1. 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

2. Dunbrack Lab, FCCC - NIGMS Workshop 2009 1 Agenda Background MolIDE in retrospect MolIDE2 Demonstration Discussion

3. Dunbrack Lab, FCCC - NIGMS Workshop 2009 2 Background Homology 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

4. Dunbrack Lab, FCCC - NIGMS Workshop 2009 3 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

5. Dunbrack Lab, FCCC - NIGMS Workshop 2009 4 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 modeling

6. Dunbrack Lab, FCCC - NIGMS Workshop 2009 5 In Retrospect MolIDE: A graphical IDE for homology modeling A. Canutescu and R.L. Dunbrack, Bioinformatics, 2005

7. Dunbrack Lab, FCCC - NIGMS Workshop 2009 6 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

8. Dunbrack Lab, FCCC - NIGMS Workshop 2009 7 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

9. Dunbrack Lab, FCCC - NIGMS Workshop 2009 8 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

10. Dunbrack Lab, FCCC - NIGMS Workshop 2009 9 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:

11. Dunbrack Lab, FCCC - NIGMS Workshop 2009 10 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:

12. Dunbrack Lab, FCCC - NIGMS Workshop 2009 11 MolIDE2 Screenshot

13. Dunbrack Lab, FCCC - NIGMS Workshop 2009 12 MolIDE2 Operation flowchart

14. Dunbrack Lab, FCCC - NIGMS Workshop 2009 13 Demonstration 1.Open sequence file 2.Run hmmpfam (generate domain file) 3.Run psiblast (generate query profile) 4.Run psipred (predict secondary structure of query sequence) 5.Open domain file 6.Search PDB for potential template; get profile-profile alignment result 7.Open alignment file 8.Manually modify sequence alignment (optional) 9.Copy backbone structure 10.Run SCWRL for sidechain replacement. 11.Build loops (not implemented yet). A typical modeling process:

15. Dunbrack Lab, FCCC - NIGMS Workshop 2009 14 Demonstration Sequences and domains

16. Dunbrack Lab, FCCC - NIGMS Workshop 2009 15 Demonstration Finding template (1)

17. Dunbrack Lab, FCCC - NIGMS Workshop 2009 16 Demonstration Finding template (2)

18. Dunbrack Lab, FCCC - NIGMS Workshop 2009 17 Demonstration Editing sequence alignment & generating model

19. Dunbrack Lab, FCCC - NIGMS Workshop 2009 18 Demonstration Editing sequence alignment & generating model (cont’d)

20. Dunbrack Lab, FCCC - NIGMS Workshop 2009 19 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 …

21. Dunbrack Lab, FCCC - NIGMS Workshop 2009 20 Acknowledge Dr. Adrian Canutescu, Dr. Mark Andrake NIH R01 GM84453 NIH R01 GM73784

22. Dunbrack Lab, FCCC - NIGMS Workshop 2009 21 Q & A