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Proceedings of the National Academy of... Dec 2016The transmembrane protein 16 (TMEM16) family of membrane proteins includes both lipid scramblases and ion channels involved in olfaction, nociception, and blood...
The transmembrane protein 16 (TMEM16) family of membrane proteins includes both lipid scramblases and ion channels involved in olfaction, nociception, and blood coagulation. The crystal structure of the fungal Nectria haematococca TMEM16 (nhTMEM16) scramblase suggested a putative mechanism of lipid transport, whereby polar and charged lipid headgroups move through the low-dielectric environment of the membrane by traversing a hydrophilic groove on the membrane-spanning surface of the protein. Here, we use computational methods to explore the membrane-protein interactions involved in lipid scrambling. Fast, continuum membrane-bending calculations reveal a global pattern of charged and hydrophobic surface residues that bends the membrane in a large-amplitude sinusoidal wave, resulting in bilayer thinning across the hydrophilic groove. Atomic simulations uncover two lipid headgroup-interaction sites flanking the groove. The cytoplasmic site nucleates headgroup-dipole stacking interactions that form a chain of lipid molecules that penetrate into the groove. In two instances, a cytoplasmic lipid interdigitates into this chain, crosses the bilayer, and enters the extracellular leaflet, and the reverse process happens twice as well. Continuum membrane-bending analysis carried out on homology models of mammalian homologs shows that these family members also bend the membrane-even those that lack scramblase activity. Sequence alignments show that the lipid-interaction sites are conserved in many family members but less so in those with reduced scrambling ability. Our analysis provides insight into how large-scale membrane bending and protein chemistry facilitate lipid permeation in the TMEM16 family, and we hypothesize that membrane interactions also affect ion permeation.
Topics: Amino Acid Sequence; Anoctamins; Biochemical Phenomena; Biological Transport; Cell Membrane; Fungal Proteins; Humans; Hydrophobic and Hydrophilic Interactions; Lipid Bilayers; Membranes; Molecular Dynamics Simulation; Phospholipid Transfer Proteins; Sequence Alignment
PubMed: 27872308
DOI: 10.1073/pnas.1607574113 -
Protein Science : a Publication of the... Nov 2016Mechanosensitive (MS) channels are evolutionarily conserved membrane proteins that play essential roles in multiple cellular processes, including sensing mechanical... (Review)
Review
Mechanosensitive (MS) channels are evolutionarily conserved membrane proteins that play essential roles in multiple cellular processes, including sensing mechanical forces and regulating osmotic pressure. Bacterial MscL and MscS are two prototypes of MS channels. Numerous structural studies, in combination with biochemical and cellular data, provide valuable insights into the mechanism of energy transfer from membrane tension to gating of the channel. We discuss these data in a unified two-state model of thermodynamics. In addition, we propose a lipid diffusion-mediated mechanism to explain the adaptation phenomenon of MscS.
Topics: Ion Channel Gating; Ion Channels; Mechanotransduction, Cellular; Membranes; Osmotic Pressure; Surface Tension
PubMed: 27530280
DOI: 10.1002/pro.3017 -
ELife Jul 2019An enigmatic step in de novo formation of the autophagosome membrane compartment is the expansion of the precursor membrane phagophore, which requires the acquisition of...
An enigmatic step in de novo formation of the autophagosome membrane compartment is the expansion of the precursor membrane phagophore, which requires the acquisition of lipids to serve as building blocks. Autophagy-related 2 (ATG2), the rod-shaped protein that tethers phosphatidylinositol 3-phosphate (PI3P)-enriched phagophores to the endoplasmic reticulum (ER), is suggested to be essential for phagophore expansion, but the underlying mechanism remains unclear. Here, we demonstrate that human ATG2A is a lipid transfer protein. ATG2A can extract lipids from membrane vesicles and unload them to other vesicles. Lipid transfer by ATG2A is more efficient between tethered vesicles than between untethered vesicles. The PI3P effectors WIPI4 and WIPI1 associate ATG2A stably to PI3P-containing vesicles, thereby facilitating ATG2A-mediated tethering and lipid transfer between PI3P-containing vesicles and PI3P-free vesicles. Based on these results, we propose that ATG2-mediated transfer of lipids from the ER to the phagophore enables phagophore expansion.
Topics: Autophagy-Related Proteins; Humans; Lipid Metabolism; Membrane Proteins; Membranes; Protein Binding
PubMed: 31271352
DOI: 10.7554/eLife.45777 -
Journal of Lipid Research Sep 1966The concept of biological membranes as vesicular or tubular continua built up of nesting repeating units has been systematically explored and some of the relevant... (Review)
Review
The concept of biological membranes as vesicular or tubular continua built up of nesting repeating units has been systematically explored and some of the relevant experimental work has been assembled. The bulk of the data have been drawn from studies on the mitochondrion, which is assumed to be a model for membranes generally. The repeating units of membranes are composite macromolecules containing both protein and lipid. The unit of the mitochondrial inner membrane is tripartite; the basepiece is the membrane-forming element. The four complexes of the electron transfer chain represent the different species of basepieces in the inner membrane. The repeating units of the outer mitochondrial membrane have a different form and size and a completely different set of enzymes (the enzymes of the citric and fatty acid oxidation cycles). The repeating units of the inner mitochondrial membrane are capable of forming membranes spontaneously. This membrane-forming capability is absolutely dependent on the presence of lipid. Evidence is presented for the view that lipid restricts the number of binding modalities and thus compels a two-dimensional alignment of repeating units. In absence of lipid three-dimensional stacking takes place, and the aggregates thus formed are, in effect, bulk phases. The membrane may be looked upon as a device for molecularizing repeating units, and it is this molecularization which underlies the essentiality of lipid for electron transfer. The theory of lipid requirement for enzymic activity is developed. The reconstitution of the electron transfer chain is shown to be essentially a membrane phenomenon rather than an expression of direct chemical interaction between the different parts of the electron transfer chain.
Topics: Lipid Metabolism; Membranes; Mitochondria
PubMed: 5339381
DOI: No ID Found -
Biophysical Journal May 2023Fluid flow near biological membranes influences cell functions such as development, motility, and environmental sensing. Flow can laterally transport extracellular...
Fluid flow near biological membranes influences cell functions such as development, motility, and environmental sensing. Flow can laterally transport extracellular membrane proteins located at the cell-fluid interface. To determine whether this transport contributes to flow signaling in cells, quantitative knowledge of the forces acting on membrane proteins is required. Here, we demonstrate a method for measuring flow-mediated lateral transport of lipid-anchored proteins. We rupture giant unilamellar vesicles to form discrete patches of supported membrane inside rectangular microchannels and then allow proteins to bind to the upper surface of the membrane. While applying flow, we observe the formation of protein concentration gradients that span the membrane patch. By observing how these gradients dynamically respond to changes in applied shear stress, we determine the flow mobility of the lipid-anchored protein. We use simplified model membranes and proteins to demonstrate our method's sensitivity and reproducibility. Our intention was to design a quantitative, reliable method and analysis for protein mobility that we will use to compare flow transport for a variety of proteins, lipid anchors, and membranes in model systems and on living cells.
Topics: Lipid Bilayers; Reproducibility of Results; Cell Membrane; Membrane Proteins; Membranes
PubMed: 37020419
DOI: 10.1016/j.bpj.2023.03.042 -
Archives of Gynecology and Obstetrics May 2024The fetal membranes are essential for the maintenance of pregnancy, and their integrity until parturition is critical for both fetal and maternal health. Preterm...
PURPOSE
The fetal membranes are essential for the maintenance of pregnancy, and their integrity until parturition is critical for both fetal and maternal health. Preterm premature rupture of the membranes (pPROM) is known to be an indicator of preterm birth, but the underlying architectural and mechanical changes that lead to fetal membrane failure are not yet fully understood. The aim of this study was to gain new insights into the anatomy of the fetal membrane and to establish a tissue processing and staining protocol suitable for future prospective cohort studies.
METHODS
In this proof of principle study, we collected fetal membranes from women undergoing vaginal delivery or cesarean section. Small membrane sections were then fixed, stained for nucleic acids, actin, and collagen using fluorescent probes, and subsequently imaged in three dimensions using a spinning disk confocal microscope.
RESULTS
Four fetal membranes of different types were successfully processed and imaged after establishing a suitable protocol. Cellular and nuclear outlines are clearly visible in all cases, especially in the uppermost membrane layer. Focal membrane (micro) fractures could be identified in several samples.
CONCLUSION
The presented method proves to be well suited to determine whether and how the occurrence of membrane (micro) fractures and cellular jamming correlate with the timing of membrane rupture and the mode of delivery. In future measurements, this method could be combined with mechanical probing techniques to compare optical and mechanical sample information.
Topics: Female; Infant, Newborn; Pregnancy; Humans; Cesarean Section; Prospective Studies; Chorion; Premature Birth; Extraembryonic Membranes; Fetal Membranes, Premature Rupture; Microscopy, Confocal
PubMed: 37184578
DOI: 10.1007/s00404-023-07070-0 -
Scientific Reports Nov 2022Crossing the cellular membrane is one of the main barriers during drug discovery; many potential drugs are rejected for their inability to integrate into the intracell...
Crossing the cellular membrane is one of the main barriers during drug discovery; many potential drugs are rejected for their inability to integrate into the intracell fluid. Although many solutions have been proposed to overcome this barrier, arguably the most promising solution is the use of cell-penetrating peptides. Recently, an array of hydrophobic penetrating peptides was discovered via high throughput screening which proved to be able to cross the membrane passively, and although these peptides proved to be effective at penetrating the cell, the details behind the underlying mechanism of this process remain unknown. In this study, we developed a method to find the equilibrium structure at the transmembrane domain of TP1, a hydrophobic penetrating peptide. In this method, we selectively deuterium-label amino acids in the peptidic chain, and employ results of [Formula: see text]H-NMR spectroscopy to find a molecular dynamics simulation of the peptide that reproduces the experimental results. Effectively finding the equilibrium orientation and dynamics of the peptide in the membrane. We employed this equilibrium structure to simulate the entire translocation mechanism and found that after the peptide reaches its equilibrium structure, it must undergo a two-step mechanism in order to completely translocate the membrane, each step involving the flip-flop of each arginine residue in the peptide. This leads us to conclude that the RLLR motif is essential for the translocating activity of the peptide.
Topics: Cell Membrane; Membranes; Cell-Penetrating Peptides; Molecular Dynamics Simulation; Hydrophobic and Hydrophilic Interactions
PubMed: 36400938
DOI: 10.1038/s41598-022-23631-w -
Proceedings of the National Academy of... Sep 2013Cell adhesion and the adhesion of vesicles to the membranes of cells or organelles are pivotal for immune responses, tissue formation, and cell signaling. The adhesion...
Cell adhesion and the adhesion of vesicles to the membranes of cells or organelles are pivotal for immune responses, tissue formation, and cell signaling. The adhesion processes depend sensitively on the binding constant of the membrane-anchored receptor and ligand proteins that mediate adhesion, but this constant is difficult to measure in experiments. We have investigated the binding of membrane-anchored receptor and ligand proteins with molecular dynamics simulations. We find that the binding constant of the anchored proteins strongly decreases with the membrane roughness caused by thermally excited membrane shape fluctuations on nanoscales. We present a theory that explains the roughness dependence of the binding constant for the anchored proteins from membrane confinement and that relates this constant to the binding constant of soluble proteins without membrane anchors. Because the binding constant of soluble proteins is readily accessible in experiments, our results provide a useful route to compute the binding constant of membrane-anchored receptor and ligand proteins.
Topics: Cell Adhesion; Cell Communication; Endocytosis; Kinetics; Membranes; Models, Molecular; Molecular Dynamics Simulation; Protein Binding; Receptors, Cell Surface
PubMed: 24006364
DOI: 10.1073/pnas.1305766110 -
Molecules (Basel, Switzerland) Jan 2017Palladium-based membranes for hydrogen separation have been studied by several research groups during the last 40 years. Much effort has been dedicated to improving the... (Review)
Review
Palladium-based membranes for hydrogen separation have been studied by several research groups during the last 40 years. Much effort has been dedicated to improving the hydrogen flux of these membranes employing different alloys, supports, deposition/production techniques, etc. High flux and cheap membranes, yet stable at different operating conditions are required for their exploitation at industrial scale. The integration of membranes in multifunctional reactors (membrane reactors) poses additional demands on the membranes as interactions at different levels between the catalyst and the membrane surface can occur. Particularly, when employing the membranes in fluidized bed reactors, the selective layer should be resistant to or protected against erosion. In this review we will also describe a novel kind of membranes, the pore-filled type membranes prepared by Pacheco Tanaka and coworkers that represent a possible solution to integrate thin selective membranes into membrane reactors while protecting the selective layer. This work is focused on recent advances on metallic supports, materials used as an intermetallic diffusion layer when metallic supports are used and the most recent advances on Pd-based composite membranes. Particular attention is paid to improvements on sulfur resistance of Pd based membranes, resistance to hydrogen embrittlement and stability at high temperature.
Topics: Alloys; Catalysis; Hydrogen; Membranes; Palladium
PubMed: 28045434
DOI: 10.3390/molecules22010051 -
Biochimica Et Biophysica Acta Jan 2009A range of physiological processes has been imputed to lateral domain formation in biological membranes. However the molecular mechanisms of these functions and the... (Review)
Review
A range of physiological processes has been imputed to lateral domain formation in biological membranes. However the molecular mechanisms of these functions and the details of how domain structures mediate these processes remain largely speculative. That domains exist in biomembranes and can be modeled in relatively simple lipid systems has contributed to our understanding of the principles governing phase behaviour in membranes. A presentation of these principles is the subject of this review. The condensing effect of sterols on phospholipids spread as monomolecular films at the air-water interface is described in terms of the dependence of the effect on sterol and phospholipid structure. The thermodynamics of sphingomyelin-cholesterol interactions are considered from calorimetric, densitometry and equilibrium cholesterol exchange measurements. Biophysical characterisation of the structure of liquid-ordered phase and its relationship with liquid-disordered phase is described from spectroscopic and X-ray scattering studies. Finally, the properties of liquid-ordered phase in the context of membrane physiology and permeability barrier properties are considered.
Topics: Cell Membrane Permeability; Cell Physiological Phenomena; Computer Simulation; Hydrophobic and Hydrophilic Interactions; Lipid Metabolism; Membrane Fluidity; Membranes; Models, Biological; Molecular Structure; Surface Properties; Thermodynamics; Water
PubMed: 18775411
DOI: 10.1016/j.bbamem.2008.08.005