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

Additional files

Additional file 1:

Nature of side chains of of substituted residues topologically equivalent with cystines of a distinct disulphide bond in their respective families. For domains where the original disulphide bond is mutated, the topologically equivalent substituted residues are extracted to verify if the interaction is conserved.

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Additional file 2:

Evolutionary dynamics of disulphides at family and superfamily level. We extended our analysis by investigating the evolutionary dynamics of disulphides between members within a homologous family and also across families in a superfamily in order to provide further insights into the biological implications of conservation and non-conservation of disulphides.

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Additional file 3:

Evolutionary dynamics of disulphides in the alpha/beta hydrolase actetylcholinesterase-like family (SCOP family code: c.69.1.1). Three highly superimposable members from this family are featured. In (a) is featured a representative (SCOP domain: d2bce__; PDB code: 2bce) from the cholesterol esterase and carboxyesterase types which display two highly conserved disulphides. In (b) is featured a representative (SCOP domain: d1dx4a_; PDB code: 1dx4) from the acetylcholinesterase type which display in addition to the two conserved disulphide, a third specific disulphide (arrow). In (c) is featured a representative from the paranitrobenzyl esterases group which do not feature any disulphide though two cysteines which are topologically equivalent to one highly conserved disulphide is present in the molecule.

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Additional file 4:

Evolutionary dynamics of disulphides in the alpha/beta hydrolase serine carboxypeptidase-like family (SCOP code: c.69.1.5). Three superimposable members from this family are featured and which display one highly conserved disulphide (arrow). In (a) is featured a representative (SCOP domain: d1ac5_; PDB: 1ac5) from the serine carboxypeptidase II type and which displays two non-conserved disulphides. In (b) is featured a representative (SCOP domain: d1cpya_; PDB: 1cpy) from the human carboxypeptidase L type which display in addition to the conserved disulphide, four specific disulphides. In (c) is featured a representative from the human protective protein group which display in addition to the conserved disulphide, three specific disulphides.

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Additional file 5:

Representation of Type-B carboxylesterase/lipase (SCOP domain: d1thga_; PDB: 1thg) from the fungal lipase family (SCOP family code: c.69.1.17). Representation of Type-B carboxylesterase/lipase (SCOP domain: d1thga_; PDB: 1thg) from the fungal lipase family (SCOP family code: c.69.1.17) that features two disulphides that are topologically equivalent to the two highly conserved disulphides from acetylcholinesterase-like family (SCOP family code: c.69.1.1).

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Additional file 6:

Localization predictions by the three programs and the consensus starting from full-length sequences of proteins in the dataset. This table provides a comparison and consensus obtained by applying the three prediction servers for cellular localization.

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Additional file 7:

Literature survey of proteins highly predicted to be cytoplasmic by all three programs. This table provides the results of literature survey on comments of cellular localization for the protein chains, that are predicted to be cytoplasmic, by all three programs or by any two out of three programs.

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Additional file 8:

Conservation of disulphide bonds in protein chains highly predicted as cytoplasmic. This table provides the results of examination of conservation (or otherwise) of distinct disulphides for proteins that have been highly predicted to be cytoplasmic.

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