Homology Modeling Seminar produced by Hanka Venselaar

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

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!

The 8 steps of Homology modeling

1: Template recognition and initial alignment

BLAST your sequence against PDB Best hit  normally template

1: Template recognition and initial alignment 2: Alignment correction

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

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

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

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

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

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

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

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

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

Molecular dynamics simulation Remove big errors Structure moves to lowest energy conformation* * Which has nothing to do with the real coordinates...

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

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

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

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