Applications of Homology Modeling

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Applications of Homology Modeling

• Hanka Venselaar

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This seminar.

• Homology Modeling
• What?
• Why?
• When?
• How?
• And a few real world examples.

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EEC syndrome
Sequence

• MSQSTQTNEFLSPEVFQHIWDFLEQPICSVQPIDLNFVDEPSEDGATNKI
  EISMDCIRMQDSDLSDMWPQYTNLGLLNSMDQQIQNGSSSTSPYNTDHAQ
  NSVTAPSPYAQPSSTFDALSPSPAIPSNTDYPGPHSFDVSFQQSSTAKSA
  TWTYSTELKKLYCQIAKTCPIQIKVMTPPPQGAVIRAMPVYKKAEHVTEV
  VKRCPNHELSREFNEGQIAPPSHLIRVEGNSHAQYVEDPITGRQSVLVPY
  EPPQVGTEFTTVLYNFMCNSSCVGGMNRRPILIIVTLETRDGQVLGRRCF
  EARICACPGRDRKADEDSIRKQQVSDSTKNGDGTKRPFRQNTHGIQMTSI
  KKRRSPDDELLYLPVRGRETYEMLLKIKESLELMQYLPQHTIETYRQQQQ
  QQHQHLLQKQTSIQSPSSYGNSSPPLNKMNSMNKLPSVSQLINPQQRNAL
  TPTTIPDGMGANIPMMGTHMPMAGDMNGLSPTQALPPPLSMPSTSHCTPP
  PPYPTDCSIVSFLARLGCSSCLDYFTTQGLTTIYQIEHYSMDDLASLKIP
  EQFRHAIWKGILDHRQLHEFSSPSHLLRTPSSASTVSVGSSETRGERVID
  AVRFTLRQTISFPPRDEWNDFNFDMDARRNKQQRIKEEGE

EEC syndrome
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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
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Homology modeling
identity

O
residues
Actually, modelling is possible, but we cannot
get an alignment
Example by 80 residues ? 30 identity sufficient
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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
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The 8 steps of Homology modeling
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1 Template recognition and initial alignment
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1 Template recognition and initial alignment

• BLAST your sequence against PDB
• Best hit ? normally template
• Initial alignment ?

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

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

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2 Alignment correction
1 Template recognition and initial alignment
3 Backbone generation
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4 Loop modeling
Known structure GVCMYIEA---LDKYACNC Your
sequence GECFMVKDLSNPSRYLCKC
Loop library, try different options
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2 Alignment correction
1 Template recognition and initial alignment
3 Backbone generation
4 Loop modeling
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5 Side-chain modeling

• Several options
• Libraries of preferred rotamers based upon
  backbone conformation

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

• Molecular dynamics simulation
• Remove big errors
• Structure moves
  to lowest
  energy conformation

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

• Second opinion by PDBreport /WHATIF
• Errors in active site? ? new alignment/ template
• No errors? ? Model!

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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
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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
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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

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EEC syndrome
P63

• MSQSTQTNEFLSPEVFQHIWDFLEQPICSVQPIDLNFVDEPSEDGATNKI
  EISMDCIRMQDSDLSDMWPQYTNLGLLNSMDQQIQNGSSSTSPYNTDHAQ
  NSVTAPSPYAQPSSTFDALSPSPAIPSNTDYPGPHSFDVSFQQSSTAKSA
  TWTYSTELKKLYCQIAKTCPIQIKVMTPPPQGAVIRAMPVYKKAEHVTEV
  VKRCPNHELSREFNEGQIAPPSHLIRVEGNSHAQYVEDPITGRQSVLVPY
  EPPQVGTEFTTVLYNFMCNSSCVGGMNRRPILIIVTLETRDGQVLGRRCF
  EARICACPGRDRKADEDSIRKQQVSDSTKNGDGTKRPFRQNTHGIQMTSI
  KKRRSPDDELLYLPVRGRETYEMLLKIKESLELMQYLPQHTIETYRQQQQ
  QQHQHLLQKQTSIQSPSSYGNSSPPLNKMNSMNKLPSVSQLINPQQRNAL
  TPTTIPDGMGANIPMMGTHMPMAGDMNGLSPTQALPPPLSMPSTSHCTPP
  PPYPTDCSIVSFLARLGCSSCLDYFTTQGLTTIYQIEHYSMDDLASLKIP
  EQFRHAIWKGILDHRQLHEFSSPSHLLRTPSSASTVSVGSSETRGERVID
  AVRFTLRQTISFPPRDEWNDFNFDMDARRNKQQRIKEEGE

EEC syndrome
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Arginine

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

Mutation R?S
Serine
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Another real world example Mutation analysis HFE
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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
ß2-microglobulin ? Facilitates trafficking of HFE
to the cellmembrane
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Hereditary Hemachromatosis ?3 occuring mutations

• C280Y
• D41H
• L161P

L161P
D41H
C280Y
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• Loss of cystein bridge
• Disturbing of ß2-microglobulin binding domain
• No trafficking to membrane

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

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

Mutation L161P
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Seriousness of mutation
Seriousness of the disease
D41H L161P C260Y
D41H L161P 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.
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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 syndrome
  and HFE can be explained