Upload
archie
View
47
Download
1
Tags:
Embed Size (px)
DESCRIPTION
Homology Modeling. Seminar produced by Hanka Venselaar. Homology modeling. Yes we can. % identity. *. # residues. * Actually, modelling is possible here, but we cannot get an alignment…. NSDSECPLSHDG || || | || NSYPGCPSSYDG. NSDSECPLSHDG. ?. - PowerPoint PPT Presentation
Citation preview
Homology ModelingHomology Modeling
Seminar produced by Hanka Venselaar
Homology modeling
# residues
% id
entit
y
*
* 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
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
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*
* 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: Iteration8: 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: Iteration8: Iteration
8: Iteration
8: Iteration
8 steps of homology modeling1: Template recognition and initial alignment2: Alignment correction3: Backbone generation4: Loop modeling5: Side-chain modeling6: Model optimization7: Model validation8: Iteration
Alignment
Modeling
Correction