Endopterygota infraclass, cannot be attributed to a single evolutionary event, but rather to multiple, independent events. Loss of selenoproteins and selenoprotein factors is usually coupled to the deletion of the entire no-longer functional genomic region, rather than to sequence degradation and consequent pseudogenisation. Such dynamics of gene extinction are consistent with the high rate of genome rearrangements observed in Drosophila. We have also found that, while many selenoprotein factors are concomitantly lost with the selenoproteins, others are present and conserved in all investigated genomes, irrespective of whether they code for selenoproteins or not, suggesting that they are involved in additional, non-selenoprotein related functions.Conclusions/significanceSelenoproteins have been independently lost in several insect species, possibly as a consequence of the relaxation in insects of the selective constraints acting across metazoans to maintain selenoproteins. The dispensability of selenoproteins in insects may be related to the fundamental differences in antioxidant defense between these animals and other metazoans.

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Relaxation of structural constraints during Amicyanin unfolding.

Publications

Relaxation of structural constraints during Amicyanin unfolding.

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