Homology Modeling

1. Homology Modeling Seminar produced by Hanka Venselaar

2. Homology modeling Yes we can % identity * # residues * Actually, modelling is possible here, but we cannot get an alignment…

3. 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

4. The 8 steps of Homology modeling

5. 1: Template recognition and initial alignment

6. 1: Template recognition and initial alignment • BLAST your sequence against PDB • Best hit  normally template

7. 2: Alignment correction 1: Template recognition and initial alignment

8. 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

9. 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

10. 3: Backbone generation 2: Alignment correction 1: Template recognition and initial alignment

11. 3: Backbone generation • Making the model…. • Copy backbone of template to model • Make deletions as discussed • (Keep conserved residues)

12. 4: Loop modeling 2: Alignment correction 1: Template recognition and initial alignment 3: Backbone generation

13. 4: Loop modeling Known structure GVCMYIEA---LDKYACNC Your sequence GECFMVKDLSNPSRYLCKC Loop library, try different options

14. 5: Sidechain modeling 2: Alignment correction 1: Template recognition and initial alignment 3: Backbone generation 4: Loop modeling

15. 5: Side-chain modeling • Several options • Libraries of preferred rotamers based upon backbone conformation

16. 6: Model optimization 2: Alignment correction 1: Template recognition and initial alignment 3: Backbone generation 4: Loop modeling 5: Sidechain modeling

17. 6: Model optimization • Molecular dynamics simulation • Remove big errors • Structure moves to lowest energy conformation* * Which has nothing to do with the real coordinates...

18. 2: Alignment correction 1: Template recognition and initial alignment 3: Backbone generation 4: Loop modeling 5: Sidechain modeling 7: Model validation 6: Model optimization

19. 7: Model Validation • Second opinion by PDBreport /WHAT IF • Errors in active site?  new alignment/ template • No errors?  Model!

20. 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

21. 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

22. 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