Asymmetry of Structural Characteristics of Lipid Bilayers Induced by Dimethylsulfoxide: An Atomistic Simulation Study

2008 ◽  
Author(s):  
Raghava Alapati ◽  
Dorel Moldovan ◽  
Ram V. Devireddy
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Cell Biology ◽  
Cell Membranes ◽  
Structural Changes ◽  
Cell Damage ◽  
Structural Characteristics ◽  
Cellular Systems ◽  
Freezing Process ◽  
Cryopreservation Protocol

In a typical cryopreservation protocol, the system to be preserved is first equilibrated with chemicals known as cryoprotective agents (CPAs). CPAs have been shown to alleviate cell damage from either the solute effects or the formation of intracellular ice during the subsequent freezing process. Thus, an extensive body of literature reporting the effects of CPAs on cellular systems has been accumulated over the last 50 years; detailing largely experimental interactions between cell systems and chemicals. Recent advances in computational methodology now offer an additional dimension in our ability to understand the molecular interactions between cell membranes, idealized as lipid bilayers and CPAs at atomistic scales. Computer simulations provide unique capabilities for analyzing biomembrane properties from atomistic perspective with a degree of detail that is hard to reach by other techniques. The excellent agreement with the experiment obtained in various molecular dynamics (MD) studies [1] on simple model membranes has raised the confidence in applying the molecular dynamics simulations to even more complex systems. Dimethylsulfoxide (DMSO) is one of the most widely used solvents in cell biology and cryopreservation. During a typical cryopreservation protocol the DMSO composition of aqueous buffers inside and outside of the cell is known to differ considerably. To model and understand the structural changes in cell membranes in such a situation we performed MD simulations of an idealized lipid bilayer membrane which separates two aqueous reservoirs with and without DMSO. Zwitterionic dimyritoylphosphatidylcholine (DMPC) lipid bilayers was chosen as the model membrane.

scholarly journals Proteins and Ions Compete for Membrane Interaction: the case of Lactadherin

2020 ◽  
Author(s):  
A. M. De Lio ◽  
D. Paul ◽  
R. Jain ◽  
J. H. Morrissey ◽  
T. V. Pogorelov
Keyword(s):  
Plasma Membrane ◽  
Blood Coagulation ◽  
Lipid Bilayers ◽  
Species Interactions ◽  
Drug Targets ◽  
Structural Changes ◽  
Lipid Membrane ◽  
Cell Damage ◽  
Experimental Studies ◽  
Coagulation Cascade

ABSTRACTCharged molecular species, such as ions, play a vital role in the life of the cell. In particular, divalent calcium ions (Ca2+) are critical for activating cellular membranes. Interactions between Ca2+ and anionic phosphatidylserine (PS) lipids result in structural changes of the plasma membrane and are vital for many signaling pathways, such as the tightly regulated blood coagulation cascade. Upon cell damage, PS lipids are externalized to the outer leaflet, where they are not only exposed to Ca2+, but also to proteins. Lactadherin is a glycoprotein, important for cell-adhesion, that can act as an anticoagulant. While a number of experimental studies have been performed on lactadherin’s C2 domain’s (LactC2) binding affinity for PS molecules, an atomistic description of LactC2 interactions with PS lipids in the plasma membrane is lacking. We performed extensive all-atom molecular dynamics simulations of mixed lipid bilayers and experimental characterization of LactC2-membrane interactions in the presence and absence of Ca2+ and characterized PS-Ca2+ and PS-LactC2 interactions to guide our understanding of how these interactions initiate and impede blood coagulation, respectively. The captured spontaneously formed long-lived PS-Ca2+ and PS-LactC2 complexes revealed that the protein side chains involved in PS-LactC2 interactions appear to be affected by the presence of Ca2+. The degree of LactC2 insertion into the lipid bilayer also appears to be dependent on the presence of Ca2+. Characterizing the interactions between Ca2+ and LactC2 with PS lipids can lead to a greater understanding of the activation and regulation of the blood coagulation cascade and of the basis of charged species interactions with the lipid membrane.STATEMENT OF SIGNIFICANCELactadherin plays an important role in cellular signaling including blood coagulation. Many of these processes involve lactadherin interacting with the lipids of the cell plasma membrane. Lactadherin acts as an anticoagulant and contributes to a number of health issues. Understanding the interactions that drive lactadherin’s anticoagulant properties can lead to potential new drug targets.

scholarly journals Assembly of hair bundles, an amazing problem for cell biology

2015 ◽  
Vol 26 (15) ◽  
pp. 2727-2732 ◽  
Author(s):  
Peter-G. Barr-Gillespie
Keyword(s):  
Systems Biology ◽  
Hair Cell ◽  
Inner Ear ◽  
Hair Cells ◽  
Cell Biology ◽  
Structural Changes ◽  
Cytoskeletal Proteins ◽  
Cellular Systems ◽  
A Cell ◽  
External Forces

The hair bundle—the sensory organelle of inner-ear hair cells of vertebrates—exemplifies the ability of a cell to assemble complex, elegant structures. Proper construction of the bundle is required for proper mechanotransduction in response to external forces and to transmit information about sound and movement. Bundles contain tightly controlled numbers of actin-filled stereocilia, which are arranged in defined rows of precise heights. Indeed, many deafness mutations that disable hair-cell cytoskeletal proteins also disrupt bundles. Bundle assembly is a tractable problem in molecular and cellular systems biology; the sequence of structural changes in stereocilia is known, and a modest number of proteins may be involved.

A Molecular Dynamics Simulation Study on the Effect of Methanol on the Structural Characteristics of Lipid Bilayers

2005 ◽  
Author(s):  
Dinesh Pinisetty ◽  
Dorel Moldovan ◽  
Ram Devireddy
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Lipid Bilayers ◽  
Structural Characteristics ◽  
Fluid Phase ◽  
Md Simulations ◽  
Bilayer Membrane ◽  
Dynamics Simulation ◽  
Equilibrium Conditions ◽  
Water Permeation

To further our understanding on the water permeation process through a lipid bilayer membrane in the presence of a commonly used cryoprotective agent (methanol), we performed detailed molecular dynamics simulation (MD) studies. The MD simulations analyzed the influence of methanol (12 mol %) on the structure of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) in the fluid phase and under equilibrium conditions at 323K.

scholarly journals Molecular Dynamics Simulation on the Interaction between Palygorskite Coating and Linear Chain Alkane Base Lubricant

Coatings ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 286
Author(s):  
Jin Zhang ◽  
Lv Yang ◽  
Yue Wang ◽  
Huaichao Wu ◽  
Jiabin Cai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Molecular Diffusion ◽  
Linear Chain ◽  
Interfacial Interaction ◽  
Dynamics Simulation ◽  
Electrostatic Energy ◽  
Experimental Development ◽  
Practical Applications ◽  
Self Diffusion

Molecular dynamics (MD) simulations were conducted to investigate the interactions between a palygorskite coating and linear chain alkanes (dodecane C12, tetradecane C14, hexadecane C16, and octadecane C18), representing base oils in this study. The simulation models were built by placing the alkane molecules on the surface of the palygorskite coating. These systems were annealed and geometrically optimized to obtain the corresponding stable configurations, followed by the analysis of the structural changes occurring during the MD process. The interfacial interaction energies, mean square displacements, and self-diffusion coefficients of the systems were evaluated to characterize the interactions between base lubricant molecules and palygorskite coating. It was found that the alkanes exhibited self-arrangement ability after equilibrium. The interfacial interaction was attractive, and the electrostatic energy was the main component of the binding energy. The chain length of the linear alkanes had a significant impact on the intensity of the interfacial interactions and the molecular diffusion behavior. Moreover, the C12 molecule exhibited higher self-diffusion coefficient values than C14, C16 and C18. Therefore, it could be the best candidate to form an orderliness and stable lubricant film on the surface of the palygorskite coating. The present work provides new insight into the optimization of the structure and composition of coatings and lubricants, which will guide the experimental development of these systems for practical applications.

scholarly journals Cell penetration efficiency analysis of different atomic force microscopy nanoneedles into living cells

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marcos Penedo ◽  
Tetsuya Shirokawa ◽  
Mohammad Shahidul Alam ◽  
Keisuke Miyazawa ◽  
Takehiko Ichikawa ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Cell Membrane ◽  
Cell Biology ◽  
Cell Damage ◽  
Efficiency Analysis ◽  
Living Cells ◽  
Biomolecular Recognition ◽  
Cell Penetration ◽  
Force Microscopy ◽  
Atomic Force

AbstractOver the last decade, nanoneedle-based systems have demonstrated to be extremely useful in cell biology. They can be used as nanotools for drug delivery, biosensing or biomolecular recognition inside cells; or they can be employed to select and sort in parallel a large number of living cells. When using these nanoprobes, the most important requirement is to minimize the cell damage, reducing the forces and indentation lengths needed to penetrate the cell membrane. This is normally achieved by reducing the diameter of the nanoneedles. However, several studies have shown that nanoneedles with a flat tip display lower penetration forces and indentation lengths. In this work, we have tested different nanoneedle shapes and diameters to reduce the force and the indentation length needed to penetrate the cell membrane, demonstrating that ultra-thin and sharp nanoprobes can further reduce them, consequently minimizing the cell damage.

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