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Anomalous diffusion of proteins in sheared lipid membranes
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 88, Issue 3 , September , 2013 ; 15393755 (ISSN) ; Jalali, M. A ; Sharif University of Technology
2013
Abstract
We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow conditions. Protein embedded membranes behave quite differently: by imposing a simple shear flow and sliding the monolayers of the membrane over each other, the motion of protein clusters becomes strongly superdiffusive in the shear direction. In such a circumstance, the subdiffusion regime is predominant perpendicular to the flow. We show that superdiffusion is a result of accelerated chaotic motions of protein-lipid complexes within the membrane voids,...
The Effect of Hydrophobic Mismatch and Rigidity of Protein on the Cluster Formation of Transmembrane Proteins in Biomembranes
, M.Sc. Thesis Sharif University of Technology ; Ahmadiyan, Mohammad Taghi (Supervisor) ; Jalali, Mir Abbas (Co-Advisor) ; Khoshnood, Atefeh (Co-Advisor)
Abstract
Membrane proteins aggregation is a very important biological phenomenon in a variety of cell functions. It has been suggested that aggregation behavior of membrane proteins is influenced by the shape of the hydrophobic domain of the proteins, proteins hydrophobic mismatch and bilayer curvature. However, in this study by means of coarse grained membrane simulations it has been found that in thermal equilibrium, protein-protein interactions also depend on protein rigidity and structural strength. Based on simulation results, we have observed stable large clusters even in the absence of hydrophobic mismatch between lipids and proteins. Interestingly, our results also indicate that proteins with...
Vesicle deformations by clusters of transmembrane proteins
, Article Journal of Chemical Physics ; Volume 134, Issue 8 , 2011 ; 00219606 (ISSN) ; Jalali, M. A ; Sharif University of Technology
2011
Abstract
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
Lipid membranes with transmembrane proteins in shear flow
, Article Journal of Chemical Physics ; Volume 132, Issue 2 , 2010 ; 00219606 (ISSN) ; Noguchi, H ; Gompper, G ; Sharif University of Technology
Abstract
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...