Applications of Homology Applications of Homology ModelingModeling

Hanka Venselaar

This seminar….

Homology Modeling…• Why?

• What?

• When?

• How?

• And a few real world examples….

Homology modeling

Example: by 80 residues 30% identity sufficient

# residues

% id

entit

y

*

* Actually, modelling is possible, but we cannot get an alignment…

O

Homology modeling in short…Prediction of structure based upon a highly similar structure

Add sidechains, Molecular Dynamics simulation on model

Unknown structure

NSDSECPLSHDG

NSDSECPLSHDG

|| || | ||

NSYPGCPSSYDG

Alignment of model and template sequence

Known structure

Known structure Back bone copiedCopy backbone and conserved residues

Model!

The 8 steps of Homology modeling

1: Template recognition and initial alignment

1: Template recognition and initial alignment

• BLAST your sequence against PDB

• Best hit normally template

• Initial alignment

NSDSECPLSHDGYCLHDGVC

|| || | ||||| |||

NSYPGCPSSYDGYCLNGGVC

1: Template recognition and initial alignment

2: Alignment correction

2: Alignment correction

• Functional residues conserved• Use multiple sequence alignments• Deletions shift gaps

CPISRTGASIFRCW CPISRTGASIFRCWCPISRTA---FRCW CPISRT---AFRCW

CPISRTAAS-FRCWCPISRTG-SMFRCWCPISRTA--TFRCWCPISRTAASHFRCWCPISRTGASIFRCW 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

I V

C

R

M

P

EV

C

R M

P

E

Correct alignment

F-D--A-V

1: Template recognition and initial alignment

2: Alignment correction

3: Backbone generation

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

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

6: Model optimization

• Molecular dynamics simulation• Remove big errors

• Structure moves to lowest energy conformation

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 /WHATIF

• 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

8: Iteration

8: Iteration

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: Iteration

8: Iteration

8: Iteration

8 steps of homology modeling

1: Template recognition and initial alignment2: Alignment correction3: Backbone generation4: Loop modeling5: Side-chain modeling6: Model optimization7: Model validation8: Iteration

Alignment

Modeling

Correction

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….

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.