1 / 39

TAS SE R: Threading ASSEmbly Refinement

TAS SE R: Threading ASSEmbly Refinement. References: Zhou et al., 2007. PROTEINS 69 (Supp 8): 90-97. Zhou, 2008. BMC Bioinformatics, 9, 40. Introduction. CASP results since 1994: Comparative modeling & threading/fold recognition is better than ab-initio

niesha
Download Presentation

TAS SE R: Threading ASSEmbly Refinement

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. TASSER: Threading ASSEmbly Refinement References: Zhou et al., 2007. PROTEINS 69 (Supp 8): 90-97. Zhou, 2008. BMC Bioinformatics, 9, 40.

  2. Introduction • CASP results since 1994: • Comparative modeling & threading/fold recognition is better than ab-initio • Good models are still difficult to generate • Meta-predictors succeed more than individual servers • Manual refinement is still essential

  3. Outline • TASSER – general information • STEP I - Threading • STEP II – Assembly & refinement • STEP III - Clustering • Results analysis • Summary

  4. What is TASSER? Automated structure prediction method of weakly homologous proteins in a genomic scale

  5. What is TASSER? Steps - • Threading through a representative template library • Assembly & Refinement of full length protein models using Monte Carlo for minimum energy • Clustering possible structures

  6. Outline • TASSER – general information • STEP I - Threading • STEP II – Assembly & refinement • STEP III - Clustering • Results analysis • Summary

  7. Step I - Threading • Threading –a method which uses the known 3D structure of proteins as a template for positioning a target sequence

  8. When to use? Step I - Threading • Weak or nonexistent sequence similarity • Poor correlation between sequence and structural homology

  9. Step I - Threading key components • structural template database (library) • an algorithm for finding an optimal placement • scoring function for measuring quality of a placement (alignment)

  10. Step I - Threading PROSPECTOR3 • TASSER method uses the PROSPECTOR3 threading program PROSPECTOR3 PROtein Structure Predictor Employing Combined Threading to Optimize Result

  11. Step I - Threading PROSPECTOR3 • an iterative sequence–structure alignment approach whose scoring function consists of: • sequence profiles • secondary structure propensities from PSIPRED • consensus contact predictions generated from the alignments in the prior threading iterations • involves six different ways for pair potential calculation enables to assign a good structural template to many types of target sequences

  12. Step I - Threading PROSPECTOR3 - Results • Results: • predicted contacts • continuous local fragments • if Z-score high, predicted templates and corresponding alignments • Targets are categorized as Easy/Medium/Hard on the basis of the score significance and alignment consistency.

  13. Step I - Threading PROSPECTOR3 - Results • Threading process ends with a gapped template and average coverage. • It is nontrivial to build a complete model that is useful for functional studies BUT… • We build a refined model using the threading template and get astonishing results that will be discussed later on.

  14. NOT ENOUGH? • NO!

  15. Outline • TASSER – general information. • STEP I - Threading • STEP II – Assembly & refinement • STEP III - Clustering • Results analysis • Summary

  16. Step II – Assembly & Refinement • The idea is to assemble tertiary structure from protein fragment pieces. • Problems • Sampling conformational space (10^100) • The energy minimum problem

  17. Step II – Assembly & Refinement Stages • Ab inito procedure - model unaligned regions on a cubic lattice to serve as linkage points of the rigid bodies rotations • Parallel Hyperbolic Monte Carlo Sampling (PHS)

  18. Step II – Assembly & Refinement PHS • Logarithmically flattens local high-energy barriers • Allows the simulation to tunnel more efficiently through energetically inaccessible regions to low energy valleys

  19. Step II – Assembly & Refinement PHS • target sequences are split into threading template aligned regions and unaligned regions • 40-80 replicas are made for each target sequence • rearranging the continuous aligned fragments building blocks • Constraints applied : • Building blocks are kept rigid • Unalignedregions serve as the linkage points of the rigid body rotations • Movements are guided by an optimized force field

  20. Step II – Assembly & Refinement Monte Carlo Force Field Optimized force field includes : • hydrogen bonding • secondary structure propensities from PSIPRED • consensus contact restraints extracted from PROSPECTOR3 identified templates/ alignment • And many many more…

  21. Outline • TASSER – general information. • STEP I - Threading • STEP II – Assembly & refinement • STEP III - Clustering • Results analysis • Summary

  22. Step III - Clustering A few numbers • 50 threading templates were used by TASSER • 40-80 replicas were exploited for each template by PHS • We can have up to 4000 possible models!

  23. Step III - Clustering • First filter – take 14 best replicas from every 40-80 replicas exploited by PHS • Still have about 700 possible models! • Want a method to filter/eliminate irrelevant structures

  24. Step III - Clustering • Clustering – combine structures with close topological structure (isomorphic) to a single model • Use the SPICKER program (an iterative structural clustering program), that identifies nearly native folds • Five highest density clusters are selected • It was found that the most populated clusters tend to be closer to the native conformation than the lowest energy structures

  25. Step III - Clustering

  26. Outline • TASSER – general information. • STEP I - Threading • STEP II – Assembly & refinement • STEP III - Clustering • Results analysis • Summary

  27. Results Analysis • 90 CASP6 targets PROSPECTOR 3 - average RMSD 8.4Å TASSER average RMSD 5.4Å

  28. Results Analysis • 90 CASP6 targets TASSER MODELLER PROSPECTOR 3

  29. Results Analysis Examples • T0267 – CM/HARD target with four loops • PROSPECTOR3 loops RMSD – 8.9Å, 7.0Å, 10.9Å, 5.2Å TASSER 2.3Å, 3.8Å, 4.1Å, 3.2Å

  30. Results Analysis Examples • T0231 – CM/Easy target with 142 residues • PROSPECTOR3 RMSD – 2.8Å TASSER 1.1Å

  31. Outline • TASSER – general information • STEP I - Threading • STEP II – Assembly & refinement • STEP III - Clustering • Results analysis • Summary

  32. TASSER - Advantages • significantly refine structures • good predictions for loops (<6.5Å) • Works on complete multi domain proteins

  33. TASSER - Disadvantages • Highly dependent on fragment orientation in the threading template • Problem generating high-resolution models for large single-domain proteins (e.g., >130 residues) • fails to split multi-domain targets into individual domains

  34. Web-servers • http://cssb.biology.gatech.edu/skolnick/webservice/TASSER/index.html (Skolnick lab, TASSER) • http://zhanglab.ccmb.med.umich.edu/I-TASSER/ (Zhang lab, I-TASSER) • Zhang homepage (including a video movie): http://zhanglab.ccmb.med.umich.edu/

  35. Applying TASSER – 1PN5 1PN5 – single domain human protein involved in apoptosis TASSER MODEL NATIVE MODEL

  36. RMSD = 1.15Å

  37. The End

More Related