Papers by John Hjort Ipsen
arXiv (Cornell University), Jul 31, 2023
Soluble alpha-amylases play an important role in the catabolism of polysaccharides. In this work,... more Soluble alpha-amylases play an important role in the catabolism of polysaccharides. In this work, we show that the enzyme can interact with the lipid membrane and further alter its mechanical properties. Vesicle fluctuation spectroscopy is used for quantitative measurement of the membrane bending rigidity of phosphatidylcholines lipid vesicles from the shape fluctuation based on the whole contour of Giant Unilamellar Vesicles (GUVs). The bending rigidity of the lipid vesicles of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine in water increases significantly with the presence of 0.14 micromolar alpha-amylase in the exterior solution. However, as the concentration increases above 1 micromolar, the bending rigidity decreases but remains higher than estimated without the protein. Contact between the alpha-amylase in the outer solution and the outer leaflet leads to spontaneous membrane curvature and the corresponding morphological changes of the
Cell Reports, Jul 1, 2018
Highlights d C24 SM functions distinctly from C16 or C18 SM in asymmetric membrane d C24 SM dicta... more Highlights d C24 SM functions distinctly from C16 or C18 SM in asymmetric membrane d C24 SM dictates cholesterol partition between the leaflets of the membrane
Springer proceedings in physics, 1991
This paper presents abrief overview induding recent results obtained from simulation studies of m... more This paper presents abrief overview induding recent results obtained from simulation studies of models of pseudo-two-dimensional systems of moleeules with translational (crystalline) as weH as internal (conformational) degrees of freedom. The models, which include both lattice-gas Potts models and models of hard discs with varying sizes, have a general sphere of applicability. The models are here being used to describe the phase transitions between the condensed phases in lipid monolayers or lipid bilayers. The simulation results reveal an intricate interplay between ordering pro ces ses governed by the two different degrees of freedom.
Langmuir, Oct 2, 2017
Experimental and theoretical studies on ion-lipid interactions predict that binding of calcium io... more Experimental and theoretical studies on ion-lipid interactions predict that binding of calcium ions to cell membranes leads to macroscopic mechanical effects and membrane remodeling. Herein, we provide experimental evidence that a point source of Ca2+ acting upon a negatively charged membrane generates spontaneous curvature and triggers the formation of tubular protrusions that point away from the ion source. This behavior is rationalized by strong binding of the divalent cations to the surface of the charged bilayer, which effectively neutralizes the surface charge density of outer leaflet of the bilayer. The mismatch in the surface charge density of the two leaflets leads to nonzero spontaneous curvature. We probe this mismatch through the use of molecular dynamics simulations and validate that calcium ion binding to a lipid membrane is sufficient to generate inward spontaneous curvature, bending the membrane. Additionally, we demonstrate that the formed tubular protrusions can be translated along the vesicle surface in a controlled manner by repositioning the site of localized Ca2+ exposure. The findings demonstrate lipid membrane remodeling in response to local chemical gradients and offer potential insights into the cell membrane behavior under conditions of varying calcium ion concentrations.
bioRxiv (Cold Spring Harbor Laboratory), May 7, 2023
We present FreeDTS software for performing computational research on biomembranes at the mesoscal... more We present FreeDTS software for performing computational research on biomembranes at the mesoscale. In this model, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included in the software to simulate complex membranes in different conditions such as framed membranes with constant tension, vesicles and high-genus membranes with various fixed volumes or constant pressure differences and applying external forces to membrane regions. Furthermore, the software allows the user to turn off the shape evolution of the membrane and focus solely on the organization of proteins. As a result, we can take realistic membrane shapes obtained from, for example, cryo-electron tomography and backmap them into a finer simulation model. In addition to many biomembrane applications, this software brings us a step closer to simulating realistic biomembranes with molecular resolution. Here we provide several interesting showcases of the power of the software but leave a wide range of potential applications for interested users.
All biomembranes share one universal construction principle: their basic structural element is a ... more All biomembranes share one universal construction principle: their basic structural element is a bilayer composed of amphiphilic lipid molecules, which primarily serves as a two-dimensional solvent for various proteins. In the plasma membrane of eucaryotic cells, the extracellular side of the lipid-bilayer is decorated by a macromolecular film called “glycocalix” extending into, or even attaching to, the extracellular matrix; the intracellular side couples to the membrane-associated cytoskeleton, a quasi two-dimensional macromolecular network which in turn couples to a three-dimensional network of actin filaments in most of cells. A large number of the talks in this workshop were devoted to the subjects both of networks of extracellular matrix and of cytoskeletal and actin networks. Our study of model lipid bilayers draws its inspiration from the lipid-bilayer component of biomembranes [1]. Lipid bilayers may form spontaneously when the types of amphiphilic lipid molecules constituting biomembranes are dispersed in an aqueous environment. They are the simplest model systems of biomembranes, which retain some of the essential physical properties, and can mimic at different levels the molecular complexity, of biological lipid bilayers. We will mainly discuss one aspect of equilibrium thermodynamic behavior of model lipid-bilayer membranes: their self-organization into lateral domains of different chemical or physical nature.
EPL, Jul 1, 2004
We have investigated the thermal fluctuations of giant unilamellar dimyristoylphosphatidlycholine... more We have investigated the thermal fluctuations of giant unilamellar dimyristoylphosphatidlycholine vesicles in the presence of both non-ionic and ionic surfactants (peptides) with identical apolar chains. Using vesicle fluctuation analysis, the effects of ionic and non-ionic surfactants upon membrane bending rigidity in the case of no added salt have been determined and the electrostatic contribution thereby isolated. We interpret these experimental findings in terms of a mean-field free-energy model for the adsorption of charged surfactants to a lipid bilayer and couple these results to describe the electrostatic contribution to membrane bending rigidity. This experimental study demonstrates how electrostatics affect the elastic properties of unilamellar bilayers.
Biochimica Et Biophysica Acta - Biomembranes, Dec 1, 2016
The structure of functional lipid domains (rafts) in biological membranes has for long time been ... more The structure of functional lipid domains (rafts) in biological membranes has for long time been unresolved due to their small length scales and transient nature. These cooperative properties of the lipid bilayer matrix are modelled by free-standing giant unilammellar vesicles (GUVs) with well-characterized lipid composition. We review a series of recent advances in preparation and analysis of GUVs, which allows for characterization of small domains by high-resolution imaging techniques. These includes a new GUV preparation method with a desired overall lipid composition achieved by mixing small unilammellar vesicles (SUVs), test of the lipids compositional uniformity in GUVs and swift adsorption of GUVs to solid support by kinetically arresting the lateral structure of membrane prior to collapse for subsequent imaging. The techniques are applied to the analysis of membrane domains in GUVs formed from mixtures of DOPC/DPPC/cholesterol with and without Na,K-ATPase (NKA), a transmembrane protein known to be associated with rafts. Two mechanisms of domain formation are revealed: 1) close to l o /l d phase coexistence, domains in size up to 100 nm appear as thermally induced droplet fluctuations, 2) NKA shows interfacial activity and cluster in l o /l d micro-emulsion droplets. Some perspectives for the application of the techniques and the understanding of the nature of raft domains are outlined.
Nature Communications, Jun 16, 2021
Gangliosides in the outer leaflet of the plasma membrane of eukaryotic cells are essential for ma... more Gangliosides in the outer leaflet of the plasma membrane of eukaryotic cells are essential for many cellular functions and pathogenic interactions. How gangliosides are dynamically organized and how they respond to ligand binding is poorly understood. Using fluorescence anisotropy imaging of synthetic, fluorescently labeled GM1 gangliosides incorporated into the plasma membrane of living cells, we found that GM1 with a fully saturated C16:0 acyl chain, but not with unsaturated C16:1 acyl chain, is actively clustered into nanodomains, which depends on membrane cholesterol, phosphatidylserine and actin. The binding of cholera toxin B-subunit (CTxB) leads to enlarged membrane domains for both C16:0 and C16:1, owing to binding of multiple GM1 under a toxin, and clustering of CTxB. The structure of the ceramide acyl chain still affects these domains, as co-clustering with the glycosylphosphatidylinositol (GPI)-anchored protein CD59 occurs only when GM1 contains the fully saturated C16:0 acyl chain, and not C16:1. Thus, different ceramide species of GM1 gangliosides dictate their assembly into nanodomains and affect nanodomain structure and function, which likely underlies many endogenous cellular processes.
Soft Matter, 2020
Associative polymers phase separate into a porous phase that mimics the structural features of bi... more Associative polymers phase separate into a porous phase that mimics the structural features of biomolecular condensates of intrinsically-disordered proteins.
Mammalian cell sphingolipids, primarily with C24 and C16 acyl chains, reside in the outer leaflet... more Mammalian cell sphingolipids, primarily with C24 and C16 acyl chains, reside in the outer leaflet of the plasma membrane. Curiously, little is known how C24 sphingolipids impact cholesterol and membrane microdomains. Here, we generated giant unilamellar vesicles and live mammalian cells with C24 or C16 sphingomyelin exclusively in the outer leaflet and compared microdomain formation. In giant unilamellar vesicles, we observed that asymmetrically placed C24 sphingomyelin suppresses microdomains. Conversely, C16 sphingomyelin facilitates microdomains. Replacing endogenous sphingolipids with C24 or C16 sphingomyelin in live HeLa cells has a similar impact on microdomains, characterized by FRET between GPI-anchored proteins: C24, but not C16, sphingomyelin suppresses submicron domains in the plasma membrane. Molecular dynamics simulations indicated that, when in the outer leaflet, the acyl chain of C24 sphingomyelin interdigitates into the opposing leaflet, thereby favouring cholesterol...
Trends in cell biology, 2018
Clustering of extracellular ligands and proteins on the plasma membrane is required to perform sp... more Clustering of extracellular ligands and proteins on the plasma membrane is required to perform specific cellular functions, such as signaling and endocytosis. Attractive forces that originate in perturbations of the membrane's physical properties contribute to this clustering, in addition to direct protein-protein interactions. However, these membrane-mediated forces have not all been equally considered, despite their importance. In this review, we describe how line tension, lipid depletion, and membrane curvature contribute to membrane-mediated clustering. Additional attractive forces that arise from protein-induced perturbation of a membrane's fluctuations are also described. This review aims to provide a survey of the current understanding of membrane-mediated clustering and how this supports precise biological functions.
Environmental science & technology, 2014
Contaminants taken up by living organisms in the environment as a result of anthropogenic contami... more Contaminants taken up by living organisms in the environment as a result of anthropogenic contamination can reduce the tolerance of natural stressors, e.g., low temperatures, but the physiological mechanisms behind these interactions of effects are poorly understood. The tolerance to low temperatures of organisms that cannot regulate their body temperature (ectotherms) depends on their ability to increase the fluidity of their cellular membranes at low temperatures. Our study shows that contaminants accumulating in lipids of organisms alter the physical state of their membranes simply by being present. Contaminants of varying chemical structures can alter the membrane fluidity in either direction and correspondingly modulate the cold tolerance of intact animals.
Soft Matter, 2019
Membranes with curvature inducing inclusions display a range of cooperative phenomena, which can ... more Membranes with curvature inducing inclusions display a range of cooperative phenomena, which can be linked to biomembrane function, e.g. membrane tubulation, vesiculation, softening and spontaneous tension.
Biophysical Journal, 1999
The crowded interior of a living cell makes experiments on simplerin vitrosystems attractive. Alt... more The crowded interior of a living cell makes experiments on simplerin vitrosystems attractive. Although these reveal interesting phenomena, their biological relevance can be questionable. A topical example is the phase separation of intrinsically-disordered proteins into biomolecular condensates, which is proposed to underlie the membraneless compartmentalisation of many cellular functions. How a cell reliably controls biochemical reactions in compartments open to the compositionally-varying cytoplasm is an important question for understanding cellular homeostasis. Computer simulations are often used to study the phase behaviour of model biomolecular condensates, but the number of relevant parameters explodes as the number of protein components increases. It is unfeasible to exhaustively simulate such models for all parameter combinations, although interesting phenomena are almost certainly hidden in the jungle of their high-dimensional parameter space. Here we have studied the phase...
Physical Review E
The properties of freestanding tensionless interfaces and membranes at low bending rigidity κ are... more The properties of freestanding tensionless interfaces and membranes at low bending rigidity κ are dominated by strong fluctuations and self-avoidance and are thus outside the range of standard perturbative analysis. We analyze this regime by a simple discretized, self-avoiding membrane model on a frame subject to periodic boundary conditions by use of Monte Carlo simulation and dynamically triangulated surface techniques. We find that at low bending rigidities, the membrane properties fall into three regimes: Below the collapse transition κ BP it is subject to branched polymer instability where the framed surface is not defined, in a range below a threshold rigidity κ c the conformational correlation function are characterized by power-law behavior with a continuously varying exponent α, 2 < α 4 and above κ c , α = 4 characteristic for linearized bending excitations. Response functions specific heat and area compressibility display pronounced peaks close to κ c. The results may be important for the description of soft interface systems, such as microemulsions and membranes with in-plane cooperative phenomena.
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Papers by John Hjort Ipsen