Interaction of Dengue Fusion Peptideswith model membrane systems
Danilo OlivierAmando Ito
April 16, 2015
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
Dengue Fever and Dengue Virus
I Aedes aegyptiI Size: 50nmI Flaviviruses, Yellow FeverI 4 Different Serotypes
1
1Source: The Journal of General Virology, 87(Pt 10), 2755–66, (2006).
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
Infection and Fusion Process
Figure : Mechanism of fusion.2
I EndocytosisI Virus mature in low pHI Fusion Peptide is exposed
2Source: The Journal of General Virology, 87(Pt 10), 2755–66, (2006).
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
Viral Fusion Peptide and Membrane Models
Peptides:I Putative Fusion Peptide: DEN II.98-112I 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 VirusPeptide sequence. Charged polar (green), Hydrophobic (blue) and non-charged polar (red). PDB Code:1OK8.
Models:I Large Unilamellar Vesicles (Experiments) - Lipid Bilayers (In Silico Experiments)I Lipids: DMPC, DMPG
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
MD: DEN II.88-123 in interaction with DMPC bilayer
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
MD: Equilibrium of DMPC bilayer
Figure : RMSD of the system during the simulation.
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
MD: Root Mean Square Fluctuation
90 100 110 120Residue Number
0
5
10
15
RM
SF
(nm
)DEN.II 88-123DEN.II 88-123 + DMPC
Figure : Root mean square fluctuation in solution and DMPC.
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
MD: Electronic Density Profile
0
0,1
0,2
0,3
0,4
0,5
Den
sity
( e
- / Å 3 )
TotalDMPCWaterPeptideTrp
-40 -20 0 20 40z-Axis ( Å )
0
0,00050,001
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
MD: Order Parameter
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15Carbon Atom Number ( # )
0
0,05
0,1
0,15
0,2
0,25
|SC
D|
DMPCDMPC + Pep
Figure : Order Parameter after 180ns of simulation.
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
MD: Area per lipid
0 20 40 60 80 100 120 140 160 180Time (ns)
54
56
58
60
62
64
66
68
Are
a (Å
2 )
Figure : Area per lipid during the simulation.
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
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 rotationalcorrelation for Trp.
System Fit A1 θ1(ns) A2 θ2(ns) A∞
DEN II.88-123 Exp. 0,11 0,35 0,02 2,03 -0,018Comp. 0,12 0,35 0,15 3,70 -0,001
DEN II.88-123 + DMPC Exp. 0,21 0,04 0,11 0,33 0,018Comp. 0,15 0,59 0,17 3,06 -0,001
Table : Steady state anisotropy.
88 - 123ABuffer 0.021ADMPC 0.034
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
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 rotationalcorrelation for Trp.
System Fit A1 θ1(ns) A2 θ2(ns) A∞
DEN II.88-123 Exp. 0,11 0,35 0,02 2,03 -0,018Comp. 0,12 0,35 0,15 3,70 -0,001
DEN II.88-123 + DMPC Exp. 0,21 0,04 0,11 0,33 0,018Comp. 0,15 0,59 0,17 3,06 -0,001
Table : Steady state anisotropy.
88 - 123ABuffer 0.021ADMPC 0.034
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
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
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
Final Configuration
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
Preliminary Conclusions
I Peptide interacts with lipid bilayer;I No significant changes in the lipid bilayer;I Differences in fluorecence anysotropy decay of Trp;I Low agreement between experiment - simulation for the
anisotropy in DMPC;I DEN II.88-123 in membrane is hindered compare with peptide
in solution;
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane
Acknowledgement
I USP - Universidade de São PauloI Rice UniversityI CNPq
Danilo Olivier Amando Ito Dengue Peptides in interaction with model membrane