Protein conformational plasticity and aggregation

Sala dos Capelos, Universidade de Coimbra, Portugal
PhD thesis defence (Biological Chemistry)

Transcript

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 CD3 OD ; 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 ; = exp[− 2 (∆ − 3 − 2 )]
5. d-toxin 1HN-1Ha fingerprint [d-toxin] ≈ 3 mM in CD3 OH ; 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-Native Native 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 #!/bin/bash HELP=`whoami` echo “Obrigado $HELP.”