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
Membrane curvature is no longer thought of as a passive property of the membrane; rather, it is considered as an ac- tive, regulated state that serves various purposes in the cell such as between cells and organelle d...Membrane curvature is no longer thought of as a passive property of the membrane; rather, it is considered as an ac- tive, regulated state that serves various purposes in the cell such as between cells and organelle definition. While transport is usually mediated by tiny membrane bubbles known as vesicles or membrane tubules, such communication requires complex interplay between the lipid bilayers and cytosolic proteins such as members of the Bin/Amphiphysin/Rvs （BAR） superfam- ily of proteins. With rapid developments in novel experimental techniques, membrane remodeling has become a rapidly emerging new field in recent years. Molecular dynamics （MD） simulations are important tools for obtaining atomistic information regarding the structural and dynamic aspects of biological systems and for understanding the physics-related aspects. The availability of more sophisticated experimental data poses challenges to the theoretical community for devel- oping novel theoretical and computational techniques that can be used to better interpret the experimental results to obtain further functional insights. In this review, we summarize the general mechanisms underlying membrane remodeling con- trolled or mediated by proteins. While studies combining experiments and molecular dynamics simulations recall existing mechanistic models, concurrently, they extend the role of different BAR domain proteins during membrane remodeling pro- cesses. We review these recent findings, focusing on how multiscale molecular dynamics simulations aid in understanding the physical basis of BAR domain proteins, as a representative of membrane-remodeling proteins.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supported by the National Natural Science Foundation of China(Grant No.21403182)the Research Grants Council of Hong Kong,China(Grant No.City U 21300014)
文摘Membrane curvature is no longer thought of as a passive property of the membrane; rather, it is considered as an ac- tive, regulated state that serves various purposes in the cell such as between cells and organelle definition. While transport is usually mediated by tiny membrane bubbles known as vesicles or membrane tubules, such communication requires complex interplay between the lipid bilayers and cytosolic proteins such as members of the Bin/Amphiphysin/Rvs （BAR） superfam- ily of proteins. With rapid developments in novel experimental techniques, membrane remodeling has become a rapidly emerging new field in recent years. Molecular dynamics （MD） simulations are important tools for obtaining atomistic information regarding the structural and dynamic aspects of biological systems and for understanding the physics-related aspects. The availability of more sophisticated experimental data poses challenges to the theoretical community for devel- oping novel theoretical and computational techniques that can be used to better interpret the experimental results to obtain further functional insights. In this review, we summarize the general mechanisms underlying membrane remodeling con- trolled or mediated by proteins. While studies combining experiments and molecular dynamics simulations recall existing mechanistic models, concurrently, they extend the role of different BAR domain proteins during membrane remodeling pro- cesses. We review these recent findings, focusing on how multiscale molecular dynamics simulations aid in understanding the physical basis of BAR domain proteins, as a representative of membrane-remodeling proteins.
