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Open Life Sciences

formerly Central European Journal of Biology


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Search for proteins with similarity to the CFTR R domain using an optimized RDBMS solution, mBioSQL

1Department of Biochemistry & Biophysics and Cystic Fibrosis T&R Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA

© 2006 Versita Warsaw. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. (CC BY-NC-ND 3.0)

Citation Information: Open Life Sciences. Volume 1, Issue 1, Pages 29–42, ISSN (Online) 2391-5412, DOI: 10.2478/s11535-006-0003-9, March 2006

Publication History

Published Online:
2006-03-01

Abstract

The cystic fibrosis transmembrane conductance regulator (CFTR) comprises ATP binding and transmembrane domains, and a unique regulatory (R) domain not found in other ATP binding cassette proteins. Phosphorylation of the R domain at different sites by PKA and PKC is obligatory for the chloride channel function of CFTR. Sequence similarity searches on the R domain were uninformative. Furthermore, R domains from different species show low sequence similarity. Since these R domains resemble each other only in the location of the phosphorylation sites, we generated different R domain patterns masking amino acids between these sites. Because of the high number of the generated patterns we expected a large number of matches from the UniProt database. Therefore, a relational database management system (RDBMS) was set up to handle the results. During the software development our system grew into a general package which we term Modular BioSQL (mBioSQL). It has higher performance than other solutions and presents a generalized method for the storage of biological result-sets in RDBMS allowing convenient further analysis. Application of this approach revealed that the R domain phosphorylation pattern is most similar to those in nuclear proteins, including transcription and splicing factors.

Keywords: Cystic fibrosis; CFTR; regulatory domain; phosphorylation; relational database management system

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