Transcript Protein Structure Prediction

Biomolecular Modeling (practical)
Dr. Kong Lesheng
Temasek Life Sciences Laboratory (TLL)
([email protected])
Objective

To predict 3D structure with good quality
when given a protein sequence
Protein structure prediction

Comparative (homology) modeling
– typically >20-30% identity

Threading/fold recognition
– cannot detect similarity in sequence level

Ab initio (de novo) modeling
– cannot detect fold
Adapted from
Sali & Baker,
Science (2001)
Adapted from
Sali & Baker,
Science (2001)
Comparative modeling
More reliable and accurate
 Computationally less intensive
 With the development of structural
genomics project, most modeling
problem will be reduced to comparative
modeling!

Before modeling

Check Protein Data Bank (PDB)
– e.g. NCBI BLAST against PDB

Check Model Databases
– SWISS-MODEL Repository
• http://swissmodel.expasy.org/repository/
– Modbase
• http://modbase.compbio.ucsf.edu/
– Caution! Those models generated by
automated comparative modeling
Few Terms

Target
– Protein sequence without structure

Template
– Known protein structure sharing detectable
sequence similarity with target sequence

Model
– Predicted 3D structure
Comparative Modeling procedure
Template selection
 Target-template alignment
 Model building
 Model evaluation

Comparative modeling

Automated server
– SDPMOD
– SWISS-MODEL
– 3D-JIGSAW

Standalone program
– Modeller
– WHATIF
Modeling using automated server
If target is small disulfide-rich
proteins (SDPs), try SDPMOD

– Length < 100 a.a. & Cys > 4
– http://proline.bic.nus.edu.sg/sdpmod/

Else, try SWISS-MODEL
– http://swissmodel.expasy.org/
A sample output by SDPMOD
http://proline.bic.nus.edu.sg/sdpmod/cgi-bin/view.py?ukey=IPC03gMxvN
Model Evaluation

Stereochemistry quality checking
– Procheck
– Whatcheck

Wrong fold vs. correct fold
– ProSA II
– Verify_3D
SAVS:Structure Analysis and
Validation Server
http://nihserver.mbi.ucla.edu/SAVS/
Want to know more?

Sali Lab
– http://salilab.org/modeller/modeller.html

Baker lab
– http://robetta.bakerlab.org/

CASP (Critical Assessment of techniques
for protein Structure Prediction)
– http://predictioncenter.gc.ucdavis.edu/casp7/
Any question?
Modeling by Modeller
Template selection
 Target-template alignment
 Model building
 Model evaluation

An example

Target: influenza hemagglutinin
(Swissprot ID: Q67087)
>Target
METISLITILLVVTVSNADKICIGYQSTNSTETVDTLTENNVPVTHAKELLHTEHNGMLCATNLGHPLIL
DTCTIEGLIYGNPSCNLLLGGREWSYIVERPSAVNGLCYPGNVENLEELRSLFSSASSFQRIQIFPDTIW
NVSYSGTSKACSDSFYRSMRWLTQKNNTYPIQDAQYTNNRGKSILFMWGINHPPTDTVQTNLYTRTDTTT
SVATEDINRTFRPLIGPRPLVNGQQGRIDYYWSVLKPGQTLRVRSNGNLIAPWYGHILSGESHGRILKTD
LNSGNCVVQCQTERGGLNTTLPFHNVSKYAFGNCPKYVGVKSLKLAVGLRNVPARSSRGLFGAIAGFIEG
GWSGLVAGWYGFQHSNDQGVGMAADRDSTQRAIDKITSKVNNIVDKMNKQYEIIDHEFSEVETRLNMINN
KIDDQIQDIWAYNAELLVLLENQKTLDEHDANVNNLYNKVKRALGSNAVEDGKGCFELYHKCDDQCMETI
RNGTYNKRKYKEESRLERQKIEGVKLESEGTYKILTIYSTVASSLVIAMGFAAFLFWAMSNGSCRCNICI
NCBI BLAST against PDB
Template selection
Download template structure
Target-template alignment

Needle at EMBOSS server
– http://sf01.bic.nus.edu.sg/EMBOSS/

Jalview
– http://www.jalview.org/
>Target
DKICIGYQSTNSTETVDTLTENNVPVTHAKELLHTEHNGMLCATNLGHPLIL
DTCTIEGLIYGNPSCNLLLGGREWSYIVERPSAVNGLCYPGNVENLEELRSLFSSASSFQRIQIFPDTIW
NVSYSGTSKACSDSFYRSMRWLTQKNNTYPIQDAQYTNNRGKSILFMWGINHPPTDTVQTNLYTRTDTTT
SVATEDINRTFRPLIGPRPLVNGQQGRIDYYWSVLKPGQTLRVRSNGNLIAPWYGHILSGESHGRILKTD
LNSGNCVVQCQTERGGLNTTLPFHNVSKYAFGNCPKYVGVKSLKLAVGLRNVPARSSRGLFGAIAGFIEG
GWSGLVAGWYGFQHSNDQGVGMAADRDSTQRAIDKITSKVNNIVDKMNKQYEIIDHEFSEVETRLNMINN
KIDDQIQDIWAYNAELLVLLENQKTLDEHDANVNNLYNKVKRALGSNAVEDGKGCFELYHKCDDQCMETI
RNGTYNKRKYKEESRLERQKIEGVKLESEGTYKILTIYSTVASSLVIAMGFAAFLFWAMSNGSCRCNICI
>1JSD
DKICIGYQSTNSTETVDTLTETNVPVTHAKELLHTSHNGMLCATNLGHPLILDTCTIEGLIYGNPSCDLL
LGGREWSYIVERPSAVNGMCYPGNVENLEELRSLFSSASSYQRIQIFPDTIWNVSYSGTSSACSDSFYRS
MRWLTQKNNAYPIQDAQYTNNRGKSILFMWGINHPPTDTVQTNLYTRTDTTTSVTTEDINRTFKPVIGPR
PLVNGLHGRIDYYWSVLKPGQTLRVRSNGNLIAPWYGHILSGESHGRILKTDLNSGNCVVQCQTERGGLN
TTLPFHNVSKYAFGNCPKYVGVKSLKLAVGLRNVPARSSGLFGAIAGFIEGGWPGLVAGWYGFQHSNDQG
VGMAADSDSTQKAIDKITSKVNNIVDKMNKQYGIIDHEFSEIETRLNMINNKIDDQIQDIWTYNAELLVL
LENQKTLDEHDANVNNLYNKVKRALGSNAMEDGKGCFELYHKCDDQCMETIRNGTYNRRKYKEESKLERQ
KIEGI
Format the alignment in PIR format