N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.
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Transcript of N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.
![Page 1: N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.](https://reader030.fdocuments.net/reader030/viewer/2022032704/56649d6a5503460f94a48737/html5/thumbnails/1.jpg)
N-term
C-term
The Folding of WW Domain The Folding of WW Domain FBP28 FBP28
(Formin binding protein):(Formin binding protein):
Xavier PerioleXavier Periole
![Page 2: N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.](https://reader030.fdocuments.net/reader030/viewer/2022032704/56649d6a5503460f94a48737/html5/thumbnails/2.jpg)
WW domainsWW domains
• Two highly conserved Two highly conserved tryptophans tryptophans
• ~ 35-45 aa. ~ 35-45 aa.
• Non-catalytic signaling Non-catalytic signaling proteins (protein-protein proteins (protein-protein recognition) recognition)
• >200 non-redundant >200 non-redundant proteins (2003)proteins (2003)
• Bind proline-rich sequences. Bind proline-rich sequences.
• 6 classes (sequence 6 classes (sequence preference).preference).
![Page 3: N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.](https://reader030.fdocuments.net/reader030/viewer/2022032704/56649d6a5503460f94a48737/html5/thumbnails/3.jpg)
WW domains:WW domains:
• Fast and reversible folding Fast and reversible folding • Highly conserved structureHighly conserved structure• Rapid formation of amyloid fibres (Rapid formation of amyloid fibres (Protein Conformational DisorderProtein Conformational Disorder))
• Collaboration with Guy Lippens (NMR-Lille)Collaboration with Guy Lippens (NMR-Lille)
WW Domain FBP28 (Formin binding protein):WW Domain FBP28 (Formin binding protein):
• Fastest folding of the family (10s of Fastest folding of the family (10s of s)s)• The fold is conserved upon mutationsThe fold is conserved upon mutations
• Temp, mutations and sequence truncation modulate a three- to two-Temp, mutations and sequence truncation modulate a three- to two-state folding pathwaystate folding pathway
• The N- (res 1-5) and C-termini (res 34-37) are not required: 28 residuesThe N- (res 1-5) and C-termini (res 34-37) are not required: 28 residues
WW Domain FBP28WW Domain FBP28
Xavier PerioleXavier Periole
![Page 4: N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.](https://reader030.fdocuments.net/reader030/viewer/2022032704/56649d6a5503460f94a48737/html5/thumbnails/4.jpg)
Very stable and highly conservedVery stable and highly conserved
slightly curved three-stranded antiparallel slightly curved three-stranded antiparallel ß-sheetß-sheet
N-term
C-term
Xavier PerioleXavier Periole
WW Domain FBP28WW Domain FBP28
![Page 5: N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.](https://reader030.fdocuments.net/reader030/viewer/2022032704/56649d6a5503460f94a48737/html5/thumbnails/5.jpg)
• 38 Replicas 38 Replicas • T: from 282 to 498KT: from 282 to 498K• in waterin water• GROMOS96 FF GROMOS96 FF
38*200ns=7.638*200ns=7.6ss
Xavier PerioleXavier Periole
WW Domain FBP28WW Domain FBP28
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RMSD from the X-ray structureRMSD from the X-ray structure
T=280KT=280K
T=500KT=500K
Xavier PerioleXavier Periole
WW Domain FBP28WW Domain FBP28
![Page 7: N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.](https://reader030.fdocuments.net/reader030/viewer/2022032704/56649d6a5503460f94a48737/html5/thumbnails/7.jpg)
X-rayX-ray rmsdrmsd0.22 nm0.22 nm
rmsdrmsd0.14 nm0.14 nm
Structures with minimum deviation from the X-rayStructures with minimum deviation from the X-ray
Xavier PerioleXavier Periole
WW Domain FBP28WW Domain FBP28
![Page 8: N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.](https://reader030.fdocuments.net/reader030/viewer/2022032704/56649d6a5503460f94a48737/html5/thumbnails/8.jpg)
RMSD from the X-ray structureRMSD from the X-ray structure
Xavier PerioleXavier Periole
WW Domain FBP28WW Domain FBP28
![Page 9: N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.](https://reader030.fdocuments.net/reader030/viewer/2022032704/56649d6a5503460f94a48737/html5/thumbnails/9.jpg)
rmsd vs. Rrmsd vs. Rgyrgyr
Xavier PerioleXavier Periole
WW Domain FBP28WW Domain FBP28
![Page 10: N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.](https://reader030.fdocuments.net/reader030/viewer/2022032704/56649d6a5503460f94a48737/html5/thumbnails/10.jpg)
Comparison with the Native StateComparison with the Native State
rmsd vs. Sec. Struct.rmsd vs. Sec. Struct.
Xavier PerioleXavier Periole
WW Domain FBP28WW Domain FBP28
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rmsd vs. native contactsrmsd vs. native contacts
Xavier PerioleXavier Periole
WW Domain FBP28WW Domain FBP28
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The Real The Real CaseCase
Build the Transition StateBuild the Transition State
1.1. Characterize the limits native/unfolded statesCharacterize the limits native/unfolded states
• Build the intermediary stateBuild the intermediary state
• Unfolding SimulationUnfolding Simulation
2.2. Use Use -values as restraints in REMD-values as restraints in REMD
Xavier PerioleXavier Periole
![Page 13: N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.](https://reader030.fdocuments.net/reader030/viewer/2022032704/56649d6a5503460f94a48737/html5/thumbnails/13.jpg)
The Real The Real CaseCase
REMD from the native state: Unfolding simulationsREMD from the native state: Unfolding simulations
Xavier PerioleXavier Periole
![Page 14: N-term C-term The Folding of WW Domain FBP28 (Formin binding protein): Xavier Periole.](https://reader030.fdocuments.net/reader030/viewer/2022032704/56649d6a5503460f94a48737/html5/thumbnails/14.jpg)
The Real The Real CaseCase
-values as restraints in MD:-values as restraints in MD:
A=1A=0Mutation does not
affect the TSEMutation doesaffect the TSE
mutDN
mutDTmut GG /
a) b)rmsd: 4.4 1.3rmsd: 4.4 1.3ÅÅ
rmsd (rmsd (ÅÅ))
Xavier PerioleXavier Periole