scholarly journals Developing Martini Coarse-Grained Nitrogen Gas Model for Lipid Nanobubble Simulations

2021 ◽  
Author(s):  
Fujia Tian ◽  
Xubo Lin
Keyword(s):  
Cell Membrane ◽  
Lipid Membranes ◽  
Molecular Mechanisms ◽  
Membrane Curvature ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Nitrogen Gas ◽  
Hydrophobic Region

<p>By integrating the advantages of lipids’ biocompatibility and nanobubbles’ potent physicochemical properties, lipid nanobubbles show a great potential in ultrasound molecular imaging and biocompatible drug/gene delivery. However, under the interactions of the ultrasound, lipid nanobubbles may fuse with the cell membrane, changing the local membrane component and re-distributing encapsulated gas molecules into the hydrophobic region of the cell membrane, which may greatly affect the dynamics of certain membrane proteins and thus functions of cells. Although molecular dynamics simulation provides a useful computational tool to reveal the related molecular mechanisms, the lack of coarse-grained gas model greatly restricts this purpose. In the current work, we developed a Martini-compatible coarse-grained gas model based on the results of previous experiments and atomistic simulations, which could be used for lipid nanobubble simulations with complicated lipid components. By comparing the results of well-designed lipid nanobubble, lipid bi-monolayer and lipid bilayer simulations, we further revealed the role of membrane curvature and interleaflet coupling in the liquid-liquid phase separation of lipid membranes. It is worth mention that our developed coarse-grained nitrogen gas model can also be used for other gas-water interface systems such as pulmonary surfactant, which may overcome the possible artefacts arising from the usage of vacuum for gas phase. </p>

scholarly journals Developing Martini Coarse-Grained Nitrogen Gas Model for Lipid Nanobubble Simulations

2021 ◽  
Author(s):  
Fujia Tian ◽  
Xubo Lin
Keyword(s):  
Cell Membrane ◽  
Lipid Membranes ◽  
Molecular Mechanisms ◽  
Membrane Curvature ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Nitrogen Gas ◽  
Hydrophobic Region

<p>By integrating the advantages of lipids’ biocompatibility and nanobubbles’ potent physicochemical properties, lipid nanobubbles show a great potential in ultrasound molecular imaging and biocompatible drug/gene delivery. However, under the interactions of the ultrasound, lipid nanobubbles may fuse with the cell membrane, changing the local membrane component and re-distributing encapsulated gas molecules into the hydrophobic region of the cell membrane, which may greatly affect the dynamics of certain membrane proteins and thus functions of cells. Although molecular dynamics simulation provides a useful computational tool to reveal the related molecular mechanisms, the lack of coarse-grained gas model greatly restricts this purpose. In the current work, we developed a Martini-compatible coarse-grained gas model based on the results of previous experiments and atomistic simulations, which could be used for lipid nanobubble simulations with complicated lipid components. By comparing the results of well-designed lipid nanobubble, lipid bi-monolayer and lipid bilayer simulations, we further revealed the role of membrane curvature and interleaflet coupling in the liquid-liquid phase separation of lipid membranes. It is worth mention that our developed coarse-grained nitrogen gas model can also be used for other gas-water interface systems such as pulmonary surfactant, which may overcome the possible artefacts arising from the usage of vacuum for gas phase. </p>

scholarly journals Martini Coarse-Grained Nitrogen Gas Model for Lipid Nanobubble Simulations

2021 ◽  
Author(s):  
Xubo Lin ◽  
Fujia Tian ◽  
Siewert-Jan Marrink
Keyword(s):  
Cell Membrane ◽  
Lipid Membranes ◽  
Molecular Mechanisms ◽  
Membrane Curvature ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Nitrogen Gas ◽  
Hydrophobic Region

<p>By integrating the advantages of lipids’ biocompatibility and nanobubbles’ potent physicochemical properties, lipid nanobubbles show a great potential in ultrasound molecular imaging and biocompatible drug/gene delivery. However, under the interactions of the ultrasound, lipid nanobubbles may fuse with the cell membrane, changing the local membrane component and re-distributing encapsulated gas molecules into the hydrophobic region of the cell membrane, which may greatly affect the dynamics of certain membrane proteins and thus functions of cells. Although molecular dynamics simulation provides a useful computational tool to reveal the related molecular mechanisms, the lack of coarse-grained gas model greatly restricts this purpose. In the current work, we developed a Martini-compatible coarse-grained gas model based on the results of previous experiments and atomistic simulations, which could be used for lipid nanobubble simulations with complicated lipid components. By comparing the results of well-designed lipid nanobubble, lipid bi-monolayer and lipid bilayer simulations, we further revealed the role of membrane curvature and interleaflet coupling in the liquid-liquid phase separation of lipid membranes. It is worth mention that our developed coarse-grained nitrogen gas model can also be used for other gas-water interface systems such as pulmonary surfactant, which may overcome the possible artefacts arising from the usage of vacuum for gas phase. </p>

Solution behaviour of poly(N-isopropylacrylamide) stereoisomers in water: a molecular dynamics simulation study

2017 ◽  
Vol 19 (19) ◽  
pp. 11892-11903 ◽  
Author(s):  
G. Paradossi ◽  
E. Chiessi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Solution Behaviour

Atomistic simulations disclose the key role of the cooperative hydration in the tacticity-dependent hydrophobicity of poly(N-isopropylacrylamide).

scholarly journals Mechanics of Microfilaments Networks: A Cross-Scales Study

2014 ◽  
Vol 553 ◽  
pp. 310-315
Author(s):  
Tong Li ◽  
Yuan Tong Gu ◽  
Bao Cheng Zhang
Keyword(s):  
Mechanical Properties ◽  
Molecular Mechanisms ◽  
Mechanical Stability ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Cellular Structures ◽  
Modelling Framework ◽  
Simulation Strategy ◽  
Mechanical Models ◽  
Mechanical Behaviours

The mechanical properties of microfilament networks are systematically summarized at different special scales in this paper. We have presented the mechanical models of single microfilaments and microfilament networks at microscale. By adopting a coarse-grained simulation strategy, the mechanical stability of microfilaments related cellular structures are analysed. Structural analysis is conducted to microfilament networks to understand the stress relaxation under compression. The nanoscale molecular mechanisms of the microfilaments deformation is also summarized from the viewpoint of molecular dynamics simulation. This paper provides the fundaments of multiscale modelling framework for the mechanical behaviours simulation of hierarchical microfilament networks.

scholarly journals Molecular dynamics simulations of membrane deformation induced by the amphiphilic helices of Epsin, Sar1p and Arf1

2017 ◽  
Author(s):  
Zhen-lu Li
Keyword(s):  
Lipid Membranes ◽  
Critical Role ◽  
Membrane Curvature ◽  
Coarse Grained ◽  
Insertion Depth ◽  
Membrane Deformation ◽  
Specific Distribution ◽  
Amphiphilic Helix ◽  
Coarse Grained Simulations ◽  
Dynamics Simulations

AbstractThe N-terminal amphiphilic helices of proteins Epsin, Sar1p and Arf1 play a critical role in initiating membrane deformation. We present here the study of the interactions of these amphiphilic helices with the lipid membranes by combining the all-atom and coarse-grained simulations. In the all-atom simulations, we find that the amphiphilic helices of Epsin and Sar1p have a shallower insertion depth into the membrane compared to the amphiphilic helix of Arf1, but remarkably, the amphiphilic helices of Epsin and Sar1p induce higher asymmetry in the lipid packing between the two monolayers of the membrane. The insertion depth of amphiphilic helix into the membrane is determined not only by the overall hydrophobicity but also by the specific distribution of polar and non-polar residues along the helix. To directly compare their ability of deforming the membrane, we further apply coarse-grained simulations to investigate the membranes deformation under the insertion of multiple helices. Importantly, it is found that the amphiphilic helices of Epsin and Sar1p generate a larger membrane curvature than that of Arf1, in accord with the experimental results qualitatively. These findings enhance our understanding of the molecular mechanism of the protein-driven membrane remodeling.

scholarly journals Physical mechanisms of amyloid nucleation on fluid membranes

2020 ◽  
Vol 117 (52) ◽  
pp. 33090-33098
Author(s):  
Johannes Krausser ◽  
Tuomas P. J. Knowles ◽  
Anđela Šarić
Keyword(s):  
Lipid Membranes ◽  
Molecular Mechanisms ◽  
Amyloid Fibrils ◽  
Lipid Membrane ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Physical Mechanisms ◽  
Fluid Membranes ◽  
Protein Membrane ◽  
Protein Rich

Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein–membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways—protein-rich and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity control the relative importance of those molecular pathways. We find that the membrane’s susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson’s disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context.

scholarly journals Concerted interactions between multiple gp41 trimers and the target cell lipidome may be required for HIV-1 entry

2020 ◽  
Author(s):  
Biswajit Gorai ◽  
Anil Kumar Sahoo ◽  
Anand Srivastava ◽  
Narendra M. Dixit ◽  
Prabal K. Maiti
Keyword(s):  
Cell Membrane ◽  
Host Cell ◽  
Target Cell ◽  
Cell Membranes ◽  
Molecular Level ◽  
Membrane Lipid ◽  
Coarse Grained ◽  
Free Energy Barrier ◽  
Hiv 1

ABSTRACTThe HIV-1 envelope glycoprotein gp41 mediates the fusion between viral and host cell membranes leading to virus entry and target cell infection. Despite years of research, important aspects of this process such as the number of gp41 trimers involved and how they orchestrate the rearrangement of the lipids in the apposed membranes along the fusion pathway remain obscure. To elucidate these molecular underpinnings, we performed coarse-grained molecular dynamics simulations of HIV-1 virions pinned to the CD4 T cell membrane by different numbers of gp41 trimers. We built realistic cell and viral membranes by mimicking their respective lipid compositions. We found that a single gp41 was inadequate for mediating fusion. Lipid mixing between membranes, indicating the onset of fusion, was efficient when 3 or more gp41 trimers pinned the membranes. The gp41 trimers interacted strongly with many different lipids in the host cell membrane, triggering lipid configurational rearrangements, exchange, and mixing. Simpler membranes, comprising fewer lipid types, displayed strong resistance to fusion, revealing the crucial role of the lipidomes in HIV-1 entry. Performing simulations at different temperatures, we estimated the free energy barrier to lipid mixing, and hence membrane stalk formation, with 4 tethering gp41 trimers to be ~6.2 kcal/mol, a >4-fold reduction over estimates without gp41. Together, these findings present molecular-level, quantitative insights into the early stages of gp41-mediated HIV-1 entry. Preventing the requisite gp41 molecules from tethering the membranes or altering membrane lipid compositions may be potential intervention strategies.SIGNIFICANCEInteractions between viral envelope proteins and host cell surface receptors leading to HIV-1 entry are well studied, however the role of membrane lipids remains obscure, although entry hinges on lipid mixing and the fusion of viral and cell membranes. We performed detailed simulations of HIV-1 and target cell membranes tethered by viral gp41 trimeric proteins to elucidate the proteo-lipidic contributions to viral entry. We found that the cooperative effects of multiple gp41 trimers and natural lipidomes of the membranes facilitate membrane fusion. The functional domains of gp41 altered local lipid concentrations, reduced membrane repulsions, and facilitated inter-membrane lipid mixing. These molecular-level insights offer a glimpse of the cryptic mechanisms underlying HIV-1 entry and suggest new interventions to combat HIV-1 infection.

scholarly journals Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Md. Iqbal Mahmood ◽  
Hiroshi Noguchi ◽  
Kei-ichi Okazaki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Complex Structure ◽  
Membrane Curvature ◽  
Coarse Grained ◽  
Lateral Interaction ◽  
Bar Domain ◽  
Dynamics Simulations

Abstract F-Bin/Amphiphysin/Rvs (F-BAR) domain proteins play essential roles in biological processes that involve membrane remodelling, such as endocytosis and exocytosis. It has been shown that such proteins transform the lipid membrane into tubes. Notably, Pacsin1 from the Pacsin/Syndapin subfamily has the ability to transform the membrane into various morphologies: striated tubes, featureless wide and thin tubes, and pearling vesicles. The molecular mechanism of this interesting ability remains elusive. In this study, we performed all-atom (AA) and coarse-grained (CG) molecular dynamics simulations to investigate the curvature induction and sensing mechanisms of Pacsin1 on a membrane. From AA simulations, we show that Pacsin1 has internal structural flexibility. In CG simulations with parameters tuned from the AA simulations, spontaneous assembly of two Pacsin1 dimers through lateral interaction is observed. Based on the complex structure, we show that the regularly assembled Pacsin1 dimers bend a tensionless membrane. We also show that a single Pacsin1 dimer senses the membrane curvature, binding to a buckled membrane with a preferred curvature. These results provide molecular insights into polymorphic membrane remodelling.

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