“Interação entre peptídeos virais de fusão com membranas modelo”, presented at http://3whpc.lcca.usp.br

1. Interaction of Dengue Fusion Peptides
with model membrane systems
Danilo Olivier
Amando Ito
April 16, 2015
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

2. Dengue Fever and Dengue Virus
Aedes aegypti
Size: 50nm
Flaviviruses, Yellow Fever
4 Different Serotypes
1
1
Source: The Journal of General Virology, 87(Pt 10), 2755–66, (2006).
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

3. Infection and Fusion Process
Figure : Mechanism of fusion.2
Endocytosis
Virus mature in low pH
Fusion Peptide is exposed
2
Source: The Journal of General Virology, 87(Pt 10), 2755–66, (2006).
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

4. Viral Fusion Peptide and Membrane Models
Peptides:
Putative Fusion Peptide: DEN II.98-112
Large Sequence: DEN II.88-123
KRFVC KHSMV DRGWG NGCGL FGKGG IVTCA MFTCKK
Figure : Top: Dengue Peptide in NewCartoon and Tryptophan in CPK representation. Bottom: Dengue Virus
Peptide sequence. Charged polar (green), Hydrophobic (blue) and non-charged polar (red). PDB Code:1OK8.
Models:
Large Unilamellar Vesicles (Experiments) - Lipid Bilayers (In Silico Experiments)
Lipids: DMPC, DMPG
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

5. MD: DEN II.88-123 in interaction with DMPC bilayer
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

6. MD: Equilibrium of DMPC bilayer
Figure : RMSD of the system during the simulation.
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

7. MD: Root Mean Square Fluctuation
90 100 110 120
Residue Number
0
5
10
15
RMSF(nm)
DEN.II 88-123
DEN.II 88-123 + DMPC
Figure : Root mean square fluctuation in solution and DMPC.
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

8. MD: Electronic Density Profile
0
0,1
0,2
0,3
0,4
0,5
Density(e
-
/Å
3
)
Total
DMPC
Water
Peptide
Trp
-40 -20 0 20 40
z-Axis ( Å )
0
0,0005
0,001
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

9. MD: Order Parameter
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Carbon Atom Number ( # )
0
0,05
0,1
0,15
0,2
0,25
|SCD
| DMPC
DMPC + Pep
Figure : Order Parameter after 180ns of simulation.
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

10. MD: Area per lipid
0 20 40 60 80 100 120 140 160 180
Time (ns)
54
56
58
60
62
64
66
68
Area(Å
2
)
Figure : Area per lipid during the simulation.
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

11. MD/FLU: Anisotropy and Rotational Correlation
A = A1 ∗ exp(−x/θ1) + A2 ∗ exp(−x/θ2) + A∞ (1)
Table : Comparison between exponential fit for fluorecence anisotropy and rotational
correlation for Trp.
System Fit A1 θ1(ns) A2 θ2(ns) A∞
DEN II.88-123
Exp. 0,11 0,35 0,02 2,03 -0,018
Comp. 0,12 0,35 0,15 3,70 -0,001
DEN II.88-123 + DMPC
Exp. 0,21 0,04 0,11 0,33 0,018
Comp. 0,15 0,59 0,17 3,06 -0,001
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

12. MD/FLU: Anisotropy and Rotational Correlation
A = A1 ∗ exp(−x/θ1) + A2 ∗ exp(−x/θ2) + A∞ (1)
Table : Comparison between exponential fit for fluorecence anisotropy and rotational
correlation for Trp.
System Fit A1 θ1(ns) A2 θ2(ns) A∞
DEN II.88-123
Exp. 0,11 0,35 0,02 2,03 -0,018
Comp. 0,12 0,35 0,15 3,70 -0,001
DEN II.88-123 + DMPC
Exp. 0,21 0,04 0,11 0,33 0,018
Comp. 0,15 0,59 0,17 3,06 -0,001
Table : Steady state anisotropy.
88 - 123
ABuffer 0.021
ADMPC 0.034
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

13. MD/FLU: Secondary Structure of DEN II.88-123 during interaction with DMPC
bilayer.
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

14. MD/FLU: Secondary Structure of DEN II.88-123 during interaction with DMPC
bilayer.
Figure : Secondary Structure colors: Yellow: Coil, Orange: Bridge, Purple: Extented,
Green: Turn, Blue: 3-10 Helix.
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

15. Final Configuration
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

16. Preliminary Conclusions
Peptide interacts with lipid bilayer;
No significant changes in the lipid bilayer;
Differences in fluorecence anysotropy decay of Trp;
Low agreement between experiment - simulation for the
anisotropy in DMPC;
DEN II.88-123 in membrane is hindered compare with peptide
in solution;
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane

17. Acknowledgement
USP - Universidade de São Paulo
Rice University
CNPq
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane