1. N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole

2. WW domains Two highly conserved tryptophansTwo highly conserved tryptophans ~ 35-45 aa.~ 35-45 aa. Non-catalytic signaling proteins (protein-protein recognition)Non-catalytic signaling proteins (protein-protein recognition) >200 non-redundant proteins (2003)>200 non-redundant proteins (2003) Bind proline-rich sequences.Bind proline-rich sequences. 6 classes (sequence preference).6 classes (sequence preference).

3. WW domains: Fast and reversible folding Fast and reversible folding Highly conserved structure Highly conserved structure Rapid formation of amyloid fibres ( Protein Conformational Disorder ) Rapid formation of amyloid fibres ( Protein Conformational Disorder ) Collaboration with Guy Lippens (NMR-Lille) Collaboration with Guy Lippens (NMR-Lille) WW Domain FBP28 (Formin binding protein): Fastest folding of the family (10s of  s) Fastest folding of the family (10s of  s) The fold is conserved upon mutations The fold is conserved upon mutations Temp, mutations and sequence truncation modulate a three- to two-state folding pathway Temp, mutations and sequence truncation modulate a three- to two-state folding pathway The N- (res 1-5) and C-termini (res 34-37) are not required: 28 residues The N- (res 1-5) and C-termini (res 34-37) are not required: 28 residues WW Domain FBP28 Xavier Periole

4. Very stable and highly conserved slightly curved three-stranded antiparallel ß-sheet N-term C-term Xavier Periole WW Domain FBP28

5. 38 Replicas 38 Replicas T: from 282 to 498K T: from 282 to 498K in water in water GROMOS96 FF GROMOS96 FF 38*200ns=7.6  s Xavier Periole WW Domain FBP28

6. RMSD from the X-ray structure T=280K T=500K Xavier Periole WW Domain FBP28

7. X-rayrmsd 0.22 nm rmsd 0.14 nm Structures with minimum deviation from the X-ray Xavier Periole WW Domain FBP28

8. RMSD from the X-ray structure Xavier Periole WW Domain FBP28

9. rmsd vs. Rgyr Xavier Periole WW Domain FBP28

10. Comparison with the Native State rmsd vs. Sec. Struct. Xavier Periole WW Domain FBP28

11. rmsd vs. native contacts Xavier Periole WW Domain FBP28

12. The Real Case Build the Transition State 1.Characterize the limits native/unfolded states Build the intermediary stateBuild the intermediary state Unfolding SimulationUnfolding Simulation 2.Use  -values as restraints in REMD Xavier Periole

13. The Real Case REMD from the native state: Unfolding simulations Xavier Periole

14. The Real Case  -values as restraints in MD:  A =1  A =0 Mutation does not affect the TSE Mutation does affect the TSE a) b) rmsd: 4.4 1.3Å rmsd (Å) Xavier Periole

15. - MD Group in Groningen; Alan Mark in AU - L. Monticelli and W. L. Ash for REMD-Gromacs (Univ. of Calgary) - E. Paci and M. Vendruscolo. European TMR - “Protein (mis)folding” Sara computer center Thanks