# Applications of Homology Modeling

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```					Applications of Homology
Modeling
Hanka Venselaar
This seminar….
Homology Modeling…
•   What?
•   Why?
•   When?
•   How?

• And a few real world examples….
EEC syndrome
Sequence:                                            No structure:
MSQSTQTNEFLSPEVFQHIWDFLEQPICSVQPIDLNFVDEPSEDGATNKI
EISMDCIRMQDSDLSDMWPQYTNLGLLNSMDQQIQNGSSSTSPYNTDHAQ
NSVTAPSPYAQPSSTFDALSPSPAIPSNTDYPGPHSFDVSFQQSSTAKSA
TWTYSTELKKLYCQIAKTCPIQIKVMTPPPQGAVIRAMPVYKKAEHVTEV
VKRCPNHELSREFNEGQIAPPSHLIRVEGNSHAQYVEDPITGRQSVLVPY
EPPQVGTEFTTVLYNFMCNSSCVGGMNRRPILIIVTLETRDGQVLGRRCF
KKRRSPDDELLYLPVRGRETYEMLLKIKESLELMQYLPQHTIETYRQQQQ
QQHQHLLQKQTSIQSPSSYGNSSPPLNKMNSMNKLPSVSQLINPQQRNAL
TPTTIPDGMGANIPMMGTHMPMAGDMNGLSPTQALPPPLSMPSTSHCTPP
PPYPTDCSIVSFLARLGCSSCLDYFTTQGLTTIYQIEHYSMDDLASLKIP
EQFRHAIWKGILDHRQLHEFSSPSHLLRTPSSASTVSVGSSETRGERVID
AVRFTLRQTISFPPRDEWNDFNFDMDARRNKQQRIKEEGE

EEC syndrome
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
Homology modeling
% identity

*                     O

# residues
* Actually, modelling is possible, but
Example: by 80 residues  30% identity sufficient       we cannot get an alignment…
Homology modeling in short…
Prediction of structure based upon a highly similar structure

NSDSECPLSHDG

NSDSECPLSHDG
||     || | ||
NSYPGCPSSYDG

Model sequence
Model!
Unknown structure
Known structure      Back bone copied
Copy backbone and
conserved residues
Known structure              Dynamics simulation on 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

NSDSECPLSHDGYCLHDGVC

• Initial alignment    ||   || | |||||   |||
NSYPGCPSSYDGYCLNGGVC
1: Template recognition   2: Alignment correction
and initial alignment
2: Alignment correction

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

CPISRTAAS-FRCW
CPISRTG-SMFRCW
CPISRTA--TFRCW
CPISRTAASHFRCW
Multipe sequence alignment
CPISRTGASIFRCW
CPISRTA---FRCW

 Sequence with known structure
CPISRTGASIFRCW          CPISRTGASIFRCW

Both are possible
Correct alignment
2: Alignment correction
E E E -A-V
F-D- I V V
• Core residues  conserved
• Use multiple sequence alignments A
C
P
CC
• Deletions in your sequence  shift gaps
R        R            M S
R

M                G
L
P
P

Known structure FDICRLPGSAEAV
Model FNVCRMP---EAI
Model FNVCR---MPEAI       Correct alignment
1: Template recognition   2: Alignment correction
and initial alignment

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   2: Alignment correction
and initial alignment

3: Backbone
generation
4: Loop
modeling
4: Loop modeling
Known structure GVCMYIEA---LDKYACNC

Loop library,
try different
options
1: Template recognition                           2: Alignment correction
and initial alignment

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                             2: Alignment correction
and initial alignment

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                             2: Alignment correction
and initial alignment

3: Backbone
generation
4: Loop
modeling

5: Sidechain modeling

7: Model
validation

6: Model
optimization
7: Model Validation
• Second opinion by PDBreport /WHATIF
• Errors in active site?  new alignment/
template

• No errors?  Model!
1: Template recognition                             2: Alignment correction
and initial alignment

3: Backbone
generation
4: Loop
modeling

5: Sidechain modeling
8: Iteration

7: Model
validation

6: Model
optimization
1: Template recognition                             2: Alignment correction
and initial alignment

3: Backbone
generation
4: Loop
modeling

5: Sidechain modeling
8: Iteration    Model!

7: Model
validation

6: Model
optimization
8 steps of homology modeling
1: Template recognition and initial
alignment                         Alignment

2: Alignment correction
3: Backbone generation
4: Loop modeling                          Modeling
5: Side-chain modeling
6: Model optimization
7: Model validation                          Correction

8: Iteration
EEC syndrome
P63                                                  Structure!
MSQSTQTNEFLSPEVFQHIWDFLEQPICSVQPIDLNFVDEPSEDGATNKI
EISMDCIRMQDSDLSDMWPQYTNLGLLNSMDQQIQNGSSSTSPYNTDHAQ
NSVTAPSPYAQPSSTFDALSPSPAIPSNTDYPGPHSFDVSFQQSSTAKSA
TWTYSTELKKLYCQIAKTCPIQIKVMTPPPQGAVIRAMPVYKKAEHVTEV
VKRCPNHELSREFNEGQIAPPSHLIRVEGNSHAQYVEDPITGRQSVLVPY
EPPQVGTEFTTVLYNFMCNSSCVGGMNRRPILIIVTLETRDGQVLGRRCF
KKRRSPDDELLYLPVRGRETYEMLLKIKESLELMQYLPQHTIETYRQQQQ
QQHQHLLQKQTSIQSPSSYGNSSPPLNKMNSMNKLPSVSQLINPQQRNAL
TPTTIPDGMGANIPMMGTHMPMAGDMNGLSPTQALPPPLSMPSTSHCTPP
PPYPTDCSIVSFLARLGCSSCLDYFTTQGLTTIYQIEHYSMDDLASLKIP
EQFRHAIWKGILDHRQLHEFSSPSHLLRTPSSASTVSVGSSETRGERVID
AVRFTLRQTISFPPRDEWNDFNFDMDARRNKQQRIKEEGE

EEC syndrome
Arginine

•Loss of negative charge
•Loss of interaction with the DNA

Mutation RS

Serine
Another real world example:
Mutation analysis HFE
Transferrin receptor (dimer)
binds iron/transferrin complex

HFE – complex:
-Signaling and regulation of iron in
bloodstream.
-Expressed in liver and colon.
-Mutations cause iron deposition disease
“Hereditary Hemachromatosis“

HFE

β2-microglobulin
 Facilitates trafficking of
HFE to the cellmembrane
Hereditary
Hemachromatosis
3 occuring mutations

•C280Y

•D41H

•L161P
L161P
D41H

C280Y
•Loss of cystein bridge
•Disturbing of β2-microglobulin
binding domain
•No trafficking to membrane

Mutation C260Y
charge
•Disturbing of hydrogen bridges
•Loss of stability in this area

Mutation H41D
•Loss hydrophobic interactions
•Major disturbance of the helix
•Less interaction of the helix with
the transferrin receptor

Mutation L161P
Seriousness of mutation           Seriousness of the disease

D41H                                        D41H

L161P                                       L161P

C260Y                                       C260Y

Conclusion: the seriousness of the mutation is related to the
seriousness of the disease and can be explained by analyzing
the mutations with the 3D structure.
To conclude….
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

• Real world examples: mutations in EEC

```
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