Dynamic Assembly/Disassembly Processes of Photoresponsive DNA Origami Nanostructures Directly Visualized on a Lipid Membrane Surface

2014 ◽  
Vol 136 (5) ◽  
pp. 1714-1717 ◽  
Author(s):  
Yuki Suzuki ◽  
Masayuki Endo ◽  
Yangyang Yang ◽  
Hiroshi Sugiyama
Keyword(s):  
Lipid Membrane ◽  
Membrane Surface ◽  
Dna Origami ◽  
Dynamic Assembly

Programming Dynamic Assembly of Viral Proteins with DNA Origami

2020 ◽  
Vol 142 (13) ◽  
pp. 5929-5932 ◽  
Author(s):  
Kun Zhou ◽  
Yihao Zhou ◽  
Victor Pan ◽  
Qiangbin Wang ◽  
Yonggang Ke
Keyword(s):  
Viral Proteins ◽  
Dna Origami ◽  
Dynamic Assembly

scholarly journals Membrane phospholipid composition affects function of potassium channels from rabbit colon epithelium

1999 ◽  
Vol 277 (1) ◽  
pp. C83-C90 ◽  
Author(s):  
Klaus Turnheim ◽  
Johannes Gruber ◽  
Christoph Wachter ◽  
Valentina Ruiz-Gutiérrez
Keyword(s):  
Surface Potential ◽  
Lipid Membrane ◽  
Single Channel ◽  
Membrane Surface ◽  
Phospholipid Composition ◽  
Distal Colon ◽  
Membrane Phospholipids ◽  
Channel Conductance ◽  
Planar Bilayers ◽  
Conduction Pathway

We tested the effects of membrane phospholipids on the function of high-conductance, Ca2+-activated K+ channels from the basolateral cell membrane of rabbit distal colon epithelium by reconstituting these channels into planar bilayers consisting of different 1:1 mixtures of phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylserine (PS), and phosphatidylinositol (PI). At low ambient K+ concentrations single-channel conductance is higher in PE/PS and PE/PI bilayers than in PE/PC bilayers. At high K+concentrations this difference in channel conductance is abolished. Introducing the negatively charged SDS into PE/PC bilayers increases channel conductance, whereas the positively charged dodecyltrimethylammonium has the opposite effect. All these findings are consistent with modulation of channel current by the charge of the lipid membrane surrounding the channel. But the K+ that permeates the channel senses only a small fraction of the full membrane surface potential of the charged phospholipid bilayers, equivalent to separation of the conduction pathway from the charged phospholipid head groups by 20Å. This distance appears to insulate the channel entrance from the bilayer surface potential, suggesting large dimensions of the channel-forming protein. In addition, in PE/PC and PE/PI bilayers, but not in PE/PS bilayers, the open-state probability of the channel decreases with time (“channel rundown”), indicating that phospholipid properties other than surface charge are required to maintain channel fluctuations.

scholarly journals Membrane Deformation of Endothelial Surface Layer Interspersed with Syndecan-4: A Molecular Dynamics Study

2019 ◽  
Vol 48 (1) ◽  
pp. 357-366 ◽  
Author(s):  
Xi Zhuo Jiang ◽  
Liwei Guo ◽  
Kai H. Luo ◽  
Yiannis Ventikos
Keyword(s):  
Molecular Dynamics ◽  
Lipid Membrane ◽  
Environmental Changes ◽  
Core Protein ◽  
Membrane Surface ◽  
Circulatory System ◽  
Endothelial Glycocalyx ◽  
Force Transmission ◽  
Membrane Deformation ◽  
The Core

Abstract The lipid membrane of endothelial cells plays a pivotal role in maintaining normal circulatory system functions. To investigate the response of the endothelial cell membrane to changes in vascular conditions, an atomistic model of the lipid membrane interspersed with Syndecan-4 core protein was established based on experimental observations and a series of molecular dynamics simulations were undertaken. The results show that flow results in continuous deformation of the lipid membrane, and the degree of membrane deformation is not in monotonic relationship with the environmental changes (either the changes in blood velocity or the alteration of the core protein configuration). An explanation for such non-monotonic relationship is provided, which agrees with previous experimental results. The elevation of the lipid membrane surface around the core protein of the endothelial glycocalyx was also observed, which can be mainly attributed to the Coulombic interactions between the biomolecules therein. The present study demonstrates that the blood flow can deform the lipid membrane directly via the interactions between water molecules and lipid membrane atoms thereby affecting mechanosensing; it also presents an additional force transmission pathway from the flow to the lipid membrane via the glycocalyx core protein, which complements previous mechanotransduction hypothesis.

scholarly journals Unsaturated fatty acids augment protein transport via the SecA:SecYEG translocon

2021 ◽  
Author(s):  
Michael Kamel ◽  
Maryna Löwe ◽  
Stephan Schott-Verdugo ◽  
Holger Gohlke ◽  
Alexej Kedrov
Keyword(s):  
Fatty Acids ◽  
Protein Transport ◽  
Unsaturated Fatty Acids ◽  
Lipid Membrane ◽  
Cell Envelope ◽  
Membrane Surface ◽  
Bacterial Cells ◽  
Hydrophobic Core ◽  
Membrane Composition ◽  
Dynamics Simulations

AbstractThe translocon SecYEG forms the primary protein-conducting channel in the cytoplasmic membrane of bacteria, and the associated ATPase SecA provides the energy for the transport of secretory and cell envelope protein precursors. The translocation requires negative charge at the lipid membrane surface, but its dependence on the properties of the membrane hydrophobic core is not known. Here, we demonstrate that SecA:SecYEG-mediated protein transport is immensely stimulated by unsaturated fatty acids (UFAs). Furthermore, UFA-rich tetraoleoyl-cardiolipin, but not bis(palmitoyloleoyl)-cardiolipin, facilitate the translocation via the monomeric translocon. Biophysical analysis and molecular dynamics simulations show that UFAs determine the loosely packed membrane interface, where the N-terminal amphipathic helix of SecA docks. While UFAs do not affect the translocon folding, they promote SecA binding to the membrane, and the effect is enhanced manifold at elevated ionic strength. Tight SecA:lipid interactions convert into the augmented translocation. As bacterial cells actively change their membrane composition in response to their habitat, the modulation of SecA:SecYEG activity via the fatty acids may be crucial for protein secretion over a broad range of environmental conditions.

scholarly journals Modelling of the Citrus CCD4 Family Members: In Silico Analysis of Membrane Binding and Substrate Preference

2021 ◽  
Vol 22 (24) ◽  
pp. 13616
Author(s):  
Jorge Cantero ◽  
Fabio Polticelli ◽  
Margot Paulino
Keyword(s):  
Lipid Membrane ◽  
Membrane Surface ◽  
Family Members ◽  
In Silico Analysis ◽  
Depth Of Penetration ◽  
Ligand Interaction ◽  
Catalytic Center ◽  
Hydrophobic Residues ◽  
Protein Ligand Interaction ◽  
Silico Analysis

Coloring is one of the most important characteristics in commercial flowers and fruits, generally due to the accumulation of carotenoid pigments. Enzymes of the CCD4 family in citrus intervene in the generation of β-citraurin, an apocarotenoid responsible for the reddish-orange color of mandarins. Citrus CCD4s enzymes could be capable of interacting with the thylakoid membrane inside chloroplasts. However, to date, this interaction has not been studied in detail. In this work, we present three new complete models of the CCD4 family members (CCD4a, CCD4b, and CCD4c), modeled with a lipid membrane. To identify the preference for substrates, typical carotenoids were inserted in the active site of the receptors and the protein–ligand interaction energy was evaluated. The results show a clear preference of CCD4s for xanthophylls over aliphatic carotenes. Our findings indicate the ability to penetrate the membrane and maintain a stable interaction through the N-terminal α-helical domain, spanning a contact surface of 2250 to 3250 Å2. The orientation and depth of penetration at the membrane surface suggest that CCD4s have the ability to extract carotenoids directly from the membrane through a tunnel consisting mainly of hydrophobic residues that extends up to the catalytic center of the enzyme.

Sealable Large Pore by DNA Origami on Lipid Membrane

2020 ◽  
Author(s):  
Shoji Iwabuchi ◽  
Ibuki Kawamata ◽  
Satoshi Murata ◽  
Shin-ichiro Nomura
Keyword(s):  
Cross Section ◽  
Lipid Membrane ◽  
Dna Origami ◽  
Single Strand ◽  
Vesicle Membrane ◽  
Giant Vesicle ◽  
Large Pore ◽  
And Function ◽  
Fluorescent Molecules

Here, we report on the design and function of a membrane nanopore through a DNA origami square tube with a cross-section of 100 nm2 . When the nanopore is added onto the giant vesicle membrane, the permeation of hydrophilic fluorescent molecules was observed. It can be sealed by the existence of the four specific single strand DNAs. A controllable artificial nanopore should help to communicate the vesicle components with their environment

Sealable Large Pore by DNA Origami on Lipid Membrane

2020 ◽  
Author(s):  
Shoji Iwabuchi ◽  
Ibuki Kawamata ◽  
Satoshi Murata ◽  
Shin-ichiro Nomura
Keyword(s):  
Cross Section ◽  
Lipid Membrane ◽  
Dna Origami ◽  
Single Strand ◽  
Vesicle Membrane ◽  
Giant Vesicle ◽  
Large Pore ◽  
And Function ◽  
Fluorescent Molecules

Here, we report on the design and function of a membrane nanopore through a DNA origami square tube with a cross-section of 100 nm2 . When the nanopore is added onto the giant vesicle membrane, the permeation of hydrophilic fluorescent molecules was observed. It can be sealed by the existence of the four specific single strand DNAs. A controllable artificial nanopore should help to communicate the vesicle components with their environment

Mechanics of a lipid bilayer subjected to thickness distension and membrane budding

2016 ◽  
Vol 23 (1) ◽  
pp. 67-84 ◽  
Author(s):  
Tsegay Belay ◽  
Kim Chun IL ◽  
Peter Schiavone
Keyword(s):  
Lipid Membrane ◽  
Transmembrane Protein ◽  
Membrane Surface ◽  
Parametric Representation ◽  
Smooth Transition ◽  
Protein Diffusion ◽  
Energy Potential ◽  
Bud Formation ◽  
Proposed Model ◽  
Shape Equation

We study the distension-induced gradient capillarity in membrane bud formation. The budding process is assumed to be primarily driven by diffusion of transmembrane proteins and acting line tensions on the protein-concentrated interface. The proposed model, based on the Helfrich-type potential, is designed to accommodate inhomogeneous elastic responses of the membrane, non-uniform protein distributions over the membrane surface and, more importantly, the thickness distensions induced by bud formations in the membrane. The latter are employed via the augmented energy potential of bulk incompressibility in a weakened manner. By computing the variations of the proposed membrane energy potential, we obtained the corresponding equilibrium equation (membrane shape equation) describing the morphological transitions of the lipid membrane undergoing bud formation and the associated thickness distensions. The effects of lipid distension on the shape equation and the necessary adjustments to the accompanying boundary conditions are also derived in detail. The resulting shape equation is solved numerically for the parametric representation of the surface which has one-to-one-correspondence with the membrane surface under consideration. The proposed model successfully predicts the bud formation phenomenon on a flat lipid membrane and the associated thickness distensions of the membrane and demonstrates a smooth transition from one phase to the other (including necking domains). It is also found that the final deformed configuration is energetically favorable and therefore is stable. Finally, we show that the inhomogeneous thickness deformation on the membrane in response to transmembrane protein diffusion makes a significant contribution to the budding and necking processes of the membrane.

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