Influence of Ganglioside GM1 Concentration on Lipid Clustering and Membrane Properties and Curvature.

Abstract:

:Gangliosides are a class of glycosphingolipids (GSLs) with amphiphilic character that are found at the outer leaflet of the cell membranes, where their ability to organize into special domains makes them vital cell membrane components. However, a molecular understanding of GSL-rich membranes in terms of their clustered organization, stability, and dynamics is still elusive. To gain molecular insight into the organization and dynamics of GSL-rich membranes, we performed all-atom molecular-dynamics simulations of bicomponent ganglioside GM1 in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) phospholipid bilayers with varying concentrations of GM1 (10%, 20%, and 30%). Overall, the simulations show very good agreement with available experimental data, including x-ray electron density profiles along the membrane normal, NMR carbohydrate proton-proton distances, and x-ray crystal structures. This validates the quality of our model systems for investigating GM1 clustering through an ordered-lipid-cluster analysis. The increase in GM1 concentration induces tighter lipid packing, driven mainly by inter-GM1 carbohydrate-carbohydrate interactions, leading to a greater preference for the positive curvature of GM1-containing membranes and larger cluster sizes of ordered-lipid clusters (with a composite of GM1 and POPC). These clusters tend to segregate and form a large percolated cluster at a 30% GM1 concentration at 293 K. At a higher temperature of 330 K, however, the segregation is not maintained.

journal_name

Biophys J

journal_title

Biophysical journal

authors

Patel DS,Park S,Wu EL,Yeom MS,Widmalm G,Klauda JB,Im W

doi

10.1016/j.bpj.2016.09.021

subject

Has Abstract

pub_date

2016-11-01 00:00:00

pages

1987-1999

issue

9

eissn

0006-3495

issn

1542-0086

pii

S0006-3495(16)30821-9

journal_volume

111

pub_type

杂志文章
  • Insulin transport within skeletal muscle transverse tubule networks.

    abstract::It has recently been observed in situ in mice that insulin takes approximately 10 min to be transported 20 microm into the t-tubule networks of skeletal muscle fibers. The mechanisms for this slow transport are unknown. It has been suggested that the biochemical composition of the t-tubular space that may include larg...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.107888

    authors: Shorten PR,McMahon CD,Soboleva TK

    更新日期:2007-11-01 00:00:00

  • Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe.

    abstract::We investigate the microsecond-timescale kinetics of the RNA hairpin ga*cUUCGguc. The fluorescent nucleotide 2-aminopurine (a*) reports mainly on base stacking. Ten kinetic traces and the temperature denaturation curve are globally fitted to four-state models of the free-energy surface. In the best-fitting sequential ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2009.06.035

    authors: Sarkar K,Meister K,Sethi A,Gruebele M

    更新日期:2009-09-02 00:00:00

  • Interaction of salicylate and a terpenoid plant extract with model membranes: reconciling experiments and simulations.

    abstract::We investigate the effects of two structurally similar small cyclic molecules: salicylic acid and perillic acid on a zwitterionic model lipid bilayer, and show that both molecules might have biological activity related to membrane thinning. Salicylic acid is a nonsteroidal antiinflammatory drug, some of the pharmacolo...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2010.11.009

    authors: Khandelia H,Witzke S,Mouritsen OG

    更新日期:2010-12-15 00:00:00

  • CW and CCW Conformations of the E. coli Flagellar Motor C-Ring Evaluated by Fluorescence Anisotropy.

    abstract::The molecular cascade that controls switching of the direction of rotation of Escherichia coli flagellar motors is well known, but the conformational changes that allow the rotor to switch are still unclear. The signaling molecule CheY, when phosphorylated, binds to the C-ring at the base of the rotor, raising the pro...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2017.12.001

    authors: Hosu BG,Berg HC

    更新日期:2018-02-06 00:00:00

  • Structure and selectivity of a monovalent cation binding site in cubic insulin crystals.

    abstract::Cubic insulin crystals contain a binding site for monovalent cations in a cavity of the crystal dyad in which the bound cation is ligated by protein atomic dipoles and water molecules. These types of interaction are analogous to interactions that occur in small cation-selective carrier and channel molecules. X-ray dif...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/s0006-3495(94)80795-7

    authors: Badger J,Kapulsky A,Gursky O,Bhyravbhatla B,Caspar DL

    更新日期:1994-02-01 00:00:00

  • Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor.

    abstract::G-protein-coupled receptors (GPCRs) are important membrane proteins that mediate cellular signaling and represent primary targets for about one-third of currently marketed drugs. Recent x-ray crystallographic studies identified distinct conformations of GPCRs in the active and inactive states. An allosteric sodium ion...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2015.03.003

    authors: Miao Y,Caliman AD,McCammon JA

    更新日期:2015-04-07 00:00:00

  • Differential polarization imaging. V. Numerical aperture effects and the contribution of preferential scattering and absorption to the circular dichroism images.

    abstract::Chiral objects which scatter and absorb preferentially left versus right circularly polarized light give rise to bright-field circular dichroism (CD) images containing contributions from both these two phenomena. These contributions are separated and characterized mathematically, and the effect of the dimensions of th...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(91)82334-7

    authors: Finzi L,Ulibarri L,Bustamante C

    更新日期:1991-06-01 00:00:00

  • Mechanical Characteristics of Ultrafast Zebrafish Larval Swimming Muscles.

    abstract::Zebrafish (Danio rerio) swim within days of fertilization, powered by muscles of the axial myotomes. Forces generated by these muscles can be measured rapidly in whole, intact larval tails by adapting protocols developed for ex vivo muscle mechanics. But it is not known how well these measurements reflect the function...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2020.06.036

    authors: Mead AF,Kennedy GG,Palmer BM,Ebert AM,Warshaw DM

    更新日期:2020-08-18 00:00:00

  • Single chromatin fiber stretching reveals physically distinct populations of disassembly events.

    abstract::Eukaryotic DNA is packaged into the cell nucleus as a nucleoprotein complex, chromatin. Despite this condensed state, access to the DNA sequence must occur during gene expression and other essential genetic events. Here we employ optical tweezers stretching of reconstituted chromatin fibers to investigate the release ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.104.053074

    authors: Pope LH,Bennink ML,van Leijenhorst-Groener KA,Nikova D,Greve J,Marko JF

    更新日期:2005-05-01 00:00:00

  • Mechanogenetic coupling of Hydra symmetry breaking and driven Turing instability model.

    abstract::The freshwater polyp Hydra can regenerate from tissue fragments or random cell aggregates. We show that the axis-defining step ("symmetry breaking") of regeneration requires mechanical inflation-collapse oscillations of the initial cell ball. We present experimental evidence that axis definition is retarded if these o...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2008.09.062

    authors: Soriano J,Rüdiger S,Pullarkat P,Ott A

    更新日期:2009-02-18 00:00:00

  • Light-induced dielectrophoretic manipulation of DNA.

    abstract::Light-induced dielectrophoretic movement of polystyrene beads and lambda-DNA is studied using thin films of amorphous hydrogenated silicon as local photoaddressable electrodes with a diameter of 4 microm. Positive (high-field seeking) dielectrophoretic movement is observed for both types of objects. The absence of str...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.106.101188

    authors: Hoeb M,Rädler JO,Klein S,Stutzmann M,Brandt MS

    更新日期:2007-08-01 00:00:00

  • Evaluation of dynamic features of Escherichia coli 16S ribosomal RNA in homogeneous physiological solution.

    abstract::There is no methodology for the estimation of the dynamic features of large-molecular-weight RNAs in homogeneous physiological media. In this report, a luminescence anisotropy-based method using a long-lifetime luminescent oligonucleotide probe for the estimation of the dynamic features of large-molecular-weight RNA i...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.105.062455

    authors: Sakamoto T,Mahara A,Yamagata K,Iwase R,Yamaoka T,Murakami A

    更新日期:2005-12-01 00:00:00

  • The Chemical Potential of Plasma Membrane Cholesterol: Implications for Cell Biology.

    abstract::Cholesterol is abundant in plasma membranes and exhibits a variety of interactions throughout the membrane. Chemical potential accounts for thermodynamic consequences of molecular interactions, and quantifies the effective concentration (i.e., activity) of any substance participating in a process. We have developed, t...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2017.12.042

    authors: Ayuyan AG,Cohen FS

    更新日期:2018-02-27 00:00:00

  • Phase-lifetime spectroscopy of photocycle processes: proton release and uptake kinetics of purple membrane.

    abstract::Phase-lifetime spectroscopy was used to measure the kinetics of light-driven proton transients and M intermediate decay of purple membrane. The kinetics were measured in distilled water and in 0.4 M KCl over the pH range of 5.3-8.8. The low ionic strength data showed results that were comparable to previous data. The ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(88)83077-7

    authors: Sinton MH,Dewey TG

    更新日期:1988-02-01 00:00:00

  • Distribution of proteins implicated in excitation-contraction coupling in rat ventricular myocytes.

    abstract::We have examined the distribution of ryanodine receptors, L-type Ca(2+) channels, calsequestrin, Na(+)/Ca(2+) exchangers, and voltage-gated Na(+) channels in adult rat ventricular myocytes. Enzymatically dissociated cells were fixed and dual-labeled with specific antibodies using standard immunocytochemistry protocols...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(00)76506-4

    authors: Scriven DR,Dan P,Moore ED

    更新日期:2000-11-01 00:00:00

  • Optimizing planar lipid bilayer single-channel recordings for high resolution with rapid voltage steps.

    abstract::We describe two enhancements of the planar bilayer recording method which enable low-noise recordings of single-channel currents activated by voltage steps in planar bilayers formed on apertures in partitions separating two open chambers. First, we have refined a simple and effective procedure for making small bilayer...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(90)82376-6

    authors: Wonderlin WF,Finkel A,French RJ

    更新日期:1990-08-01 00:00:00

  • A molecular dynamics investigation of vinculin activation.

    abstract::Vinculin activation plays a critical role in focal adhesion initiation and formation. In its native state, vinculin is in an autoinhibitory conformation in which domain 1 prevents interaction of the vinculin tail domain with actin by steric hindrance. Once activated, vinculin is able to interact with both actin and ta...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2010.05.024

    authors: Golji J,Mofrad MR

    更新日期:2010-08-09 00:00:00

  • The influence of lysolipids on the spontaneous curvature and bending elasticity of phospholipid membranes.

    abstract::The effects of lysolipids on phospholipid layer curvature and bending elasticity were examined using x-ray diffraction and the osmotic stress method. Lysolipids with two different head groups, phosphatidylcholine (PC) and phosphatidylethanolamine (PE), and differing hydrocarbon chains were mixed with the hexagonal-for...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(01)75695-0

    authors: Fuller N,Rand RP

    更新日期:2001-07-01 00:00:00

  • Digitized precision measurements of the movements of sea urchin sperm flagella.

    abstract::High speed cinemicrographs were made of sea urchin sperm at temperatures varying from 22 to 6 degrees C. Apparatus, combining a television camera and a video digitizer, was constructed to scan individual flagellar images and to digitize the flagellar waveforms. With appropriate smoothing and averaging procedures, the ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(85)83931-X

    authors: Rikmenspoel R,Isles CA

    更新日期:1985-03-01 00:00:00

  • Resolution of two substrate-binding sites in an engineered cytochrome P450eryF bearing a fluorescent probe.

    abstract::To elucidate the mechanisms of cooperativity of cytochrome P450eryF an SH-reactive fluorescent probe was introduced close to the substrate-binding site. Cys-154, the only accessible cysteine, was eliminated by site-directed mutagenesis, and a novel cysteine was substituted for Ser-93 in the B'/C loop. S93C, C154A, C15...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.104.058479

    authors: Davydov DR,Botchkareva AE,Davydova NE,Halpert JR

    更新日期:2005-07-01 00:00:00

  • Rate constant of muscle force redevelopment reflects cooperative activation as well as cross-bridge kinetics.

    abstract::The rate of muscle force redevelopment after release-restretch protocols has previously been interpreted using a simple two-state cross-bridge cycling model with rate constants for transitions between non-force-bearing and force-bearing states, f, and between force-bearing and non-force-bearing states, g. Changes in t...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(97)78664-8

    authors: Campbell K

    更新日期:1997-01-01 00:00:00

  • Molecular mechanisms of how mercury inhibits water permeation through aquaporin-1: understanding by molecular dynamics simulation.

    abstract::Aquaporin (AQP) functions as a water-conducting pore. Mercury inhibits the water permeation through AQP. Although site-directed mutagenesis has shown that mercury binds to Cys189 during the inhibition process, it is not fully understood how this inhibits the water permeation through AQP1. We carried out 40 ns molecula...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2009.12.4310

    authors: Hirano Y,Okimoto N,Kadohira I,Suematsu M,Yasuoka K,Yasui M

    更新日期:2010-04-21 00:00:00

  • A procedure for refining a coiled coil protein structure using x-ray fiber diffraction and modeling.

    abstract::We describe a combined use of experimental and simulation techniques to configure side chains in a coiled coil structure. As already demonstrated in a previous work, x-ray diffraction patterns from hard alpha-keratin fibers in the 5.15 A meridian zone reflect the global configuration of the chi(1) dihedral angle of th...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(02)73943-X

    authors: Briki F,Doucet J,Etchebest C

    更新日期:2002-10-01 00:00:00

  • The fast tumble signal in bacterial chemotaxis.

    abstract::We have analyzed repellent signal processing in Escherichia coli by flash photorelease of leucine from photolabile precursors. We found that 1). response amplitudes of free-swimming cell populations increased with leucine jump concentration, with an apparent Hill coefficient of 1.3 and a half-maximal dose of 14.4 micr...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.103.033043

    authors: Khan S,Jain S,Reid GP,Trentham DR

    更新日期:2004-06-01 00:00:00

  • Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations.

    abstract::RNA junctions are common secondary structural elements present in a wide range of RNA species. They play crucial roles in directing the overall folding of RNA molecules as well as in a variety of biological functions. In particular, there has been great interest in the dynamics of RNA junctions, including conformation...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2013.12.008

    authors: Jung S,Schlick T

    更新日期:2014-01-21 00:00:00

  • Dissecting elastic heterogeneity along DNA molecules coated partly with Rad51 using concurrent fluorescence microscopy and optical tweezers.

    abstract::Nucleoprotein filament formation by recombinases is central to homologous recombination. To follow this process, we used fluorescent human Rad51 recombinase to visualize the interactions with double-stranded DNA (dsDNA). Fluorescence imaging revealed that Rad51 filament formation on dsDNA initiates from multiple nucle...

    journal_title:Biophysical journal

    pub_type: 信件

    doi:10.1529/biophysj.106.089466

    authors: Mameren Jv,Modesti M,Kanaar R,Wyman C,Wuite GJ,Peterman EJ

    更新日期:2006-10-15 00:00:00

  • SAXS study of crotapotin at low pH.

    abstract::The structure of crotapotin, a protein extracted, from the venom of the Crotalus durissus terrificus, in solution at pH = 1.5, was studied by SAXS. The experimental results yield structural parameter values of the molecular radius of gyration Rg = 13.6 A, volume v = 16.2 x 10(3) A3 A3 and maximal dimension Dmax = 46 A...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(93)81395-X

    authors: Abrego JR,Craievich AF,Mascarenhas YP,Laure CJ

    更新日期:1993-02-01 00:00:00

  • Analysis of a Functional Dimer Model of Ubiquinol Cytochrome c Oxidoreductase.

    abstract::Ubiquinol cytochrome c oxidoreductase (bc1 complex) serves as an important electron junction in many respiratory systems. It funnels electrons coming from NADH and ubiquinol to cytochrome c, but it is also capable of producing significant amounts of the free radical superoxide. In situ and in other experimental system...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2017.08.018

    authors: Bazil JN

    更新日期:2017-10-03 00:00:00

  • Quantum mechanics/molecular mechanics calculation of the Raman spectra of the phycocyanobilin chromophore in alpha-C-phycocyanin.

    abstract::We have established a quantum mechanics (QM)/molecular mechanics (MM) hybrid method for calculating the Raman spectra of protein-bound cofactors using the alpha-subunit of C-phycocyanin containing a phycocyanobilin (PCB) chromophore as a test case. The PCB cofactor was described with density functional theory, whereas...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.108878

    authors: Mroginski MA,Mark F,Thiel W,Hildebrandt P

    更新日期:2007-09-15 00:00:00

  • Triphasic force dependence of E-selectin/ligand dissociation governs cell rolling under flow.

    abstract::During inflammation, flowing leukocytes tether to and roll on vascular surfaces through the association and dissociation of selectin/ligand bonds. The interactions of P- and L- selectins with their respective ligands exhibit catch-slip bonds, such that increasing force initially prolongs and then shortens bond lifetim...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2010.05.040

    authors: Wayman AM,Chen W,McEver RP,Zhu C

    更新日期:2010-08-09 00:00:00