Presentation is loading. Please wait.

Presentation is loading. Please wait.

Christophe Schmitz Thomas Huber group The University of Queensland ECPM2009 Coffs Harbour.

Similar presentations


Presentation on theme: "Christophe Schmitz Thomas Huber group The University of Queensland ECPM2009 Coffs Harbour."— Presentation transcript:

1 Christophe Schmitz Thomas Huber group The University of Queensland ECPM2009 Coffs Harbour

2 1.NMR effect induced by a paramagnetic lanthanide. 2.Measured on active spin ( 1 H, 15 N, 13 C…) 3.Long range effect. 4.Effect described within the Δχ-tensor. 5.Combine distance and angular dependence. 40 Å The Pseudocontact shift (PCS)

3 What is PCS used for? Structure refinement Allegrozzi, M.; Bertini, I.; Janik, M. B. L.; Lee, Y. M.; Lin, G. H.; Luchinat, C. JACS 2000, 122, (17), Chemical shift assignment Schmitz, C.; John, M.; Park, A. Y.; Dixon, N. E.; Otting, G.; Pintacuda, G.; Huber, T., JBNMR 2006, 35, Protein-protein complex Pintacuda, G.; Park, A. Y.; Keniry, M. A.; Dixon, N. E.; Otting, G. JACS 2006, 128, (11), What about structure determination?

4 PCS for structure determination?

5 Rosetta for structure prediction

6 Fragment picking …GFMDYEFSL………….. RQIVLDTET…………..TGMNQIGAH… High resolution refinement Abinitio Rosetta structure prediction protocol

7 ψ ϕ Fragment picking Yang Shen, Oliver Lange, Frank Delaglio, et al. PNAS, (2008) 105, Rosetta Fragments CS-Rosetta Fragments Native fragment ϕ ψ Fragment picking with CS-ROSETTA

8 PCS into ROSETTA Fragment picking High resolution refinement Abinitio

9 List of protein targets ArgN repressor 78 residues 1AOY Calbindin 75 residues 1KQV Myoglobin 153 residues 1BZR Protein G 56 residues 3GB1 Calmodulin 146 residues 2K61 N-t Calmodulin 79 residues 1SW8 Thioredoxin 108 residues 1XOA ε subunit 186 residues 1J54 Parvalbumin 110 residues 1RJV θ subunit 76 residues 2AE9

10 PCS SCORE Cα RMSD 1000 decoys from low to high RMSD Native structure ArgN repressor 78 residues 1AOY Cα RMSD Density 3 PCS data sets N and H Example 1 - ROSETTA only - PCS only - PCS-ROSETTA ■ Native ■ Best PCS-ROSETTA decoy

11 PCS SCORE Cα RMSD Density 1 PCS data sets H Parvalbumin 110 residues 1RJV 1000 decoys from low to high RMSD Native structure Example 2 (it doesn’t work well, but we sort of know why) - ROSETTA only - PCS only - PCS-ROSETTA ■ Native ■ Best PCS-ROSETTA decoy

12 PCS SCORE Cα RMSD Density - ROSETTA only - PCS only - PCS-ROSETTA 4 PCS data sets H Calmodulin 146 residues 2K decoys from low to high RMSD Native structure Example 3 (it works and it’s cool because it’s a big one) ■ Native ■ Best PCS-ROSETTA decoy

13 PCS SCORE Cα RMSD Density - ROSETTA only - PCS only - PCS-ROSETTA 5 PCS data sets C, N and H ε subunit 186 residues 1J decoys from low to high RMSD Native structure Example 5 (it doesn't' work yet, but it really should, and we are going to keep working hard on that one) Coming soon…

14 ArgN repressor 78 residues 1AOY Calbindin 75 residues 1KQV Myoglobin 153 residues 1BZR Protein G 56 residues 3GB1 Calmodulin 146 residues 2K61 N-t Calmodulin 79 residues 1SW8 Thioredoxin 108 residues 1XOA ε subunit 186 residues 1J54 Parvalbumin 110 residues 1RJV Theta 76 residues 2AE List of protein targets

15 Conclusion 1. New road for structure determination 2. PCS and Rosetta work hand in hand 3. PCS are awesome

16 Acknowledgments GSRTG Dr Thomas Huber (UQ) Prof. David Baker (UW) Robert Vernon (UW)Dr Guido Pintacuda (ENS-Lyon) Dr Xun-Cheng Su (ANU) Dr Michael John (GAU) Prof. Gottfried Otting (ANU)

17 Different paramagnetic lanthanides…

18 PCS SCORE Cα RMSD Density - ROSETTA only - PCS only - PCS-ROSETTA θ subunit 76 residues 2AE9 ■ θ ■ ε■ θ ■ ε Example 4: it works and it’s a good surprise because we thought it wouldn’t. 2 PCS data sets H 1000 decoys from low to high RMSD Native structure

19 1000 decoys from low to high RMSD Native structure PCS SCORE Cα RMSD Density - ROSETTA only - PCS only - PCS-ROSETTA 11 PCS data sets C, N and H Calbindin 75 residues 1KQV

20 PCS SCORE Cα RMSD Density - ROSETTA only - PCS only - PCS-ROSETTA 3 PCS data sets H Protein G 56 residues 3GB decoys from low to high RMSD Native structure

21 PCS SCORE Cα RMSD Density - ROSETTA only - PCS only - PCS-ROSETTA 1 PCS data sets H and N Thioredoxin 108 residues 1XOA 1000 decoys from low to high RMSD Native structure

22 PCS SCORE Cα RMSD Density - ROSETTA only - PCS only - PCS-ROSETTA 2 PCS data sets H Myoglobin 153 residues 1BZR 1000 decoys from low to high RMSD Native structure

23 Fragment picking High resolution refinement Abinitio PCS into ROSETTA


Download ppt "Christophe Schmitz Thomas Huber group The University of Queensland ECPM2009 Coffs Harbour."

Similar presentations


Ads by Google