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CysMap and CysJoin: Database and tools for protein disulphides localisation
Author(s) -
Caporale Carlo,
Bertini Laura,
Pucci Piero,
Buonocore Vincenzo,
Caruso Carla
Publication year - 2005
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2005.04.061
Subject(s) - edman degradation , database , computer science , chemistry , sequence database , protein sequencing , proteases , sequence (biology) , identification (biology) , data mining , computational biology , combinatorial chemistry , peptide sequence , biochemistry , biology , botany , gene , enzyme
We have developed a computer program able to make user‐customised databases derived from the public PIR non‐redundant reference protein database. When the database of interest has been created, the user will generate the map of all the possible linear peptides containing one and two cysteines for each protein and combine them to calculate the mass of all the possible clusters of linear peptides linked by a disulphide bridge with a cysteine pair. It is also possible to create selected maps corresponding to peptides formed by the action of specific proteases. In this way, mass spectrometric data obtained from the hydrolysis of proteins of unknown sequence can be related to that contained in the database for quick disulphide assignment and protein identification. To confirm signal attribution, the program will also furnish the expected mass of cluster peptides after performing a cycle of Edman degradation. The utility of the program is discussed and examples of application are given.