scholarly journals Free energies of membrane stalk formation from a lipidomics perspective

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chetan S. Poojari ◽  
Katharina C. Scherer ◽  
Jochen S. Hub
Keyword(s):  
Lipid Composition ◽  
Chemical Species ◽  
Coarse Grained ◽  
Free Energies ◽  
Computationally Efficient ◽  
Membrane Biology ◽  
Biologically Relevant ◽  
Outer Leaflet ◽  
Head Groups ◽  
Complex Lipid

AbstractMany biological membranes are asymmetric and exhibit complex lipid composition, comprising hundreds of distinct chemical species. Identifying the biological function and advantage of this complexity is a central goal of membrane biology. Here, we study how membrane complexity controls the energetics of the first steps of membrane fusions, that is, the formation of a stalk. We first present a computationally efficient method for simulating thermodynamically reversible pathways of stalk formation at coarse-grained resolution. The method reveals that the inner leaflet of a typical plasma membrane is far more fusogenic than the outer leaflet, which is likely an adaptation to evolutionary pressure. To rationalize these findings by the distinct lipid compositions, we computed ~200 free energies of stalk formation in membranes with different lipid head groups, tail lengths, tail unsaturations, and sterol content. In summary, the simulations reveal a drastic influence of the lipid composition on stalk formation and a comprehensive fusogenicity map of many biologically relevant lipid classes.

scholarly journals Free energies of stalk formation in the lipidomics era

2021 ◽  
Author(s):  
Chetan S Poojari ◽  
Katharina C Scherer ◽  
Jochen S Hub
Keyword(s):  
Lipid Composition ◽  
Biological Function ◽  
Chemical Species ◽  
Free Energies ◽  
Computationally Efficient ◽  
Membrane Biology ◽  
Biologically Relevant ◽  
Outer Leaflet ◽  
Head Groups ◽  
Complex Lipid

Many biological membranes are asymmetric and exhibit complex lipid composition, comprising hundreds of distinct chemical species. Identifying the biological function and advantage of this complexity is a central goal of membrane biology. Here, we study how membrane complexity controls the energetics of the first steps of membrane fusions, that is, the formation of a stalk. We first present a computationally efficient method for simulating thermodynamically reversible pathways of stalk formation at near-atomic resolution. The new method reveals that the inner leaflet of a typical plasma membrane is far more fusogenic than the outer leaflet, which is likely an adaptation to evolutionary pressure. To rationalize these findings by the distinct lipid compositions, we computed ~200 free energies of stalk formation in membranes with different lipid head groups, tail lengths, tail unsaturations, and sterol content. In summary, the simulations reveal a drastic influence of the lipid composition on stalk formation and a comprehensive fusogenicity map of many biologically relevant lipid classes.

Simulation studies of the interactions between membrane proteins and detergents

2005 ◽  
Vol 33 (5) ◽  
pp. 910-912 ◽  
Author(s):  
P.J. Bond ◽  
J. Cuthbertson ◽  
M.S.P. Sansom
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Self Assembly ◽  
Kinetic Mechanism ◽  
Coarse Grained ◽  
Simulation Studies ◽  
High Resolution Data ◽  
Biologically Relevant ◽  
Structure And Dynamics ◽  
Detergent Interactions

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.

scholarly journals Lipid Bilayer Composition Affects Transmembrane Protein Orientation and Function

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Katie D. Hickey ◽  
Mary M. Buhr
Keyword(s):  
Lipid Bilayer ◽  
Lipid Composition ◽  
Protein Function ◽  
Transmembrane Protein ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Outer Leaflet ◽  
Lipid Environment ◽  
Protein Incorporation ◽  
And Function

Sperm membranes change in structure and composition upon ejaculation to undergo capacitation, a molecular transformation which enables spermatozoa to undergo the acrosome reaction and be capable of fertilization. Changes to the membrane environment including lipid composition, specifically lipid microdomains, may be responsible for enabling capacitation. To study the effect of lipid environment on proteins, liposomes were created using lipids extracted from bull sperm membranes, with or without a protein (Na+K+-ATPase or -amylase). Protein incorporation, function, and orientation were determined. Fluorescence resonance energy transfer (FRET) confirmed protein inclusion in the lipid bilayer, and protein function was confirmed using a colourometric assay of phosphate production from ATP cleavage. In the native lipid liposomes, ATPase was oriented with the subunit facing the outer leaflet, while changing the lipid composition to 50% native lipids and 50% exogenous lipids significantly altered this orientation of Na+K+-ATPase within the membranes.

scholarly journals Multi-city modeling of epidemics using spatial networks: Application to 2019-nCov (COVID-19) coronavirus in India

2020 ◽  
Author(s):  
Bhalchandra S. Pujari ◽  
Snehal Shekatkar
Keyword(s):  
Hybrid Approach ◽  
Coarse Grained ◽  
Spatial Networks ◽  
Computationally Efficient ◽  
Transport Networks ◽  
Epidemiological Modeling ◽  
Fine Grained ◽  
City Modeling ◽  
Coupling Parameters

The ongoing pandemic of 2019-nCov (COVID-19) coronavirus has made reliable epidemiological modeling an urgent necessity. Unfortunately, most of the existing models are either too fine-grained to be efficient or too coarse-grained to be reliable. Here we propose a computationally efficient hybrid approach that uses SIR model for individual cities which are in turn coupled via empirical transportation networks that facilitate migration among them. The treatment presented here differs from existing models in two crucial ways: first, self-consistent determination of coupling parameters so as to maintain the populations of individual cities, and second, the incorporation of distance dependent temporal delays in migration. We apply our model to Indian aviation as well as railway networks taking into account populations of more than 300 cities. Our results project that through the domestic transportation, the significant population is poised to be exposed within 90 days of the onset of epidemic. Thus, serious supervision of domestic transport networks is warranted even after restricting international migration.

scholarly journals A mass-conserving and multi-tracer efficient transport scheme in the online integrated Enviro-HIRLAM model

2013 ◽  
Vol 6 (4) ◽  
pp. 1029-1042 ◽  
Author(s):  
B. Sørensen ◽  
E. Kaas ◽  
U. S. Korsholm
Keyword(s):  
Prediction Model ◽  
Weather Prediction ◽  
Three Dimensional ◽  
Chemical Species ◽  
Numerical Weather Prediction Model ◽  
Computationally Efficient ◽  
Long Time ◽  
Dimensional Version ◽  
The Stability ◽  
Lagrangian Scheme

Abstract. In this paper a new advection scheme for the online coupled chemical–weather prediction model Enviro-HIRLAM is presented. The new scheme is based on the locally mass-conserving semi-Lagrangian method (LMCSL), where the original two-dimensional scheme has been extended to a fully three-dimensional version. This means that the three-dimensional semi-implicit semi-Lagrangian scheme which is currently used in Enviro-HIRLAM is largely unchanged. The HIRLAM model is a computationally efficient hydrostatic operational short-term numerical weather prediction model, which is used as the base for the online integrated Enviro-HIRLAM. The new scheme is shown to be efficient, mass conserving, and shape preserving, while only requiring minor alterations to the original code. It still retains the stability at long time steps, which the semi-Lagrangian schemes are known for, while handling the emissions of chemical species accurately. Several mass-conserving filters have been tested to assess the optimal balance of accuracy vs. efficiency.

scholarly journals Accurate Phase Separation of Complex Lipid Mixtures (DPPC/DOPC/CHOL) with a Refined Coarse Grained Martini Model

2018 ◽  
Vol 114 (3) ◽  
pp. 102a
Author(s):  
Timothy S. Carpenter ◽  
Cesar A. Lopez ◽  
Chris Neale ◽  
Helgi I. Ingolfsson ◽  
Cameron Montour ◽  
...  
Keyword(s):  
Phase Separation ◽  
Coarse Grained ◽  
Lipid Mixtures ◽  
Complex Lipid

scholarly journals An efficient approach for limited-data chemical species tomography and its error bounds

2016 ◽  
Vol 472 (2187) ◽  
pp. 20150875 ◽  
Author(s):  
N. Polydorides ◽  
S.-A. Tsekenis ◽  
H. McCann ◽  
V.-D. A. Prat ◽  
P. Wright
Keyword(s):  
Chemical Species ◽  
Dimensional Subspace ◽  
Concentration Function ◽  
Reconstruction Method ◽  
Limited Data ◽  
Computationally Efficient ◽  
Data Errors ◽  
Low Dimensional ◽  
The Impact ◽  
Simple Flow

We present a computationally efficient reconstruction method for the limited-data chemical species tomography problem that incorporates projection of the unknown gas concentration function onto a low-dimensional subspace, and regularization using prior information obtained from a simple flow model. In this context, the contribution of this work is on the analysis of the projection-induced data errors and the calculation of bounds for the overall image error incorporating the impact of projection and regularization errors as well as measurement noise. As an extension to this methodology, we present a variant algorithm that preserves the positivity of the concentration image.

scholarly journals Reversible host cell remodeling underpins deformability changes in malaria parasite sexual blood stages

2016 ◽  
Vol 113 (17) ◽  
pp. 4800-4805 ◽  
Author(s):  
Megan Dearnley ◽  
Trang Chu ◽  
Yao Zhang ◽  
Oliver Looker ◽  
Changjin Huang ◽  
...  
Keyword(s):  
Erythrocyte Membrane ◽  
Malaria Parasite ◽  
Membrane Skeleton ◽  
Peripheral Circulation ◽  
Coarse Grained ◽  
Mature Stage ◽  
Computationally Efficient ◽  
Vertical Coupling ◽  
Coarse Grained Model ◽  
Cell Remodeling

The sexual blood stage of the human malaria parasitePlasmodium falciparumundergoes remarkable biophysical changes as it prepares for transmission to mosquitoes. During maturation, midstage gametocytes show low deformability and sequester in the bone marrow and spleen cords, thus avoiding clearance during passage through splenic sinuses. Mature gametocytes exhibit increased deformability and reappear in the peripheral circulation, allowing uptake by mosquitoes. Here we define the reversible changes in erythrocyte membrane organization that underpin this biomechanical transformation. Atomic force microscopy reveals that the length of the spectrin cross-members and the size of the skeletal meshwork increase in developing gametocytes, then decrease in mature-stage gametocytes. These changes are accompanied by relocation of actin from the erythrocyte membrane to the Maurer’s clefts. Fluorescence recovery after photobleaching reveals reversible changes in the level of coupling between the membrane skeleton and the plasma membrane. Treatment of midstage gametocytes with cytochalasin D decreases the vertical coupling and increases their filterability. A computationally efficient coarse-grained model of the erythrocyte membrane reveals that restructuring and constraining the spectrin meshwork can fully account for the observed changes in deformability.

scholarly journals Transient anchorage of cross-linked glycosyl-phosphatidylinositol–anchored proteins depends on cholesterol, Src family kinases, caveolin, and phosphoinositides

2006 ◽  
Vol 175 (1) ◽  
pp. 169-178 ◽  
Author(s):  
Yun Chen ◽  
William R. Thelin ◽  
Bing Yang ◽  
Sharon L. Milgram ◽  
Ken Jacobson
Keyword(s):  
Transmembrane Protein ◽  
Cross Linking ◽  
Cholesterol Depletion ◽  
Transmembrane Conductance Regulator ◽  
Membrane Biology ◽  
Glycosyl Phosphatidylinositol ◽  
Caveolin 1 ◽  
Outer Leaflet ◽  
Membrane Components ◽  
Open Question

How outer leaflet plasma membrane components, including glycosyl-phosphatidylinositol–anchored proteins (GPIAPs), transmit signals to the cell interior is an open question in membrane biology. By deliberately cross-linking several GPIAPs under antibody-conjugated 40-nm gold particles, transient anchorage of the gold particle–induced clusters of both Thy-1 and CD73, a 5′ exonucleotidase, occurred for periods ranging from 300 ms to 10 s in fibroblasts. Transient anchorage was abolished by cholesterol depletion, addition of the Src family kinase (SFK) inhibitor PP2, or in Src-Yes-Fyn knockout cells. Caveolin-1 knockout cells exhibited a reduced transient anchorage time, suggesting the partial participation of caveolin-1. In contrast, a transmembrane protein, the cystic fibrosis transmembrane conductance regulator, exhibited transient anchorage that occurred without deliberately enhanced cross-linking; moreover, it was only slightly inhibited by cholesterol depletion or SFK inhibition and depended completely on the interaction of its PDZ-binding domain with the cytoskeletal adaptor EBP50. We propose that cross-linked GPIAPs become transiently anchored via a cholesterol-dependent SFK-regulatable linkage between a transmembrane cluster sensor and the cytoskeleton.

scholarly journals Purification, characterization and influence on membrane properties of the plant-specific sphingolipids GIPC

2020 ◽  
Author(s):  
Adiilah Mamode Cassim ◽  
Yotam Navon ◽  
Yu Gao ◽  
Marion Decossas ◽  
Laetitia Fouillen ◽  
...  
Keyword(s):  
Fluid Phase ◽  
Membrane Properties ◽  
Neutron Reflectivity ◽  
Temperature Variations ◽  
Signal Perception ◽  
H Nmr ◽  
Lipidomic Analysis ◽  
Outer Leaflet ◽  
Head Groups ◽  
Plant Plasma Membrane

AbstractThe plant plasma membrane (PM) is an essential barrier between the cell and the external environment. The PM is crucial for signal perception and transmission. It consists of an asymmetrical lipid bilayer made up of three different lipid classes: sphingolipids, sterols and phospholipids. The most abundant sphingolipids in the plant PM are the Glycosyl Inositol Phosphoryl Ceramides (GIPCs), representing up to 40% of total sphingolipids, assumed to be almost exclusively in the outer leaflet of the PM. In this study, we investigated the structure of GIPCs and their role in membrane organization. Since GIPCs are not commercially available, we developed a protocol to extract and isolate GIPC-enriched fractions from eudicots (cauliflower and tobacco) and monocots (leek and rice). Lipidomic analysis confirmed the presence of different long chain bases and fatty acids. The glycan head groups of the different GIPC series from monocots and dicots were analysed by GC-MS showing different sugar moieties. Multiple biophysics tools namely Langmuir monolayer, ζ-Potential, light scattering, neutron reflectivity, solid state 2H-NMR and molecular modelling were used to investigate the physical properties of the GIPCs, as well as their interaction with free and conjugated phytosterols. We showed that GIPCs increase the thickness and electronegativity of model membranes, interact differentially with the phytosterols species and regulate the gel-to-fluid phase transition during temperature variations.

Sign in / Sign up

Export Citation Format

Share Document