Thesis.20101115
1 like347 views
This document discusses several topics related to protein conformational plasticity and aggregation including: 1) Probing protein aggregation using pulsed field gradient NMR and presenting NMR structure data of d-toxin. 2) Simulating a lipid bilayer and d-toxin interaction using molecular dynamics. 3) Modeling how secondary structure of d-toxin changes with different solvents. 4) Describing amyloid fibril formation by transthyretin protein.
![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](https://image.slidesharecdn.com/thesis-141117074326-conversion-gate02/85/Thesis-20101115-3-320.jpg)
![Attenuation plots
D ≈ 3 x 10-10 m2 s-1 ; 𝐸 = exp[−𝑫 𝛾 𝐺𝑧 𝛿 2
(∆ − 𝛿 3 − 𝜏 2)]](https://image.slidesharecdn.com/thesis-141117074326-conversion-gate02/85/Thesis-20101115-4-320.jpg)
![d-toxin1HN-1Ha fingerprint
[d-toxin] ≈ 3 mM in CD3OH ; pH* = 3 ; T = 298 K](https://image.slidesharecdn.com/thesis-141117074326-conversion-gate02/85/Thesis-20101115-5-320.jpg)
![Amyloid fibril formation by TTR
Polymorphism : Tclass (- EPR) = 7-9 dimers ; Tclass (+ EPR) = 8-10 dimers ; diameter ≈ [42 - 54] Å](https://image.slidesharecdn.com/thesis-141117074326-conversion-gate02/85/Thesis-20101115-16-320.jpg)
Thesis.20101115
- 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 #!/bin/bash HELP=`whoami` echo “Obrigado $HELP.”