1. Homology Profile-HMMs Domains Protein-family Databases How to build a new (Pfam) protein family EMBO Workshop, Cape Town, 2014 Function annotation transfer Outline Pfam database

2. Homology EMBO Workshop, Cape Town, 2014

3. Definition: Two proteins are homologous if they share a common ancestor, i.e. they are evolutionary related EMBO Workshop, Cape Town, 2014

4. Symmetric A A B B homologous Transitive B B A A homologous A A B B AND B B C C homologous A A C C

5. Detecting homology EMBO Workshop, Cape Town, 2014

6. Human: 1 MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE 60 MGLSDGEWQLVLNVWGKVEAD GHGQEVLI LFK HPETL KFDKFK LKSE MK SE Mouse: 1 MGLSDGEWQLVLNVWGKVEADLAGHGQEVLIGLFKTHPETLDKFDKFKNLKSEEDMKGSE 60 Human: 61 DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKH 120 DLKKHG TVLTALG ILKKKG H AEI PLAQSHATKHKIPVKYLEFISE II VL H Mouse: 61 DLKKHGCTVLTALGTILKKKGQHAAEIQPLAQSHATKHKIPVKYLEFISEIIIEVLKKRH 120 Human: 121 PGDFGADAQGAMNKALELFRKDMASNYKELGFQG 154 GDFGADAQGAM KALELFR D A YKELGFQG Mouse: 121 SGDFGADAQGAMSKALELFRNDIAAKYKELGFQG 154 By excess similarity (see Pearson Curr Protoc Bioinformatics 2013 ) Statistical significance (e.g. E-values) Sequence similarity EMBO Workshop, Cape Town, 2014

7. 2G2X: 1 MAYWLMKSEPDELSIEALARLGEARWDGVRNYQARNFLRAMSVGDEFFFYH-----SSCP 55 MAYWL D W Y N VGD Y 2P5D: 4 MAYWLCITNEDNWKVIKEKKI----WGVAERY--KNTINKVKVGDKLIIYEIQRSGKDYK 57 2G2X: 56 QPGIAGIARITRAAYPD------PTALDPESHY 82 P I G Y D PT P 2P5D: 58 PPYIRGVYEVVSEVYKDSSKIFKPTPRNPNEKF 90 Excess sequence similarity? Structural similarity EMBO Workshop, Cape Town, 2014

8. 2G2X 2P5D Structural similarity EMBO Workshop, Cape Town, 2014

9. Structural similarity 2G2X 2P5D

10. Structural similarity 2G2X 2P5D Z-score = 12.2 RMSD = 2.9 Lali = 122 %id =20 DALI: http://ekhidna.biocenter.helsinki.fi/dali_lite/start

11. http://www.microbesonline.org EMBO Workshop, Cape Town, 2014 Genomic context See e.g. Jun et al. BMC Genomics 2009

12. http://www.microbesonline.org EMBO Workshop, Cape Town, 2014 Genomic context Homology See e.g. Jun et al. BMC Genomics 2009

13. http://www.microbesonline.org EMBO Workshop, Cape Town, 2014 Genomic context See e.g. Jun et al. BMC Genomics 2009 Homology?

14. http://www.microbesonline.org EMBO Workshop, Cape Town, 2014 Genomic context Mostly used for distinguishing orthology from paralogy

15. Origins of homology in proteins EMBO Workshop, Cape Town, 2014

16. Origin of homology in proteins Speciation (orthology) Gene duplication (paralogy) Horizontal gene transfer (xenology) Whole genome duplication (ohnology) Gametology EMBO Workshop, Cape Town, 2014

17. Myoglobin: Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles. Orthology EMBO Workshop, Cape Town, 2014

18. Speciation (orthology) Gene duplication (paralogy) Horizontal gene transfer (xenology) Whole genome duplication (ohnology) Gametology Origin of protein homology EMBO Workshop, Cape Town, 2014

19. Myoglobin: Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles. Hemoglobin: Oxygen-transport protein in red-blood cells of vertebrates Paralogy

20. EMBO Workshop, Cape Town, 2014

21. Ancestral Globin B C Myo A Hemo EMBO Workshop, Cape Town, 2014

22. Ancestral Globin B C Myo A Hemo EMBO Workshop, Cape Town, 2014

23. Ancestral Globin B C Myo A Hemo Myo Hemo Myo Hemo EMBO Workshop, Cape Town, 2014

24. Origin of protein homology EMBO Workshop, Cape Town, 2014 Speciation (orthology) Gene duplication (paralogy) Horizontal gene transfer (xenology) Whole genome duplication (ohnology) Gametology, Synology

25. Mindell and Meyer Trends in Ecology and Evolution 2001

26. EMBO Workshop, Cape Town, 2014 Homology: why bother? Slide courtesy of Alex Mitchell (EMBL-EBI)

27. Homology Function? Structure (homology modeling) EMBO Workshop, Cape Town, 2014 Homology: why bother?

28. Schubert et al. Nat. Struct. Biol. 5 (1998) Protein function(s) EMBO Workshop, Cape Town, 2014

29. A way to capture biological knowledge in a written and computable form A set of concepts and their relationships to each other www.ebi.ac.uk/QuickGO EMBO Workshop, Cape Town, 2014 Slide courtesy of Alex Mitchell (EMBL-EBI) The Gene Ontology (GO)

30. 1. Molecular Function 2. Biological Process 3. Cellular Component An elemental activity or task or job protein kinase activity insulin receptor activity A commonly recognised series of events cell division Where a gene product is located mitochondrion mitochondrial matrix mitochondrial inner membrane EMBO Workshop, Cape Town, 2014 Slide courtesy of Alex Mitchell (EMBL-EBI) GO: 3 ontologies in 1

34. Protein Families EMBO Workshop, Cape Town, 2014

35. http://www.studyblue.com/notes/note/n/exam-3/deck/8955883 Globins in Human

36. Definition: We call ‘family’ a group of evolutionary related proteins or protein regions EMBO Workshop, Cape Town, 2014

37. P P A A Why protein families?

38. Human: 1 MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE 60 MGLSDGEWQLVLNVWGKVEAD GHGQEVLI LFK HPETL KFDKFK LKSE MK SE Mouse: 1 MGLSDGEWQLVLNVWGKVEADLAGHGQEVLIGLFKTHPETLDKFDKFKNLKSEEDMKGSE 60 Human: 61 DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKH 120 DLKKHG TVLTALG ILKKKG H AEI PLAQSHATKHKIPVKYLEFISE II VL H Mouse: 61 DLKKHGCTVLTALGTILKKKGQHAAEIQPLAQSHATKHKIPVKYLEFISEIIIEVLKKRH 120 Human: 121 PGDFGADAQGAMNKALELFRKDMASNYKELGFQG 154 GDFGADAQGAM KALELFR D A YKELGFQG Mouse: 121 SGDFGADAQGAMSKALELFRNDIAAKYKELGFQG 154 Why protein families? EMBO Workshop, Cape Town, 2014

39. Human: 1 MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE 60 MGLSDGEWQLVLNVWGKVEAD GHGQEVLI LFK HPETL KFDKFK LKSE MK SE Mouse: 1 MGLSDGEWQLVLNVWGKVEADLAGHGQEVLIGLFKTHPETLDKFDKFKNLKSEEDMKGSE 60 Human: 61 DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKH 120 DLKKHG TVLTALG ILKKKG H AEI PLAQSHATKHKIPVKYLEFISE II VL H Mouse: 61 DLKKHGCTVLTALGTILKKKGQHAAEIQPLAQSHATKHKIPVKYLEFISEIIIEVLKKRH 120 Human: 121 PGDFGADAQGAMNKALELFRKDMASNYKELGFQG 154 GDFGADAQGAM KALELFR D A YKELGFQG Mouse: 121 SGDFGADAQGAMSKALELFRNDIAAKYKELGFQG 154 Why protein families? EMBO Workshop, Cape Town, 2014

40. P P A A B B H H G G E E C C D D F F

41. We can detect functionally important residues EMBO Workshop, Cape Town, 2014

42. We can detect functionally important residues EMBO Workshop, Cape Town, 2014

43. We have a window open on evolutionary diversity Human: 1 MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE 60 MGLSDGEWQLVLNVWGKVEAD GHGQEVLI LFK HPETL KFDKFK LKSE MK SE Mouse: 1 MGLSDGEWQLVLNVWGKVEADLAGHGQEVLIGLFKTHPETLDKFDKFKNLKSEEDMKGSE 60 Human: 61 DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKH 120 DLKKHG TVLTALG ILKKKG H AEI PLAQSHATKHKIPVKYLEFISE II VL H Mouse: 61 DLKKHGCTVLTALGTILKKKGQHAAEIQPLAQSHATKHKIPVKYLEFISEIIIEVLKKRH 120 Human: 121 PGDFGADAQGAMNKALELFRKDMASNYKELGFQG 154 GDFGADAQGAM KALELFR D A YKELGFQG Mouse: 121 SGDFGADAQGAMSKALELFRNDIAAKYKELGFQG 154 EMBO Workshop, Cape Town, 2014

44. We have a window open on evolutionary diversity

45. Example (using homology for protein annotation) EMBO Workshop, Cape Town, 2014

46. H. influenzae protein (3M71) 1.20 Å Chen et al. Nature 467 (2010) TUM, January 2013 EMBO Workshop, Cape Town, 2014 New York Consortium on Membrane Protein Structure (NYCOMPS)

47. TUM, January 2013

48. Thomine and Barbier-Brygoo Nature 467:1058-59 (2010) EMBO Workshop, Cape Town, 2014

49. Thomine and Barbier-Brygoo Nature 467:1058-59 (2010) EMBO Workshop, Cape Town, 2014

50. Chen et al. Nature 467 (2010)

51. EMBO Workshop, Cape Town, 2014 Chen et al. Nature 467 (2010)

52. EMBO Workshop, Cape Town, 2014 Chen et al. Nature 467 (2010)

53. TUM, January 2013

54. EMBO Workshop, Cape Town, 2014 OPEN Jalview 1. 2. File -> Input Alignment -> From File “PF03595_seed.txt”

55. EMBO Workshop, Cape Town, 2014 Colour -> BLOSUM62 1.

56. EMBO Workshop, Cape Town, 2014 OPEN Chimera 1. File -> Open “3M71.pdb” 2.

57. EMBO Workshop, Cape Town, 2014

58. out

59. EMBO Workshop, Cape Town, 2014 Actions -> Atoms/Bonds -> wire 1. Actions -> Atoms/Bonds -> show 2.

60. out EMBO Workshop, Cape Town, 2014 Actions -> Atoms/Bonds -> wire 1. Actions -> Atoms/Bonds -> show 2.