molide2: homology modeling of protein oligomers and complexes
DESCRIPTION
MolIDE2: Homology Modeling Of Protein Oligomers And Complexes. Qiang Wang, Qifang Xu, Guoli Wang, and Roland L. Dunbrack, Jr. Fox Chase Cancer Center Philadelphia, PA 19111. Agenda. Background MolIDE in retrospect MolIDE2 Demonstration Discussion. - PowerPoint PPT PresentationTRANSCRIPT
MolIDE2: Homology Modeling Of Protein Oligomers And ComplexesQiang Wang, Qifang Xu, Guoli Wang, and Roland L. Dunbrack, Jr.
Fox Chase Cancer CenterPhiladelphia, PA 19111
Dunbrack Lab, FCCC - NIGMS Workshop 2009 2
Agenda
Background MolIDE in retrospect MolIDE2 Demonstration Discussion
Dunbrack Lab, FCCC - NIGMS Workshop 2009 3
Background
Homology ModellingHomology Modelling What is it and why do we need it?
Given a protein without known structure, predict its 3D structure based on its sequence:
• Search structure databases for homologous sequences
• Transfer coordinates of known protein onto unknown
MQEQLTDFSKVETNLISW-QGSLETVEQMEPWAGSDANSQTEAY
MHQQVSDYAKVEHQWLYRVAGTIETLDNMSPANHSDAQTQAA| |..|. ||| ... |..||.|.| | |||..|
| = Identity
. = positively related
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Background
An inconvenient truth: huge gap between known structures and known sequences.
Experimentally determined structures (through x-ray crystallography & NMR spectroscopy.)As of 2/24/2009, PDB has 56,066 entries (< 52K protein structures)
Decoded protein sequences As of 2/10/2009, UniProtKB/Swiss-Prot (Release 56.8 ) contains 410,518
sequence entries. As of 2/10/2009, UniProtKB/TrEMBL(Release 39.8 ) contains 7,157,600
sequence entries
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Background
Various methods Swiss-model – fully automated modeling server Modeller – satisfaction of spatial restraints Nest – based on artificial evolution
Similar steps Template identification Sequence alignment Backbone generation Side-chain prediction & loop modeling Structure refinement
Homology modelingHomology modeling
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In RetrospectMolIDE: A graphical IDE for homology modeling
A. Canutescu and R.L. Dunbrack, Bioinformatics, 2005
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In Retrospect
sequence search
MolIDE: open-source, cross-platform
multiple-round psiblast alignments secondary structure prediction assisted alignment editing (joint with a template
viewer) side chain conformation prediction loop building
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In Retrospect
MolIDE automatically downloads these large sequence databases (nr or uniref100) and formats them for use with BLAST.
MolIDE1.6 (released on July 1, 2008)
Easy installer for Windows version One-step updating of PDB and Non-redundant protein
sequence databases PSI-BLAST search of non-redundant database can be opened
as a sortable table for browsing homologues of query List of templates from PDB includes protein names and
species Works with current remediated XML files from the PDB NCBI's non-redundant protein database (nr) can be replaced
with Uniprot's Uniref100 database:
Wang et al. Nature Protocols, Dec., 2008
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In Retrospect
Some examples: Structure with ligands Multi-chain protein complex Modeling of biological unit Modeling with multiple templates Structural or functional restraints in modeling …
Previous MolIDE CAN NOT deal with protein oligomers and protein complexes
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MolIDE2
• Identify an appropriate template;• One-to-many sequence alignment;• Better understanding of Biological Unit (BU).
Challenge:
Develop a new homology modeling program capable of modeling protein oligomers and protein complexes.
Goal:
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MolIDE2
Able to model protein oligomers and complexes; Modeling process based on Biological Unit (BU). Identifying structural template based on domain and family
information; Integrated database providing protein structural and sequence
information; Better organization and representation of template information; User-friendly graphical interface for selecting template; Integration of profile-profile sequence alignment method; Improved graphical editing of sequence alignment;
Key features:
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MolIDE2Screenshot
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MolIDE2Operation flowchart
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Demonstration
1. Open sequence file2. Run hmmpfam (generate domain file)3. Run psiblast (generate query profile)4. Run psipred (predict secondary structure of query sequence)5. Open domain file6. Search PDB for potential template; get profile-profile alignment result7. Open alignment file8. Manually modify sequence alignment (optional)9. Copy backbone structure10.Run SCWRL for sidechain replacement.11.Build loops (not implemented yet).
A typical modeling process:
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DemonstrationSequences and domains
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DemonstrationFinding template (1)
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DemonstrationFinding template (2)
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DemonstrationEditing sequence alignment & generating model
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DemonstrationEditing sequence alignment & generating model (cont’d)
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Discussion
Some future work
Loop modeling component dealing with space symmetry
Involvement of protein-protein interaction information (ProtBuD)
Modeling with multiple templates
modeling of ligands
refinement of models with Rosetta and RosettaDock
…
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Acknowledge
Dr. Adrian Canutescu,
Dr. Mark Andrake
NIH R01 GM84453
NIH R01 GM73784
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Q & A