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Camps 2.0: Exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins
Author(s) -
Neumann Sindy,
Hartmann Holger,
MartinGaliano Antonio J.,
Fuchs Angelika,
Frishman Dmitrij
Publication year - 2012
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.23242
Subject(s) - transmembrane protein , computational biology , sequence (biology) , sequence space , structural similarity , membrane protein , transmembrane domain , similarity (geometry) , biology , structural classification of proteins database , homogeneous , protein structure , sequence alignment , peptide sequence , markov chain , crystallography , membrane , chemistry , physics , computer science , biochemistry , mathematics , image (mathematics) , artificial intelligence , gene , statistical physics , receptor , pure mathematics , banach space , machine learning
Structural bioinformatics of membrane proteins is still in its infancy, and the picture of their fold space is only beginning to emerge. Because only a handful of three-dimensional structures are available, sequence comparison and structure prediction remain the main tools for investigating sequence-structure relationships in membrane protein families. Here we present a comprehensive analysis of the structural families corresponding to α-helical membrane proteins with at least three transmembrane helices. The new version of our CAMPS database (CAMPS 2.0) covers nearly 1300 eukaryotic, prokaryotic, and viral genomes. Using an advanced classification procedure, which is based on high-order hidden Markov models and considers both sequence similarity as well as the number of transmembrane helices and loop lengths, we identified 1353 structurally homogeneous clusters roughly corresponding to membrane protein folds. Only 53 clusters are associated with experimentally determined three-dimensional structures, and for these clusters CAMPS is in reasonable agreement with structure-based classification approaches such as SCOP and CATH. We therefore estimate that ∼1300 structures would need to be determined to provide a sufficient structural coverage of polytopic membrane proteins. CAMPS 2.0 is available at http://webclu.bio.wzw.tum.de/CAMPS2.0/.