1. Applications of Homology Modeling Hanka Venselaar

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

3. Hearing loss No structure: MGTPWRKRKGIAGPGLPDLSCALVLQPRAQVGTMSPAI ALAFLPLVVTLLVRYRHYFRLLVRTVLLRSLRDCLSGLRI EERAFSYVLTHALPGDPGHILTTLDHWSSRCEYLSHMG PVKGQILMRLVEEKAPACVLELGTYCGYSTLLIARALPP GGRLLTVERDPRTAAVAEKLIRLAGFDEHMVELIVGSSE DVIPCLRTQYQLSRADLVLLAHRPRCYLRDLQLLEAHAL LPAGATVLADHVLFPGAPRFLQYAKSCGRYRCRLHHTG LPDFPAIKDGIAQLTYAGPG DFNB 63 Sequence:

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 Example: by 80 residues  30% identity is (just) sufficient # residues % identity * * Actually, modelling is possible here, but we cannot get an alignment… O Yes we can O

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

7. The 8 steps of Homology modeling

8. 1: Template recognition and initial alignment

9. BLAST your sequence against PDB Best hit  normally template Initial alignment  NSDSECPLSHDGYCLHDGVC || || | ||||| ||| NSYPGCPSSYDGYCLNGGVC

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

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

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

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

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

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

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

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

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

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

20. Molecular dynamics simulation Remove big errors Structure moves to lowest energy conformation

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

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

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

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

25. 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 Alignment Modeling Correction

26. 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 To conclude….

27. Think about the ligand (keep/put it in template) Optimize with the right type of ligand either the real drug, or a generic average agonist / antagonist. Think of details in the active site (ions, waters, pH, etc) Think where the molecule sits in the cell, in the human, in life… And for drug design:

28. And now…. After the next seminar go to the course website: http://swift.cmbi.ru.nl/teach/B4/ Thanks to Hanka Venselaar for making nearly all slides in this seminar.