Search for: lipid-bilayers
Article Journal of Membrane Biology ; Volume 246, Issue 1 , 2013 , Pages 67-73 ; 00222631 (ISSN) ; Amininasab, M ; Vali, M ; Ejtehadi, M ; Kowsari, F ; Sharif University of Technology
A very important part of the living cells of biological systems is the lipid membrane. The mechanical properties of this membrane play an important role in biophysical studies. Investigation as to how the insertion of additional phospholipids in one leaflet of a bilayer affects the physical properties of the obtained asymmetric lipid membrane is of recent practical interest. In this work a coarse-grained molecular dynamics simulation was carried out in order to compute the pressure tensor, the lateral pressure, the surface tension and the first moment of lateral pressure in each leaflet of such a bilayer. Our simulations indicate that adding more phospholipids into one monolayer results in...
The effect of local bending on gating of MscL using a representative volume element and finite element simulation, Article Channels ; Vol. 8, issue. 4 , 2014 , p. 344-349 ; Vossoughi, M ; Naghdabadi, R ; Jamali, Y ; Sharif University of Technology
Many physiological processes such as cell division, endocytosis and exocytosis cause severe local curvature of the cell membrane. Local curvature has been shown experimentally to modulate numerous mechanosensitive (MS) ion channels. In order to quantify the effects of local curvature we introduced a coarse grain representative volume element for the bacterial mechanosensitive ion channel of large conductance (MscL) using continuum elasticity. Our model is designed to be consistent with the channel conformation in the closed and open states to capture its major continuum rheological behavior in response to the local membrane curvature. Herein we show that change in the local curvature of the...
Article Nanotechnology ; Vol. 25, issue. 50 , Dec , 2014 ; Bahadori, A ; Ott, D ; Kyrsting, A ; Reihani, S. N. S ; Bendix, P. M ; Sharif University of Technology
The diverse physical properties of membranes play a critical role in many membrane associated biological processes. Proteins responsible for membrane transport can be affected by the lateral membrane order and lateral segregation of proteins is often controlled by the preference of certain membrane anchors for membrane phases having a physically ordered state. The dynamic properties of coexisting membrane phases are often studied by investigating their thermal behavior. Optical trapping of gold nanoparticles is a useful tool to generate local phase transitions in membranes. The high local temperatures surrounding an irradiated gold nanoparticle can be used to melt a part of a giant...
Modeling and stability analysis of truncated high density lipoprotein (HDL) system using MARTINI coarse grain technique, Article ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE) ; Volume 3 A , November , 2013 ; 9780791856215 (ISBN) ; Rouhollahi, A ; Sohrabi, S ; Mehr, S. M. N ; Sharif University of Technology
American Society of Mechanical Engineers (ASME) 2013
Lipoproteins are biochemical compounds containing both proteins and lipids. These particles carry chemicals like cholesterol and triglycerides that are not soluble in aqueous solutions. This paper presents modeling of lipoprotein system using coarse grain molecular dynamics technique and stability analysis of this system in a water solution like blood. A high density lipoprotein (HDL) that consists of two annular monomers is modeled. Also there are lipid bilayers located in center of the rings, so the whole HDL and lipid bilayers are called lipoprotein system. First, all atom model is provided and then coarse-grain model is obtained using MARTINI technique. Modeling of the system in all atom...
Article Journal of Chemical Physics ; Volume 134, Issue 8 , 2011 ; 00219606 (ISSN) ; Jalali, M. A ; Sharif University of Technology
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters change the shapes of their host vesicles. The effects of depletion force and vesiculation on protein clustering are also investigated. By increasing the protein concentration, clusters are fragmented to smaller bundles, which are then redistributed to form more symmetric structures corresponding to lower bending energies. Big clusters and highly aspherical vesicles cannot be formed when the fraction of protein to lipid molecules is large
Modeling self-assembly of the surfactants into biological bilayer membranes with special chemical structures using dissipative particle dynamics method, Article Scientia Iranica ; Volume 23, Issue 3 , 2016 , Pages 942-950 ; 10263098 (ISSN) ; Pishevar, A. R ; Saidi, M. S ; Shirani, E ; Sharif University of Technology
Sharif University of Technology 2016
The aim of this study is to simulate the self-assembly of the surfactant molecules with special chemical structure and bending stiffiness into bilayer membranes using a mesoscopic Dissipative Particle Dynamics (DPD) method. The surfactants are modeled with special chemical structure and bending stiffiness. To confirm that the novel model is physical, we determine the interaction parameters based on matching the compressibility and solubility of the DPD system with real physics of the uid. To match the mutual solubility for binary uids, we use the relation between DPD parameters and x-parameters in Flory-Huggins-type models. Unsaturated bonds can change the stiffiness of a lipid membrane,...
Article Journal of the Mechanical Behavior of Biomedical Materials ; Volume 117 , 2021 ; 17516161 (ISSN) ; Jamali, Y ; Tajkhorshid, E ; Bavi, O ; Pishkenari, H. N ; Sharif University of Technology
Elsevier Ltd 2021
In addition to its biological importance, DPhPC lipid bilayers are widely used in droplet bilayers, study of integral membrane proteins, drug delivery systems as well as patch-clamp electrophysiology of ion channels, yet their mechanical properties are not fully measured. Herein, we examined the effect of the ether linkage on the mechanical properties of ester- and ether-DPhPC lipid bilayers using all-atom molecular dynamics simulation. The values of area per lipid, thickness, intrinsic lateral pressure profile, order parameter, and elasticity moduli were estimated using various computational frameworks and were compared with available experimental values. Overall, a good agreement was...
M.Sc. Thesis Sharif University of Technology ; Jalali, Mir Abbas ; Khoshnood, Atefeh
Studying the dynamics of vesicles in simple shear flow is the first step to decipher the dynamics of cells in flows or the motion of vesicle-based nanoparticles in vessels for drug delivery. The deformation of vesicle in shear flow changes the permeability of its membrane and may lead to its rupture, both of which correlate with the transportation of vesicle cargos to their environment, especially important in drug delivery. The deformation of vesicles in shear flow not only depends on the physical properties of the whole system, such as temperature, but also on the mechanical properties of three media: vesicle membrane plus vesicle’s inner and outer fluid. The effect of the mechanical...
Kinetics of Animal Cell Adhesion Mediated by the Diffusion of Cell Wall Receptors: Effect of Mechanical Stiffness and Electrical Charges of the Substrate, M.Sc. Thesis Sharif University of Technology ; Mohammadi Shoja, Hossein
Viability and proliferation of cells in cell culture mainly depends on i) cell culture medium, ii) cell-cell interaction, and iii) the supporting scaffold. Among these factors, and within recent years, surface and mechanical properties of the supporting ECM has attracted many researchers. Experiment results show that the animal cell adhesion is accelerated on stiffer scaffolds. Electrical charge of the scaffold is also a determinant term in the kinetics of adhesion and on a relatively charged scaffold, one can expect an increment in kinetics of adhesion front movement. This is due to the natural negative charges of the cell wall membrane. In this thesis, an analytical model is proposed to...
M.Sc. Thesis Sharif University of Technology ; Jalali, Mir Abbas ; Ejtehadi, Mohammad Reza
Aggregation of membrane proteins plays a determinative role in many biological processes، such as signal transduction, cell division and endocytosis. In the present study, we have investigated the interaction between proteins in vesicles by means of coarse-grained molecular dynamics simulations. In the first step, a number of periodic lipid bilayers were simulated and their physical properties were calculated. Then, bilayers were immersed in water and converted into spherical vesicles via a selforganizing process . Finally two proteins were embedded into the vesicle and the potential of mean force (PMF) respect to the angle between them was obtained using umbrella sampling. This process was...
Article European Biophysics Journal ; Vol. 43, Issue. 12 , 2014 , pp. 595-602 ; ISSN: 1432-1017 ; Oddershede, L. B ; Reihani, S. N. S ; Bendix, P. M ; Sharif University of Technology
Membrane nanotubes, ubiquitous in cellular systems, adopt a spectrum of curvatures and shapes that are dictated by their intrinsic physical characteristics as well as their interactions with the local cellular environment. A high bending flexibility is needed in the crowded cytoplasm where tubes often need to bend significantly in the axial direction at sub-micron length scales. We find the stiffness of spontaneously formed membrane nanotubes by measuring the persistence length of reconstituted membrane nanotubes freely suspended in solution and imaged by fluorescence microscopy. By quantifying the tube diameter we demonstrate for the first time that the persistence length scales linearly...
Article ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology, NEMB 2013 ; 2013 ; ISBN: 9780791845332 ; Amininasab, M ; Ejtehadi, M ; Kowsari, F ; Sharif University of Technology
One of the most important biological components is lipid nanobio membrane. The lipid membranes of alive cells and their mechanical properties play an important role in biophysical investigations. Some proteins affect the shape and properties of the nanobio membrane while interacting with it. In this study a multiscale approach is experienced: first a 100ns all atom (fine-grained) molecular dynamics simulation is done to investigate the binding of CTX A3, a protein from snake venom, to a phosphatidylcholine lipid bilayer, second, a 5 micro seconds coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment of...
Article Scientia Iranica ; Volume 23, Issue 2 , 2016 , Pages 600-608 ; 10263098 (ISSN) ; Saidi, M. S ; Rismanian, M ; Firoozabadi, B ; Amininasab, M ; Sharif University of Technology
Sharif University of Technology 2016
High Density Lipoprotein (HDL) is a lipid-protein complex responsible for transporting cholesterol and triglyceride molecules, as these compounds are unable to dissolve in aqueous environments such as a bloodstream. Among the most well-known possible structures, the belt-like structure is the most common shape proposed for this vital bimolecular complex. In this structure, the protein scaffold encompasses the lipid bilayer and a planar circular structure is formed. Several HDL simulations with embedded components in the lipid section were performed. Here, we applied a series of molecular dynamic simulations using the MARTINI coarse grain force field to investigate an HDL model, with pores of...
Nanomechanical properties of lipid bilayer: Asymmetric modulation of lateral pressure and surface tension due to protein insertion in one leaflet of a bilayer, Article Journal of Chemical Physics ; Volume 138, Issue 6 , 2013 ; 00219606 (ISSN) ; Amininasab, M ; Ejtehadi, M. R ; Kowsari, F ; Dastvan, R ; Sharif University of Technology
The lipid membranes of living cells form an integral part of biological systems, and the mechanical properties of these membranes play an important role in biophysical investigations. One interesting problem to be evaluated is the effect of protein insertion in one leaflet of a bilayer on the physical properties of lipid membrane. In the present study, an all atom (fine-grained) molecular dynamics simulation is used to investigate the binding of cytotoxin A3 (CTX A3), a cytotoxin from snake venom, to a phosphatidylcholine lipid bilayer. Then, a 5 ms coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment...
Article Journal of Chemical Physics ; Volume 132, Issue 2 , 2010 ; 00219606 (ISSN) ; Noguchi, H ; Gompper, G ; Sharif University of Technology
The effects of embedded proteins on the dynamical properties of lipid bilayer membranes are studied in shear flow. Coarse-grained molecular simulations are employed, in which lipids are modeled as short polymers consisting of hydrophilic head groups and hydrophobic tail monomers; similarly, transmembrane proteins are modeled as connected hydrophobic double- or triple-chain molecules with hydrophilic groups at both ends. In thermal equilibrium, rigid proteinlike molecules aggregate in a membrane of flexible lipids, while flexible proteins do not aggregate. In shear flow parallel to the membrane, the monolayers of lipid bilayer slide over each other. The presence of transmembrane proteins...
Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 93, Issue 1 , 2016 ; 15393755 (ISSN) ; Khoshnood, A ; Jalali, M. A ; Sharif University of Technology
American Physical Society
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as α-helices and β-sheets have different structural rigidities. We use molecular dynamics simulation of a coarse-grained model of protein-embedded lipid membranes to investigate the mechanisms of protein clustering. For a variety of protein concentrations, our simulations under thermal equilibrium conditions reveal that the structural rigidity of transmembrane domains dramatically affects interactions and changes the shape of the cluster. We have observed stable large aggregates even in the absence of hydrophobic mismatch,...