PowerPoint-presentatie

1
The Folding of WW Domain FBP28 (Formin binding
protein)
C-term
N-term
Xavier Periole
2

• WW domains
• Two highly conserved tryptophans
• 35-45 aa.
• Non-catalytic signaling proteins
  (protein-protein recognition)
• gt200 non-redundant proteins (2003)
• Bind proline-rich sequences.
• 6 classes (sequence preference).

3
WW Domain FBP28

• WW domains
• Fast and reversible folding
• Highly conserved structure
• Rapid formation of amyloid fibres (Protein
  Conformational Disorder)
• Collaboration with Guy Lippens (NMR-Lille)
• WW Domain FBP28 (Formin binding protein)
• Fastest folding of the family (10s of ?s)
• The fold is conserved upon mutations
• 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

Xavier Periole
4
WW Domain FBP28
Very stable and highly conserved slightly curved
three-stranded antiparallel ß-sheet
C-term
N-term
Xavier Periole
5
WW Domain FBP28

• 38 Replicas
• T from 282 to 498K
• in water
• GROMOS96 FF

38200ns7.6ms
Xavier Periole
6
WW Domain FBP28
RMSD from the X-ray structure
T280K
T500K
Xavier Periole
7
WW Domain FBP28
Structures with minimum deviation from the X-ray
X-ray
rmsd 0.22 nm
rmsd 0.14 nm
Xavier Periole
8
WW Domain FBP28
RMSD from the X-ray structure
Xavier Periole
9
WW Domain FBP28
rmsd vs. Rgyr
Xavier Periole
10
WW Domain FBP28
Comparison with the Native State
rmsd vs. Sec. Struct.
Xavier Periole
11
WW Domain FBP28
rmsd vs. native contacts
Xavier Periole
12
Build the Transition State

• Characterize the limits native/unfolded states
• Build the intermediary state
• Unfolding Simulation
• Use F-values as restraints in REMD

Xavier Periole
13
REMD from the native state Unfolding simulations
Xavier Periole
14
F-values as restraints in MD
b)
a)
rmsd 4.4 1.3Å
rmsd (Å)
?A1
?A0
Mutation does not affect the TSE
Mutation does affect the TSE
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