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Protein conformational plasticity and aggregation
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Nuno L Ferreira
November 15, 2010
1
40
Protein conformational plasticity and aggregation
Sala dos Capelos, Universidade de Coimbra, Portugal
PhD thesis defence (Biological Chemistry)
Nuno L Ferreira
November 15, 2010
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Transcript
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 CD3 OD
; 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 ;
= exp[− 2 (∆ − 3 − 2 )]
d-toxin 1HN-1Ha fingerprint [d-toxin] ≈ 3 mM in CD3 OH
; 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 #!/bin/bash HELP=`whoami` echo “Obrigado $HELP.”