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)simul...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.展开更多
The comparable feature analysis of NAMD and GROMACS molecular dy-namics packages has been done.The benchmarks of 72 and 128 Dipalmitoylphos-phatidylcholine(DPPC)/water have been constructed using a cluster(3GHz-Xeon p...The comparable feature analysis of NAMD and GROMACS molecular dy-namics packages has been done.The benchmarks of 72 and 128 Dipalmitoylphos-phatidylcholine(DPPC)/water have been constructed using a cluster(3GHz-Xeon proces-sors and Myrinet network)and the comparison has been performed using GROMOS87 and CHARMM27 force fields modified for lipids with GROMACS and NAMD software packages,respectively.The GROMACS has been displayed as faster than NAMD,likely due to united-atom character of GROMACS and good implementation features.The GROMACS reaches saturation and goes to the worst results,the reason of which is that the program spends more time on communications between processors.展开更多
基金supported by the Susan Mann Dissertation Scholarship Award of York UniversityNatural Science and Engineering Research Council(NSERC)of Canada+1 种基金Mathematics for Information Technology and Complex System(MITACS)of CanadaResearch and Development of the Next-Generation Integrated Simulation of Living Matter,a part of the Development and Use of the Next-Generation Supercomputer Project of the Ministry of Education,Culture,Sports,Science and Technology(MEXT),Japan.
文摘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.
基金the INTAS under YS Fellowship Ref.Number 03-55-699.
文摘The comparable feature analysis of NAMD and GROMACS molecular dy-namics packages has been done.The benchmarks of 72 and 128 Dipalmitoylphos-phatidylcholine(DPPC)/water have been constructed using a cluster(3GHz-Xeon proces-sors and Myrinet network)and the comparison has been performed using GROMOS87 and CHARMM27 force fields modified for lipids with GROMACS and NAMD software packages,respectively.The GROMACS has been displayed as faster than NAMD,likely due to united-atom character of GROMACS and good implementation features.The GROMACS reaches saturation and goes to the worst results,the reason of which is that the program spends more time on communications between processors.
