Applications of Homology Modeling
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Transcript of Applications of Homology Modeling
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Applications of Homology Applications of Homology ModelingModeling
Hanka Venselaar
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This seminar….
Homology Modeling…• Why?
• What?
• When?
• How?
• And a few real world examples….
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Hearing loss
No structure:
MGTPWRKRKGIAGPGLPDLSCALVLQPRAQVGTMSPAIALAFLPLVVTLLVRYRHYFRLLVRTVLLRSLRDCLSGLRIEERAFSYVLTHALPGDPGHILTTLDHWSSRCEYLSHMGPVKGQILMRLVEEKAPACVLELGTYCGYSTLLIARALPPGGRLLTVERDPRTAAVAEKLIRLAGFDEHMVELIVGSSEDVIPCLRTQYQLSRADLVLLAHRPRCYLRDLQLLEAHALLPAGATVLADHVLFPGAPRFLQYAKSCGRYRCRLHHTGLPDFPAIKDGIAQLTYAGPG
DFNB 63 Sequence:
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KKIALSDARSMKHALREIKIIRRLDHDNIVKVYEVLGPKGTDLQGELFKFSVAYIVQEYMETDLARLLEQGTLAEEHAKLFMYQLLRGLKYIHSANVLHRDLPANIFISTEDLVLKIGDFGLARIVDQHYSHKGYLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCILAEMLTGRMLFAGAHELEQMQLLETIPVIREEDKDELLRVMPSFVSS ??
Why homology modeling?
Lab Translation Bioinformatics
ATOM 1 N GLN A 117 -42.882 10.838 12.153 1.00 58.09 N ATOM 2 CA GLN A 117 -42.770 10.783 10.668 1.00 58.36 C ATOM 3 C GLN A 117 -41.435 11.371 10.185 1.00 57.07 C ATOM 4 O GLN A 117 -41.264 12.582 10.210 1.00 57.81 O ATOM 5 CB GLN A 117 -43.966 11.532 10.028 1.00 59.40 C ATOM 6 CG GLN A 117 -45.344 10.768 10.084 1.00 62.58 C ATOM 7 CD GLN A 117 -45.254 9.261 9.651 1.00 67.37 C ATOM 8 OE1 GLN A 117 -44.260 8.554 9.948 1.00 68.20 O ATOM 9 NE2 GLN A 117 -46.304 8.778 8.955 1.00 67.47 N ATOM 10 N SER A 118 -40.488 10.545 9.741 1.00 54.71 N ATOM 11 CA SER A 118 -39.144 11.089 9.506 1.00 52.44 C ATOM 12 C SER A 118 -38.389 10.616 8.251 1.00 50.58 C ATOM 13 O SER A 118 -38.692 9.566 7.734 1.00 50.83 O ATOM 14 CB SER A 118 -38.317 10.815 10.736 1.00 52.75 C ATOM 15 OG SER A 118 -38.273 9.437 10.917 1.00 53.04 O ATOM 16 N CYS A 119 -37.428 11.398 7.755 1.00 48.00 N ATOM 17 CA CYS A 119 -36.748 11.070 6.507 1.00 46.41 C ATOM 18 C CYS A 119 -35.339 10.829 6.835 1.00 45.44 C ATOM 19 O CYS A 119 -34.845 11.360 7.805 1.00 45.36 O ATOM 20 CB CYS A 119 -36.721 12.232 5.504 1.00 45.97 C ATOM 21 SG CYS A 119 -38.275 12.940 5.114 1.00 47.29 S ATOM 22 N LEU A 120 -34.657 10.098 5.972 1.00 44.91 N
4
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Protein structures – 4 levels
Primary Secondary
Tertiary Quaternary
Shape of the protein determines its function…..
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Protein structures…where can we find them?
Protein DataBank = www.pdb.org
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PDB-file: contains the coördinaties for every atom in a protein
Visualisation with PDB-viewers-Jmol-PyMol-SwissPDB viewer-YASARA
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So, 3D Protein-structures provide useful information
But……Not enough protein structures in the PDB database
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Predictions/Annotations
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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
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 – When?
Example: by 80 residues 30% identity sufficient
O
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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 Model sequence
Known structure
Known structureBack bone copied
Copy backbone and conserved residues
Model!
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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
• Initial alignment
• Best hit is usually your template
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1: Template recognition and initial alignment
2: Alignment correction
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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
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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
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1: Template recognition and initial alignment
2: Alignment correction
3: Backbone generation
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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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1: Template recognition and initial alignment
2: Alignment correction
3: Backbone generation
4: Loop modeling
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4: Loop modeling
Known structure GVCMYIEA---LDKYACNC
Your sequence GECFMVKDLSNPSRYLCKC
Loop library,
try different options
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1: Template recognition and initial alignment
2: Alignment correction
3: Backbone generation
4: Loop modeling
5: Sidechain modeling
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5: Side-chain modeling
• Several options
• Libraries of preferred rotamers based upon backbone conformation
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1: Template recognition and initial alignment
2: Alignment correction
3: Backbone generation
4: Loop modeling
5: Sidechain modeling
6: Model optimization
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6: Model optimization
• Molecular dynamics simulation• Remove big errors
• Structure moves to lowest energy conformation
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1: Template recognition and initial alignment
2: Alignment correction
3: Backbone generation
4: Loop modeling
5: Sidechain modeling
6: Model optimization
7: Model validation
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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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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
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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
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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
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Hearing loss
Structure!
MGTPWRKRKGIAGPGLPDLSCALVLQPRAQVGTMSPAIALAFLPLVVTLLVRYRHYFRLLVRTVLLRSLRDCLSGLRIEERAFSYVLTHALPGDPGHILTTLDHWSSRCEYLSHMGPVKGQILMRLVEEKAPACVLELGTYCGYSTLLIARALPPGGRLLTVERDPRTAAVAEKLIRLAGFDEHMVELIVGSSEDVIPCLRTQYQLSRADLVLLAHRPRCYLRDLQLLEAHALLPAGATVLADHVLFPGAPRFLQYAKSCGRYRCRLHHTGLPDFPAIKDGIAQLTYAGPG
DFNB 63 Sequence:
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Mutation:
•Tryptophan 105 -> Arginine
Hydrophobic contacts from the Tryoptohan are lost, introduction of an hydrophilic and charged residue
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The three mutated residues are all important for the correct positioning of Tyrosine 111
Tyrosine 111 is important for substrate binding
Published in
Nature Genetics: 2008 Oct 26.
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Voorbeeld: C-terminale deletie van 10 aa in Dectine
Afdeling: Interne geneeskunde of Internal Medicine
>Dectin_1_Isoform_a MEYHPDLENLDEDGYTQLHFDSQSNTRIAVVSEKGSCAASPPWRLIAVILGILCLVILVIAVVLGTMAIWRSNSGSNTLENGYFLSRNKENHSQPTQSSLEDSVTPTKAVKTTGVLSSPCPPNWIIYEKSCYLFSMSLNSWDGSKRQCWQLGSNLLKIDSSNELGFIVKQVSSQPDNSFWIGLSRPQTEVPWLWEDGSTFSSNLFQIRTTATQENPSPNCVWIHVSVIYDQLCSVPSYSICEKKFSM
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MSQSTQTNEFLSPEVFQHIWDFLEQPICSVQPIDLNFVDEPSEDGATNKIEISMDCIRMQDSDLSDMWPQYTNLGLLNSMDQQIQNGSSSTSPYNTDHAQNSVTAPSPYAQPSSTFDALSPSPAIPSNTDYPGPHSFDVSFQQSSTAKSATWTYSTELKKLYCQIAKTCPIQIKVMTPPPQGAVIRAMPVYKKAEHVTEVVKRCPNHELSREFNEGQIAPPSHLIRVEGNSHAQYVEDPITGRQSVLVPYEPPQVGTEFTTVLYNFMCNSSCVGGMNRRPILIIVTLETRDGQVLGRRCFEARICACPGRDRKADEDSIRKQQVSDSTKNGDGTKRPFRQNTHGIQMTSIKKRRSPDDELLYLPVRGRETYEMLLKIKESLELMQYLPQHTIETYRQQQQQQHQHLLQKQTSIQSPSSYGNSSPPLNKMNSMNKLPSVSQLINPQQRNALTPTTIPDGMGANIPMMGTHMPMAGDMNGLSPTQALPPPLSMPSTSHCTPPPPYPTDCSIVSFLARLGCSSCLDYFTTQGLTTIYQIEHYSMDDLASLKIPEQFRHAIWKGILDHRQLHEFSSPSHLLRTPSSASTVSVGSSETRGERVIDAVRFTLRQTISFPPRDEWNDFNFDMDARRNKQQRIKEEGE
P63 sequence Structure!
EEC syndrome
EEC syndrome
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Arginine
Serine
Mutation RS
•Loss of negative charge
•Loss of interaction with the DNA
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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
Use the models for mutant analysis, experimental design and understanding of the protein in general
To conclude….