||October 11, 2011
||Prof. Dmitrij Frishman, Technische Universitat Munich
||Exploring the fold space of membrane proteins
Recent progress in structure determination techniques has led to a significant growth in the number of known membrane protein structures.
The first structural genomics projects focusing on membrane proteins have been initiated, warranting an investigation of appropriate bioinformatics
strategies for optimal structural target selection for these molecules. What determines a membrane protein fold? How many structures need to be solved
to provide sufficient structural coverage of the membrane protein sequence space? In my talk I will describe the CAMPS database (Computational Analysis
of the Membrane Protein Space) that automatically classifies α-helical membrane proteins into fold classes. I will also present our latest results
on predicting interacting helices in membrane proteins and deriving helix connectivity diagrams that represent a convenient level of abstraction for
comparing predicted membrane protein structures. Finally, I will review the difficulties in classifying experimentally determined three-dimensional structures
of membrane proteins, focusing on the differences between the SCOP and CATH databases.
1. Frishman, D. (Ed) Structural bioinformatics of membrane proteins. Springer, Wien 2009. ISBN 978-3709100448.
2. Fuchs A, Frishman D. (2010) Structural comparison and classification of alpha-helical transmembrane domains based on helix interaction patterns. Proteins, 78, 2587-2599.
3. Neumann S., Fuchs A., Mulkidjanian A, and Frishman D. (2010) Current status of membrane protein structure classification. Proteins, 78, 1760-1773.
4. Fuchs, A., Kirschner, A., Frishman D. (2009) Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks. Proteins, 74, 857-71
5. Fuchs, A., Martin-Galiano, A.J., Kalman, M., Fleishman, S., Ben-Tal, S., and Frishman, D. (2007) Co-Evolving Residues in Membrane Proteins. Bioinformatics, 23, 3312-3319.
6. Martin-Galiano, A.J., Frishman, D. (2006) Defining the Fold Space of Membrane Proteins: the CAMPS Database. Proteins, 64, 906-22.