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• Fonseca, R
• Drury, B
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• Drury, B
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• Fonseca, R
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• Melo, A

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Int. J. Mol. Sci. 2010, 11(11), 4673-4686; doi:10.3390/ijms11114673

Article

Amino Acid Patterns around Disulfide Bonds

José R. F. Marques ¹ , Rute R. da Fonseca ² , Brett Drury ³  and André Melo ^1,*

¹ REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal ² CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal ³ LIAAD-INESC, Rua de Ceuta, 118, 6º, 4050-190 Porto, Portugal

* Author to whom correspondence should be addressed.

Received: 17 October 2010; in revised form: 4 November 2010 / Accepted: 11 November 2010 / Published: 18 November 2010

(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

Download PDF Full-Text [563 KB, uploaded 18 November 2010 10:50 CET]

Abstract: Disulfide bonds provide an inexhaustible source of information on molecular evolution and biological specificity. In this work, we described the amino acid composition around disulfide bonds in a set of disulfide-rich proteins using appropriate descriptors, based on ANOVA (for all twenty natural amino acids or classes of amino acids clustered according to their chemical similarities) and Scheffé (for the disulfide-rich proteins superfamilies) statistics. We found that weakly hydrophilic and aromatic amino acids are quite abundant in the regions around disulfide bonds, contrary to aliphatic and hydrophobic amino acids. The density distributions (as a function of the distance to the center of the disulfide bonds) for all defined entities presented an overall unimodal behavior: the densities are null at short distances, have maxima at intermediate distances and decrease for long distances. In the end, the amino acid environment around the disulfide bonds was found to be different for different superfamilies, allowing the clustering of proteins in a biologically relevant way, suggesting that this type of chemical information might be used as a tool to assess the relationship between very divergent sets of disulfide-rich proteins.

Keywords: disulfide bond; neighborhood; classification; frequency; diversity

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