Predicting sub-Golgi localization of type II membrane proteins.
BACKGROUND
Recent research underlines the importance of finegrained knowledge on protein localization. In particular, subcompartmental localization in the Golgi apparatus is important, for example, for the order of reactions performed in glycosylation pathways or the sorting functions of SNAREs, but is currently poorly understood.


RESULTS
We assemble a dataset of type II transmembrane proteins with experimentally determined sub-Golgi localizations and use this information to develop a predictor based on the transmembrane domain of these proteins, making use of a dedicated proteinstructure based kernel in an SVM. Various applications demonstrate the power of our approach. In particular, comparison with a large set of glycan structures illustrates the applicability of our predictions on a 'glycomic' scale and demonstrates a significant correlation between sub-Golgi localization and the ordering of different steps in glycan biosynthesis.


BACKGROUND
Supplementary data are available at Bioinformatics online.
van Dijk
A D J
AD
Applied Bioinformatics, PRI, Wageningen UR, Wageningen, The Netherlands.
Bosch
D
D
ter Braak
C J F
CJ
van der Krol
A R
AR
van Ham
R C H J
RC
D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D003198:Computer Simulation; D006056:Golgi Apparatus / Q000378:metabolism*; D008954:Models, Biological; D008956:Models, Chemical; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D050600:SNARE Proteins / Q000737:chemistry* / Q000378:metabolism*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013329:Structure-Activity Relationship
D050600:SNARE Proteins