Protein conformational plasticity and aggregation

Nuno L. Ferreira 20101115 @ Coimbra, PT

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

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

Attenuation plots

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

d-toxin 1HN-1Ha fingerprint

[d-toxin] ≈ 3 mM in CD3OH ; pH* = 3 ; T = 298 K

d-toxin NMR restraints data

100% MetOH DMSO

d-toxin NMR structure

PDB ID : 2KAM

DMPC : molecular dynamics

System = 64 * 2 DMPC + 3655 SPC ; FF = GROMOS96 45A3 variants

Area / Volume per DMPC molecule

AL (exp) = 0.606 nm2 ; VL (exp) = 1.101 nm3

Electron & density profile

DHH (exp) = 3.5 nm ; DHH (MD) = 3.4 nm

Simulated model systems

Solvents : MetOH, SPC, DMSO

Secondary structure vs solvent

SPC

MetOH

DMSO

d-toxin interaction with DMPC

Amyloid fibril formation by TTR

Quintas et al. (2001) J. Biol. Chem. 276(29):27207-27213

Amyloid fibril formation by TTR

Near-Native Non-Native Native monomer

Amyloid fibril formation by TTR

Polymorphism : Tclass (- EPR) = 7-9 dimers ; Tclass (+ EPR) = 8-10 dimers ; diameter ≈ [42 - 54] Å

Protein conformational plasticity and aggregation

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