On the evolution of membrane proteins

1. Arne Elofsson (arne@bioinfo.se) On the evolution of membrane proteins Homology detection Blast, PSIBLAST are they good ? SHRIMP (Bernsel, submitted) Evolution of TM-helices Internal duplications >50% of +6TM proteins

2. Problems with homology detection of TM proteins Arne Elofsson (arne@bioinfo.se) • Methods optimized on globular proteins • High scoring false positives due to similarity between unrelated TM regions • Hedman et al, 1998 (Pmembr): • Fold recognition methods improve this fact • Globular detections improved by profile-profile (HMM-HMM) comparisons

3. Profile-profile methods improve detection of membrane proteins Arne Elofsson (arne@bioinfo.se)

4. Classification of GPCRs at 1% FPR Arne Elofsson (arne@bioinfo.se)

5. How does TM proteins evolve Arne Elofsson (arne@bioinfo.se) • Mutation rates any differences in respect to the different compartments. • Few “multi-domain” membrane proteins • Many complexes • Internal symmetry

6. Arne Elofsson (arne@bioinfo.se) Slower evolution in the membrane

7. Internal duplications on sequence level Arne Elofsson (arne@bioinfo.se) Searched for internal duplication events in 87 prokaryotic genomes Out of 38,124 membrane proteins, 377 duplication events could be detected (~1%) Internal duplications has been hard to detect on sequence level α α α α α α X A B C J. Mol. Biol. 2004, 339:1-15

8. Arne Elofsson (arne@bioinfo.se) Lactose Permease

9. Arne Elofsson (arne@bioinfo.se) 1xqf (NH3-channel) Antiparallel duplication

10. Arne Elofsson (arne@bioinfo.se) 12-TM chain from Cytochrome C-oxidase(Triplication)

11. Internal symmetry in α-helical inner membrane proteins Arne Elofsson (arne@bioinfo.se) Antiparallel:LeuTSecYBtuCDAQP1GlpFAmtBClC H+/Cl- exchange transporterNhaA N 2-fold symmetry axis • Parallel to membrane • Odd number of TMH • Domains anti-parallel to each other • In plane with membrane • Even number of TMH • Domains parallel to each other C middle Parallel:LacYGlpTSav1866 ABC transporterAcrBEmrDADP/ATP carrier N C

12. Arne Elofsson (arne@bioinfo.se) Many (most) proteins have internal duplications

13. Arne Elofsson (arne@bioinfo.se) Duplications in TM proteins

14. Arne Elofsson (arne@bioinfo.se) Both parallel and antiparallel duplications exist

15. But in order to have antiparallel domains, they must be inserted with opposing topology! Arne Elofsson (arne@bioinfo.se) N C inside membrane outside N C • In order for an antiparallel symmetry to be explained by a duplication event, each subunit of the homodimer must be inserted with opposite topology • That implies that a sequence can have dual topology, be inserted either way in the membrane • Have been constructed in labs (Cell 62, 1135-1141 & Cell 77, 401-412)

16. Hypothesis for antiparallel internal symmetry Arne Elofsson (arne@bioinfo.se) Nat. Struct. Mol. Biol. 2006, 13: 94-96

17. Detection of internal duplications Arne Elofsson (arne@bioinfo.se) • Structural alignments • Finds most of the manually detected examples. • Sequence alignments • Sequence alignments do not find most. • Using SHRIMP about 80% can be found • Also finds a few extra. • Some problems defining exact duplication unit • Genome scanning • Ongoing.

18. Acknowledgements Arne Elofsson (arne@bioinfo.se) • Erik Granseth • Anni Kauko • Jenny Falk • Andreas Bernsel • Kristoffer Illergård

19. Arne Elofsson (arne@bioinfo.se) Final comments Thanks to EMBRACE Please fill out the questionaire..