1. Protein conformational
plasticity and aggregation
Nuno L. Ferreira
20101115 @ Coimbra, PT

2. Outline
• Probing protein aggregation by PFG NMR
• NMR structure of d-toxin
• Lipid bilayer simulation
• Plasticity and aggregation of d-toxin
• Modeling of amyloid protofilaments

3. BPPLED 1H NMR d-toxin
[d-toxin]= 1 mM in CD3OD ; T = 298 K ; d = 2 * t = 3 ms ; te = 300 ms; D = 40 ms ; Gz ≤ 0.47 Tm-1

4. Attenuation plots
D ≈ 3 x 10-10 m2 s-1 ; 𝐸 = exp[−𝑫 𝛾 𝐺𝑧 𝛿 2
(∆ − 𝛿 3 − 𝜏 2)]

5. d-toxin1HN-1Ha fingerprint
[d-toxin] ≈ 3 mM in CD3OH ; pH* = 3 ; T = 298 K

6. d-toxin NMR restraints data
100% MetOH DMSO

7. d-toxin NMR structure
PDB ID : 2KAM

8. DMPC : molecular dynamics
System = 64 * 2 DMPC + 3655 SPC ; FF = GROMOS96 45A3 variants

9. Area / Volume per DMPC molecule
AL (exp) = 0.606 nm2 ; VL (exp) = 1.101 nm3

10. Electron & density profile
DHH (exp) = 3.5 nm ; DHH (MD) = 3.4 nm

11. Simulated model systems
Solvents : MetOH, SPC, DMSO

12. Secondary structure vs solvent
SPC
MetOH
DMSO

13. d-toxin interaction with DMPC

14. Amyloid fibril formation by TTR
Quintas et al. (2001) J. Biol. Chem. 276(29):27207-27213

15. Amyloid fibril formation by TTR
Near-Native Non-NativeNative monomer

16. Amyloid fibril formation by TTR
Polymorphism : Tclass (- EPR) = 7-9 dimers ; Tclass (+ EPR) = 8-10 dimers ; diameter ≈ [42 - 54] Å

17. Protein conformational plasticity
and aggregation
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