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Open Access Highly Accessed Research article

Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families

Ratna R Thangudu14, Malini Manoharan2, N Srinivasan3, Frédéric Cadet1, R Sowdhamini2* and Bernard Offmann1*

Author Affiliations

1 Laboratoire de Biochimie et Génétique Moléculaire, Université de La Réunion, BP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France

2 National Centre for Biological Sciences, GKVK Campus, Bangalore, India

3 Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India

4 National Center for Biotechnology Information, U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA

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BMC Structural Biology 2008, 8:55  doi:10.1186/1472-6807-8-55

Published: 26 December 2008

Abstract

Background

Disulphide bridges are well known to play key roles in stability, folding and functions of proteins. Introduction or deletion of disulphides by site-directed mutagenesis have produced varying effects on stability and folding depending upon the protein and location of disulphide in the 3-D structure. Given the lack of complete understanding it is worthwhile to learn from an analysis of extent of conservation of disulphides in homologous proteins. We have also addressed the question of what structural interactions replaces a disulphide in a homologue in another homologue.

Results

Using a dataset involving 34,752 pairwise comparisons of homologous protein domains corresponding to 300 protein domain families of known 3-D structures, we provide a comprehensive analysis of extent of conservation of disulphide bridges and their structural features. We report that only 54% of all the disulphide bonds compared between the homologous pairs are conserved, even if, a small fraction of the non-conserved disulphides do include cytoplasmic proteins. Also, only about one fourth of the distinct disulphides are conserved in all the members in protein families. We note that while conservation of disulphide is common in many families, disulphide bond mutations are quite prevalent. Interestingly, we note that there is no clear relationship between sequence identity between two homologous proteins and disulphide bond conservation. Our analysis on structural features at the sites where cysteines forming disulphide in one homologue are replaced by non-Cys residues show that the elimination of a disulphide in a homologue need not always result in stabilizing interactions between equivalent residues.

Conclusion

We observe that in the homologous proteins, disulphide bonds are conserved only to a modest extent. Very interestingly, we note that extent of conservation of disulphide in homologous proteins is unrelated to the overall sequence identity between homologues. The non-conserved disulphides are often associated with variable structural features that were recruited to be associated with differentiation or specialisation of protein function.