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

Dunbrack Lab, FCCC - NIGMS Workshop 2009 4

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

Dunbrack Lab, FCCC - NIGMS Workshop 2009 5

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

Dunbrack Lab, FCCC - NIGMS Workshop 2009 6

In RetrospectMolIDE: A graphical IDE for homology modeling

A. Canutescu and R.L. Dunbrack, Bioinformatics, 2005

Dunbrack Lab, FCCC - NIGMS Workshop 2009 7

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

Dunbrack Lab, FCCC - NIGMS Workshop 2009 8

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

Dunbrack Lab, FCCC - NIGMS Workshop 2009 9

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

Dunbrack Lab, FCCC - NIGMS Workshop 2009 10

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:

Dunbrack Lab, FCCC - NIGMS Workshop 2009 11

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:

Dunbrack Lab, FCCC - NIGMS Workshop 2009 12

MolIDE2Screenshot

Dunbrack Lab, FCCC - NIGMS Workshop 2009 13

MolIDE2Operation flowchart

Dunbrack Lab, FCCC - NIGMS Workshop 2009 14

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:

Dunbrack Lab, FCCC - NIGMS Workshop 2009 15

DemonstrationSequences and domains

Dunbrack Lab, FCCC - NIGMS Workshop 2009 16

DemonstrationFinding template (1)

Dunbrack Lab, FCCC - NIGMS Workshop 2009 17

DemonstrationFinding template (2)

Dunbrack Lab, FCCC - NIGMS Workshop 2009 18

DemonstrationEditing sequence alignment & generating model

Dunbrack Lab, FCCC - NIGMS Workshop 2009 19

DemonstrationEditing sequence alignment & generating model (cont’d)

Dunbrack Lab, FCCC - NIGMS Workshop 2009 20

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

…

Dunbrack Lab, FCCC - NIGMS Workshop 2009 21

Acknowledge

Dr. Adrian Canutescu,

Dr. Mark Andrake

NIH R01 GM84453

NIH R01 GM73784

Dunbrack Lab, FCCC - NIGMS Workshop 2009 22

Q & A