scholarly journals Curvature sensing by cardiolipin in simulated buckled membranes

Soft Matter ◽  
2019 ◽  
Vol 15 (4) ◽  
pp. 792-802 ◽  
Author(s):  
Federico Elías-Wolff ◽  
Martin Lindén ◽  
Alexander P. Lyubartsev ◽  
Erik G. Brandt
Keyword(s):  
Lipid Membranes ◽  
Elastic Theory ◽  
Coarse Grained ◽  
Curvature Sensing

Simulated buckling of coarse-grained lipid membranes and elastic theory predicts that cardiolipin strongly prefers negative membrane curvatures.

Exploring gas permeability of lipid membranes using coarse-grained molecular dynamics

2009 ◽  
Vol 35 (10-11) ◽  
pp. 953-961 ◽  
Author(s):  
Huajun Yuan ◽  
Cynthia J. Jameson ◽  
Sohail Murad
Keyword(s):  
Molecular Dynamics ◽  
Lipid Membranes ◽  
Gas Permeability ◽  
Coarse Grained ◽  
Coarse Grained Molecular Dynamics

scholarly journals Atomistic and Coarse-Grained Molecular Simulations of Mixed Lamellar/Nonlamellar Lipid Membranes

2016 ◽  
Vol 110 (3) ◽  
pp. 572a
Author(s):  
Wei Ding ◽  
Michail Palaiokostas ◽  
Wen Wang ◽  
Mario Orsi
Keyword(s):  
Lipid Membranes ◽  
Molecular Simulations ◽  
Coarse Grained

scholarly journals Predicting Nanoparticle Uptake by Biological Membranes: Theory and Simulation

2020 ◽  
Author(s):  
M. Schneemilch ◽  
N Quirke
Keyword(s):  
Physical Property ◽  
Elastic Theory ◽  
Coarse Grained ◽  
Nanoparticle Uptake ◽  
Nanoparticle Toxicity ◽  
New Approach ◽  
Nanoscale Particles ◽  
Property Data ◽  
Coarse Grained Simulations ◽  
Physical Property Data

We describe a new approach which predicts the level of internalisation or complete wrapping of nanoparticles by liposomes in solution. It is based on a generalisation of elastic theory to nanoscale particles with physical property data obtained from atomistic and coarse-grained simulations. We apply this approach to determine the maximum number of nanoparticles of a given type that can be internalised by a given liposome and give examples of how our approach might be used to identify and/or design nanoparticles with different uptakes: New data that could be correlated with nanoparticle toxicity experiments . We briefly discuss the possibility of designing nanoscale separations process.

scholarly journals Inverse design of cholesterol attracting transmembrane helices reveals a paradoxical role of hydrophobic length

2021 ◽  
Author(s):  
Jeroen Methorst ◽  
Niek van Hilten ◽  
Herre Jelger Risselada
Keyword(s):  
Molecular Dynamics ◽  
Lipid Membranes ◽  
Transmembrane Domain ◽  
Optimal Solution ◽  
Molecular Shape ◽  
Global Optimum ◽  
Coarse Grained ◽  
Hydrophobic Core ◽  
Recognition Motifs ◽  
Dynamics Simulations

The occurrence of linear cholesterol-recognition motifs in alpha-helical transmembrane domains has long been debated. Here, we demonstrate the ability of a genetic algorithm guided by coarse-grained molecular dynamics simulations---a method coined evolutionary molecular dynamics (evo-MD)---to directly resolve the sequence which maximally attracts/sorts cholesterol within a single-pass alpha-helical transmembrane domain (TMDs). We illustrate that the evolutionary landscape of cholesterol attraction in membrane proteins is characterized by a sharp, well-defined global optimum. Surprisingly, this optimal solution features an unusual short hydrophobic block, consisting of typically only eight short chain hydrophobic amino acids, surrounded by three successive lysines. Owing to the membrane thickening effect of cholesterol, cholesterol-enriched ordered phases favor TMDs characterized by a long rather than a short hydrophobic length. However, this short hydrophobic pattern evidently offers a pronounced net advantage for the binding of free cholesterol in both coarse-grained and atomistic simulations. Attraction is mediated by the unique ability of cholesterol to snorkel within the hydrophobic core of the membrane and thereby shield deeply located lysines from the unfavorable hydrophobic surrounding. Since this mechanism of attraction is of a thermodynamic nature and is not based on molecular shape specificity, a large diversity of sub-optimal cholesterol attracting sequences can exist. The puzzling sequence variability of proposed linear cholesterol-recognition motifs is thus consistent with sub-optimal, unspecific binding of cholesterol. Importantly, since evo-MD uniquely enables the targeted design of recognition motifs for distinct fluid lipid membranes, we foresee wide applications for evo-MD in the biological and biomedical fields.

Entropic elasticity based coarse-grained model of lipid membranes

2018 ◽  
Vol 148 (16) ◽  
pp. 164705 ◽  
Author(s):  
Shuo Feng ◽  
Yucai Hu ◽  
Haiyi Liang
Keyword(s):  
Lipid Membranes ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Entropic Elasticity

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.

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