scholarly journals Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation

2021 ◽  
Author(s):  
Karina van den Broek ◽  
Matthias Epple ◽  
Lisa Sophie Kersten ◽  
Hubert Kuhn ◽  
Achim Zielesny
Keyword(s):  
Quantitative Estimation ◽  
Activity Patterns ◽  
Lipid Extraction ◽  
Dissipative Particle Dynamics ◽  
Interaction Model ◽  
Membrane Lipid ◽  
Membrane Disruption ◽  
Kinetic Rate Constant ◽  
Mesoscopic Simulation ◽  
Kalata B1

Cyclotide-induced membrane disruption is studied at the microsecond timescale by Dissipative Particle Dynamics (DPD) to quantitatively estimate a kinetic rate constant for membrane lipid extraction with a “sandwich” interaction model where two bilayer membranes enclose a cyclotide/water compartment. The obtained bioactivity trends for cyclotides Kalata B1, Cycloviolacin O2 and selected mutants with different membrane types are in agreement with experimental findings: For all membranes investigated, Cycloviolacin O2 shows a higher lipid extraction activity than Kalata B1. The presence of cholesterol leads to a decreased cyclotide activity compared to cholesterol-free membranes. Phosphoethanolamine-rich membranes exhibit an increased membrane disruption. A cyclotide’s “hydrophobic patch” surface area is important for its bioactivity. A replacement of or with charged amino acid residues may lead to super-mutants with above-native activity but without simple charge-activity patterns. Cyclotide mixtures show linearly additive bioactivities without significant sub- or over-additive effects.<br>

scholarly journals Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation

2021 ◽  
Author(s):  
Karina van den Broek ◽  
Matthias Epple ◽  
Lisa Sophie Kersten ◽  
Hubert Kuhn ◽  
Achim Zielesny
Keyword(s):  
Quantitative Estimation ◽  
Activity Patterns ◽  
Lipid Extraction ◽  
Dissipative Particle Dynamics ◽  
Interaction Model ◽  
Membrane Lipid ◽  
Membrane Disruption ◽  
Kinetic Rate Constant ◽  
Mesoscopic Simulation ◽  
Kalata B1

Cyclotide-induced membrane disruption is studied at the microsecond timescale by Dissipative Particle Dynamics (DPD) to quantitatively estimate a kinetic rate constant for membrane lipid extraction with a “sandwich” interaction model where two bilayer membranes enclose a cyclotide/water compartment. The obtained bioactivity trends for cyclotides Kalata B1, Cycloviolacin O2 and selected mutants with different membrane types are in agreement with experimental findings: For all membranes investigated, Cycloviolacin O2 shows a higher lipid extraction activity than Kalata B1. The presence of cholesterol leads to a decreased cyclotide activity compared to cholesterol-free membranes. Phosphoethanolamine-rich membranes exhibit an increased membrane disruption. A cyclotide’s “hydrophobic patch” surface area is important for its bioactivity. A replacement of or with charged amino acid residues may lead to super-mutants with above-native activity but without simple charge-activity patterns. Cyclotide mixtures show linearly additive bioactivities without significant sub- or over-additive effects.<br>

scholarly journals The structure and flexibility analysis of the Arabidopsis Synaptotagmin 1 reveal the basis of its regulation at membrane contact sites

2021 ◽  
Author(s):  
Juan Luis Benavente ◽  
Dritan Siliqi ◽  
Lourdes Infantes ◽  
Laura Lagartera ◽  
Alberto Mills ◽  
...  
Keyword(s):  
Cell Function ◽  
Lipid Extraction ◽  
Membrane Lipid ◽  
Lipid Binding ◽  
Lipid Transfer ◽  
C2 Domains ◽  
Membrane Contact Sites ◽  
Contact Sites ◽  
Cellular Environment ◽  
Synaptotagmin 1

Cell function requires the maintenance of membrane lipid homeostasis as changes in cellular environment unbalance this equilibrium. The non-vesicular lipid transfer at endoplasmic reticulum (ER) and plasma membrane (PM) contact sites (CS) is central to restore it. Extended synaptotagmins (E-Syts) are ER proteins that play a central role in this process as they act as molecular tethers with PM and as lipid transfer proteins between these organelles. E-Syts are constitutively anchored to the ER through an N-terminal hydrophobic segment and bind to the PM via C-terminal C2 domains. In plants, synaptotagmins (SYTs) are orthologous of E-Syts and regulate the ER-PM communication by the activity of their two C2 domains in response to abiotic stresses. We have combined macromolecular crystallography, small-angle X-ray scattering, structural bioinformatics and biochemical data to analyze the regulation of plant synaptotagmin 1 (SYT1). Our data show that the binding of SYT1 to the PM is regulated by the interaction of the first C2 domain through a Ca2+-dependent lipid binding site and by a site for phosphorylated forms of phosphatidylinositol in such a way that two different molecular signals are integrated in response to stress. In addition, our data show that SYT1 is highly flexible by virtue of up to three hinge points, including one that connects the two C2 domains. This feature provides conformational freedom to SYT1 to define a large and complementary interaction surface with the PM. This structural plasticity, in turn, may facilitate lipid extraction, protein loading and subsequent transfer between PM and ER.

DISSIPATIVE PARTICLE DYNAMICS IN SOFT MATTER AND POLYMERIC APPLICATIONS — A REVIEW

2010 ◽  
Vol 02 (01) ◽  
pp. 161-190 ◽  
Author(s):  
E. MOEENDARBARY ◽  
T. Y. NG ◽  
M. ZANGENEH
Keyword(s):  
Soft Matter ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Efficient Manner ◽  
Mesoscopic Simulation ◽  
Polymeric Systems ◽  
In Vivo Experiments ◽  
Simulation Techniques ◽  
Complex Fluid

Computer simulations and in particular mesoscopic simulation techniques such as the dissipative particle dynamics (DPD) technique, enable researchers to study the complexities of soft material and polymeric systems by performing in silico experimentations alongside in vivo experiments. In addition, these mesoscopic simulations allow scientists and engineers to characterize and optimize the actual experiments in a more efficient manner. The DPD is one the most reliable mesoscopic simulation techniques for phenomenological investigation of soft matter and polymeric systems. In this review, which is complimentary to an earlier review also by the present authors on DPD methodology and complex fluid application (Moeendarbary et al., 2009), we categorize and review the notable published works, and document efforts that applied the DPD simulation technique to various important soft matter and polymeric applications, over the last decade.

Simulation of Dripping Using Dissipative Particle Dynamics

2010 ◽  
Author(s):  
Sorush Khajepor ◽  
Meysam Joulaian ◽  
Ahmadreza Pishevar ◽  
Yaser Afshar
Keyword(s):  
Dissipative Particle Dynamics ◽  
Thermal Fluctuations ◽  
Particle Dynamics ◽  
Fluid Density ◽  
Mesoscopic Simulation ◽  
Wall Boundary Condition ◽  
Wide Range ◽  
Breakup Time ◽  
Dpd Simulation ◽  
Good Agreement

Dissipative Particle Dynamics (DPD) is a mesoscopic simulation approach used in wide range of applications and length scales. In this paper, a DPD simulation is carried out to study dripping flow from a nozzle. The results of this study are used to answer this question that whether DPD is capable of simulating the free surface fluid on all different scales. A novel wall boundary condition is developed for the nozzle surface that controls its penetrability, near wall fluid density oscillations and the fluid slip close to the wall. We also utilize a new method to capture the real-time instantaneous geometry of the drop. The obtained results are in good agreement with the macroscopic experiment except near the breakup time, when the fluid thread that connects the primitive drop to the nozzle, becomes tenuous. At this point, the DPD simulation can be justified by thermal length of DPD fluid and the finest accuracy of the simulation that is the radius of a particle. We finally conclude that in spite of the fact that DPD can be used potentially for simulating flow on different scales, it is restricted to the nanoscale problems, due to the surface thermal fluctuations.

scholarly journals Phospholipid synthesis rates in the eastern subtropical South Pacific Ocean

2007 ◽  
Vol 4 (4) ◽  
pp. 2793-2808
Author(s):  
B. A. S. Van Mooy ◽  
T. Moutin ◽  
S. Duhamel ◽  
P. Rimmelin ◽  
F. Van Wambeke
Keyword(s):  
Heterotrophic Bacteria ◽  
Membrane Lipids ◽  
Cell Metabolism ◽  
Lipid Extraction ◽  
High Surface ◽  
High Surface Area ◽  
South Pacific ◽  
Membrane Lipid ◽  
Phosphorus Cycle ◽  
Phospholipid Synthesis

Abstract. Membrane lipid molecules are a major component of planktonic organisms and this is particularly true of the microbial picoplankton that dominate the open ocean; with their high surface-area to volume ratios, the synthesis of membrane lipids places a major demand on their overall cell metabolism. The synthesis of one class of membrane lipids, the phospholipids, also creates a demand for the nutrient phosphorus, and we sought to refine our understanding of the role of phospholipids in the upper ocean phosphorus cycle. We measured the rates of phospholipid synthesis in a transect of the eastern subtropical South Pacific from Easter Island to Concepcion, Chile as part of the BIOSOPE program. Our approach combined standard phosphorus radiotracer incubations and lipid extraction methods. We found that phospholipid synthesis rates varied from less than 1 to greater than 200 pmol P L−1 h−1, and that phospholipid synthesis contributed between less than 5% to greater than 22% of the total PO43− incorporation rate. Changes in the percentage that phospholipid synthesis contributed to total PO43− incorporation were strongly correlated with the ratio of primary production to bacterial production, which supported our hypothesis that heterotrophic bacteria were the primary agents of phospholipid synthesis. The spatial variation in phospholipid synthesis rates underscored the importance of heterotrophic bacteria in the phosphorus cycle of the eastern subtropical South Pacific, particularly the hyperoligotrophic South Pacific subtropical gyre.

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