Applications of Homology Modeling

1. Applications of Homology Modeling Hanka Venselaar

2. This seminar…. Homology Modeling… • Why? • What? • When? • How? • And a few real world examples….

3. No structure: ? DFNB 63 Sequence: MGTPWRKRKGIAGPGLPDLSCALVLQPRAQVGTMSPAIALAFLPLVVTLLVRYRHYFRLLVRTVLLRSLRDCLSGLRIEERAFSYVLTHALPGDPGHILTTLDHWSSRCEYLSHMGPVKGQILMRLVEEKAPACVLELGTYCGYSTLLIARALPPGGRLLTVERDPRTAAVAEKLIRLAGFDEHMVELIVGSSEDVIPCLRTQYQLSRADLVLLAHRPRCYLRDLQLLEAHALLPAGATVLADHVLFPGAPRFLQYAKSCGRYRCRLHHTGLPDFPAIKDGIAQLTYAGPG Hearing loss

4. Homology modeling in short… Prediction of structure based upon a highly similar structure • 2 basic assumptions: • Structure defines function • During evolution structures are more conserved than sequence Use one structure to predict another

5. Homology modeling % identity * O # residues * Actually, modelling is possible, but we cannot get an alignment… Example: by 80 residues  30% identity sufficient

6. NSDSECPLSHDG || || | || NSYPGCPSSYDG NSDSECPLSHDG ? Alignment of model and template sequence Unknown structure Known structure Back bone copied Homology modeling in short… Prediction of structure based upon a highly similar structure Model! Copy backbone and conserved residues Add sidechains, Molecular Dynamics simulation on model Known structure

7. The 8 steps of Homology modeling

8. 1: Template recognition and initial alignment

9. NSDSECPLSHDGYCLHDGVC || || | ||||| ||| NSYPGCPSSYDGYCLNGGVC 1: Template recognition and initial alignment • BLAST your sequence against PDB • Best hit  normally template • Initial alignment 

10. 2: Alignment correction 1: Template recognition and initial alignment

11. CPISRTAAS-FRCW CPISRTG-SMFRCW CPISRTA--TFRCW CPISRTAASHFRCW CPISRTGASIFRCW CPISRTA---FRCW CPISRTGASIFRCW CPISRTGASIFRCW CPISRTA---FRCW CPISRT---AFRCW Correct alignment 2: Alignment correction • Functional residues  conserved • Use multiple sequence alignments • Deletions  shift gaps Multipe sequence alignment  Sequence with known structure Your sequence Both are possible

12. E I E E V V A P C C C S R R M R G L M P P 2: Alignment correction -A-V F-D- • Core residues  conserved • Use multiple sequence alignments • Deletions in your sequence  shift gaps Known structure FDICRLPGSAEAV Model FNVCRMP---EAI Model FNVCR---MPEAI  Correct alignment

13. 3: Backbone generation 2: Alignment correction 1: Template recognition and initial alignment

14. 3: Backbone generation • Making the model…. • Copy backbone of template to model • Make deletions as discussed • (Keep conserved residues)

15. 4: Loop modeling 2: Alignment correction 1: Template recognition and initial alignment 3: Backbone generation

16. 4: Loop modeling Known structure GVCMYIEA---LDKYACNC Your sequence GECFMVKDLSNPSRYLCKC Loop library, try different options

17. 5: Sidechain modeling 2: Alignment correction 1: Template recognition and initial alignment 3: Backbone generation 4: Loop modeling

18. 5: Side-chain modeling • Several options • Libraries of preferred rotamers based upon backbone conformation

19. 6: Model optimization 2: Alignment correction 1: Template recognition and initial alignment 3: Backbone generation 4: Loop modeling 5: Sidechain modeling

20. 6: Model optimization • Molecular dynamics simulation • Remove big errors • Structure moves to lowest energy conformation

21. 2: Alignment correction 1: Template recognition and initial alignment 3: Backbone generation 4: Loop modeling 5: Sidechain modeling 7: Model validation 6: Model optimization

22. 7: Model Validation • Second opinion by PDBreport /WHATIF • Errors in active site?  new alignment/ template • No errors?  Model!

23. 2: Alignment correction 1: Template recognition and initial alignment 3: Backbone generation 4: Loop modeling 8: Iteration 8: Iteration 5: Sidechain modeling 8: Iteration 8: Iteration 7: Model validation 6: Model optimization

24. 2: Alignment correction 1: Template recognition and initial alignment 3: Backbone generation 4: Loop modeling 8: Iteration 8: Iteration 5: Sidechain modeling Model! 8: Iteration 8: Iteration 7: Model validation 6: Model optimization

25. Alignment Modeling Correction 8 steps of homology modeling 1: Template recognition and initial alignment 2: Alignment correction 3: Backbone generation 4: Loop modeling 5: Side-chain modeling 6: Model optimization 7: Model validation 8: Iteration

26. Structure! DFNB 63 Sequence: MGTPWRKRKGIAGPGLPDLSCALVLQPRAQVGTMSPAIALAFLPLVVTLLVRYRHYFRLLVRTVLLRSLRDCLSGLRIEERAFSYVLTHALPGDPGHILTTLDHWSSRCEYLSHMGPVKGQILMRLVEEKAPACVLELGTYCGYSTLLIARALPPGGRLLTVERDPRTAAVAEKLIRLAGFDEHMVELIVGSSEDVIPCLRTQYQLSRADLVLLAHRPRCYLRDLQLLEAHALLPAGATVLADHVLFPGAPRFLQYAKSCGRYRCRLHHTGLPDFPAIKDGIAQLTYAGPG Hearing loss

27. Mutations: • Arginine 81 -> Glutamic acid • Glutamic acid 110 -> Lysine Saltbridge between Arginine and Glutamic acid is lost in both cases

28. Mutation: • Tryptophan 105 -> Arginine Hydrophobic contacts from the Tryoptohan are lost, introduction of an hydrophilic and charged residue

29. The three mutated residues are all important for the correct positioning of Tyrosine 111 Tyrosine 111 is important for substrate binding Accepted in Nature Genetics

30. To conclude…. Homology Modeling… • What? Prediction of an unknown structure based on an homologous and known structure • Why? To answer biological and medical questions when the “real” structure is unknown • When? A template with enough identity must be available • How? 8 Steps • Real world examples: mutations in DFNB63 gene can lead to hearing disorders.

31. And now…. • Go to the course website: http://swift.cmbi.ru.nl/teach/graduateCourse • Follow the steps on the site • A few hints…. Login with username: c01 – c13 (number of your pc is written on the pc itself) Click on the icon to open a terminal Run Yasara by typing “yasara” in that terminal Save your files on the Desktop