Volume 2, Issue 4
Coarse Grained Molecular Dynamics Simulation of Interaction between Hemagglutinin Fusion Peptides and Lipid Bilayer Membranes

Naveen K. Vaidya, Huaxiong Huang & Shu Takagi

Adv. Appl. Math. Mech., 2 (2010), pp. 430-450.

Published online: 2010-02

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  • Abstract

Microscopic level interaction between fusion-peptides and lipid bilayer membranes plays a crucial role in membrane fusion, a key step of viral infection. In this paper, we use coarse-grained molecular dynamics (CGMD) simulations to study the interaction between hemagglutinin fusion-peptides and phospholipid bilayer membranes. With CGMD, we are able to simulate the interaction of fusion peptides with a relatively large piece of membrane for a sufficiently long time period, which is necessary for a detailed understanding of the fusion process. A conformation of the peptide with a kink at the level of phosphate group is obtained, consistent with NMR and EPR studies. Our results show that the N-terminal segment of the peptide inserts more deeply into the membrane bilayer compared to the C-terminal segment, as observed in previous experiments. Our simulations also show that the presence of fusion peptides inside the membrane may cause bilayer thinning and lipid molecule disorder. Finally, our results reveal that peptides tend to aggregate, indicating cluster  formation as seen in many experiments.

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@Article{AAMM-2-430, author = {Naveen K. Vaidya, Huaxiong Huang and Shu Takagi}, title = {Coarse Grained Molecular Dynamics Simulation of Interaction between Hemagglutinin Fusion Peptides and Lipid Bilayer Membranes}, journal = {Advances in Applied Mathematics and Mechanics}, year = {2010}, volume = {2}, number = {4}, pages = {430--450}, abstract = {

Microscopic level interaction between fusion-peptides and lipid bilayer membranes plays a crucial role in membrane fusion, a key step of viral infection. In this paper, we use coarse-grained molecular dynamics (CGMD) simulations to study the interaction between hemagglutinin fusion-peptides and phospholipid bilayer membranes. With CGMD, we are able to simulate the interaction of fusion peptides with a relatively large piece of membrane for a sufficiently long time period, which is necessary for a detailed understanding of the fusion process. A conformation of the peptide with a kink at the level of phosphate group is obtained, consistent with NMR and EPR studies. Our results show that the N-terminal segment of the peptide inserts more deeply into the membrane bilayer compared to the C-terminal segment, as observed in previous experiments. Our simulations also show that the presence of fusion peptides inside the membrane may cause bilayer thinning and lipid molecule disorder. Finally, our results reveal that peptides tend to aggregate, indicating cluster  formation as seen in many experiments.

}, issn = {2075-1354}, doi = {https://doi.org/10.4208/aamm.09-m0987}, url = {http://global-sci.org/intro/article_detail/aamm/8339.html} }
TY - JOUR T1 - Coarse Grained Molecular Dynamics Simulation of Interaction between Hemagglutinin Fusion Peptides and Lipid Bilayer Membranes AU - Naveen K. Vaidya, Huaxiong Huang & Shu Takagi JO - Advances in Applied Mathematics and Mechanics VL - 4 SP - 430 EP - 450 PY - 2010 DA - 2010/02 SN - 2 DO - http://doi.org/10.4208/aamm.09-m0987 UR - https://global-sci.org/intro/article_detail/aamm/8339.html KW - AB -

Microscopic level interaction between fusion-peptides and lipid bilayer membranes plays a crucial role in membrane fusion, a key step of viral infection. In this paper, we use coarse-grained molecular dynamics (CGMD) simulations to study the interaction between hemagglutinin fusion-peptides and phospholipid bilayer membranes. With CGMD, we are able to simulate the interaction of fusion peptides with a relatively large piece of membrane for a sufficiently long time period, which is necessary for a detailed understanding of the fusion process. A conformation of the peptide with a kink at the level of phosphate group is obtained, consistent with NMR and EPR studies. Our results show that the N-terminal segment of the peptide inserts more deeply into the membrane bilayer compared to the C-terminal segment, as observed in previous experiments. Our simulations also show that the presence of fusion peptides inside the membrane may cause bilayer thinning and lipid molecule disorder. Finally, our results reveal that peptides tend to aggregate, indicating cluster  formation as seen in many experiments.

Naveen K. Vaidya, Huaxiong Huang & Shu Takagi. (1970). Coarse Grained Molecular Dynamics Simulation of Interaction between Hemagglutinin Fusion Peptides and Lipid Bilayer Membranes. Advances in Applied Mathematics and Mechanics. 2 (4). 430-450. doi:10.4208/aamm.09-m0987
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