Protein modelling

http://biome.ngic.re.kr/ProteinModelling/

Problem (문제정의)

• Build 3D structural models of given or interested proteins
  • Initial input: amino acid sequence of the target protein
  • Final output: its predicted 3D structure

Method

• Find one or more structural templates of the target protein via sequence homology search against known structures (program: BLASTP or PSI-BLAST, database: PDB)

• Download template structures in PDB format (web server: RCSB PDB)
• Align the amino acid sequence of the target protein with that(those) of the template protein(s) (program: CLUSTALW, output: PIR format)
• Build 3D structural models based on the multiple sequence alignment and the template 3D structure(s) (program: MODELLER, input: ATM, ALI, and TOP files)
  • manual build
    • manually convert file formats from PDB to ATM and PIR to ALI, respectively
    • write a TOP script file
    • run MODELLER
  • automatic build (some PDB and PIR files are not successfully converted to correct ATM and ALI files due to amino-acid sequence mismatch)
    • perl script to generate ATM, ALI, and TOP files from PDB and PIR files: txt, gz
    • command-line arguments in order: base_directory_path pir_file_name target_protein_id(exactly 4 letters) one_or_more_PDB_file_names(exactly 4-letter prefix)
    • run the perl script (e.g. ../bin/makeModellerInput.pl /home/user/Protein3DModelling/KCIP KCIP.pir KCIP 1QJA.pdb)
    • run MODELLER (e.g. mod7v7 KCIP.top)
  • example
    • ATM file: 5fd1.atm
    • ALI file: alignment.ali
    • TOP file: model-default.top
    • command: mod7v7 model-default.top
    • output PDB file (predicted model): 1fdx.B99990001.pdb
  • MODELLER manual
    • PDF, HTML
• Display and compare the 3D structures of the model and the template proteins (program: RasMol)

Sample proteins (단백질 예제들)

• Sample protein A: 14-3-3 protein gamma (Protein kinase C inhibitor protein-1; KCIP-1)

>sw|P61981|143G_HUMAN 14-3-3 protein gamma (Protein kinase C inhibitor protein-1) (KCIP-1) VDREQLVQKARLAEQAERYDDMAAAMKNVTELNEPLSNEERNLLSVAYKNVVGARRSSWR VISSIEQKTSADGNEKKIEMVRAYREKIEKELEAVCQDVLSLLDNYLIKNCSETQYESKV FYLKMKGDYYRYLAEVATGEKRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYSV FYYEIQNAPEQACHLAKTAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDDD GGEGNN

• Sample protein B: GAK_HUMAN Cyclin G-associated kinase (GAKH)

>sw|O14976|GAK_HUMAN Cyclin G-associated kinase MSLLQSALDFLAGPGSLGGASGRDQSDFVGQTVELGELRLRVRRVLAEGGFAFVYEAQDV GSGREYALKRLLSNEEEKNRAIIQEVCFMKKLSGHPNIVQFCSAASIGKEESDTGQAEFL LLTELCKGQLVEFLKKMESRGPLSCDTVLKIFYQTCRAVQHMHRQKPPIIHRDLKVENLL LSNQGTIKLCDFGSATTISHYPDYSWSAQRRALVEEEITRNTTPMYRTPEIIDLYSNFPI GEKQDIWALGCILYLLCFRQHPFEDGAKLRIVNGKYSIPPHDTQYTVFHSLIRAMLQVNP EERLSIAEVVHQLQEIAAARNVNPKSPITELLEQNGGYGSATLSRGPPPPVGPAGSGYSG GLALAEYDQPYGGFLDILRGGTERLFTNLKDTSSKVIQSVANYAKGDLDISYITSRIAVM SFPAEGVESALKNNIEDVRLFLDSKHPGHYAVYNLSPRTYRPSRFHNRVSECGWAARRAP HLHTLYNICRNMHAWLRQDHKNVCVVHCMDGRAASAVAVCSFLCFCRLFSTAEAAVYMFS MKRCPPGIWPSHKRYIEYMCDMVAEEPITPHSKPILVRAVVMTPVPLFSKQRSGCRPFCE VYVGDERVASTSQEYDKMRDFKIEDGKAVIPLGVTVQGDVLIVIYHARSTLGGRLQAKMA SMKMFQIQFHTGFVPRNATTVKFAKYDLDACDIQEKYPDLFQVNLEVEVEPRDRPSREAP PWENSSMRGLNPKILFSSREEQQDILSKFGKPELPRQPGSTAQYDAGAGSPEAEPTDSDS PPSSSADASRFLHTLDWQEEKEAETGAENASSKESESALMEDRDESEVSDEGGSPISSEG QEPRADPEPPGLAAGLVQQDLVFEVETPAVLPEPVPQEDGVDLLGLHSEVGAGPAVPPQA CKAPSSNTDLLSCLLGPPEAASQGPPEDLLSEDPLLLASPAPPLSVQSTPRGGPPAAADP FGPLLPSSGNNSQPCSNPDLFGEFLNSDSVTVPPSFPSAHSAPPPSCSADFLHLGDLPGE PSKMTASSSNPDLLGGWAAWTETAASAVAPTPATEGPLFSPGGQPAPCGSQASWTKSQNP DPFADLGDLSSGLQGSPAGFPPGGFIPKTATTPKGSSSWQTSRPPAQGASWPPQAKPPPK ACTQPRPNYASNFSVIGAREERGVRAPSFAQKPKVSENDFEDLLSNQGFSSRSDKKGPKT IAEMRKQDLAKDTDPLKLKLLDWIEGKERNIRALLSTLHTVLWDGESRWTPVGMADLVAP EQVKKHYRRAVLAVHPDKAAGQPYEQHAKMIFMELNDAWSEFENQGSRPLF

Available Online Tool Servers

1. BLASTP:
   1. 'NCBI BLASTP'
   2. EBI SRS BLASTP
2. PSI-BLAST:
   1. 'NCBI PSI-BLAST'
3. CLUSTALW: 'EBI ClustalW', 'Genebee ClustalW'
4. SRS servers: 'NGIC SRS', 'Public SRS servers'
5. Search engine: Google (Search online servers by yourself!)

Available Online Databases

1. PDB amino-acid FASTA file: NCBI BLAST DB (local: pdbaa.gz)
2. PDB: RCSB, 'UK PDB mirror', 'Japan PDB mirror'

Downloadable programs

1. BLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/ (local: DOS)
2. CLUSTALW: ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/ (local: DOS[WindowsXP])
3. MODELLER: http://salilab.org/modeller/ (local: DOS)
4. RasMol: http://www.openrasmol.org/ (local: Windows)
5. Perl: http://www.perl.org/ (local: DOS[WindowsXP])
6. Other utilities: ALZip.exe (for unzip, untar, and ungzip)

Solution Example

1. Found templates (PDB format)
   1. Sample protein A: 1QJA.pdb
   2. Sample protein B: 1N4C.pdb

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1. Multiple sequence alignments (PIR format)
   1. Sample protein A: KCIP.pir
   2. Sample protein B: GAKH.pir.ORG

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• MODELLER input files
  • Sample protein A:
    • ATM,
    • ALI,
    • TOP files (automatically generated)
  • Sample protein B:
    • ATM,
    • ALI,
    • TOP files (manually edited; C-terminal only)

• MODELLER output files
  • Sample protein A: KCIP.pdb
  • Sample protein B: GAKH.pdb