Gramicidin Increases Lipid Flip-Flop in Symmetric and Asymmetric Lipid Vesicles.

Abstract:

:Unlike most transmembrane proteins, phospholipids can migrate from one leaflet of the membrane to the other. Because this spontaneous lipid translocation (flip-flop) tends to be very slow, cells facilitate the process with enzymes that catalyze the transmembrane movement and thereby regulate the transbilayer lipid distribution. Nonenzymatic membrane-spanning proteins with unrelated primary functions have also been found to accelerate lipid flip-flop in a nonspecific manner and by various hypothesized mechanisms. Using deuterated phospholipids, we examined the acceleration of flip-flop by gramicidin channels, which have well-defined structures and known functions, features that make them ideal candidates for probing the protein-membrane interactions underlying lipid flip-flop. To study compositionally and isotopically asymmetric proteoliposomes containing gramicidin, we expanded a recently developed protocol for the preparation and characterization of lipid-only asymmetric vesicles. Channel incorporation, conformation, and function were examined with small angle x-ray scattering, circular dichroism, and a stopped-flow spectrofluorometric assay, respectively. As a measure of lipid scrambling, we used differential scanning calorimetry to monitor the effect of gramicidin on the melting transition temperatures of the two bilayer leaflets. The two calorimetric peaks of the individual leaflets merged into a single peak over time, suggestive of scrambling, and the effect of the channel on the transbilayer lipid distribution in both symmetric 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and asymmetric 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles was quantified from proton NMR measurements. Our results show that gramicidin increases lipid flip-flop in a complex, concentration-dependent manner. To determine the molecular mechanism of the process, we used molecular dynamics simulations and further computational analysis of the trajectories to estimate the extent of membrane deformation. Together, the experimental and computational approaches were found to constitute an effective means for studying the effects of transmembrane proteins on lipid distribution in both symmetric and asymmetric model membranes.

journal_name

Biophys J

journal_title

Biophysical journal

authors

Doktorova M,Heberle FA,Marquardt D,Rusinova R,Sanford RL,Peyear TA,Katsaras J,Feigenson GW,Weinstein H,Andersen OS

doi

10.1016/j.bpj.2019.01.016

subject

Has Abstract

pub_date

2019-03-05 00:00:00

pages

860-873

issue

5

eissn

0006-3495

issn

1542-0086

pii

S0006-3495(19)30051-7

journal_volume

116

pub_type

杂志文章
  • A model for protein translation: polysome self-organization leads to maximum protein synthesis rates.

    abstract::The genetic information in DNA is transcribed to mRNA and then translated to proteins, which form the building blocks of life. Translation, or protein synthesis, is hence a central cellular process. We have developed a gene-sequence-specific mechanistic model for the translation machinery, which accounts for all the e...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.106.087825

    authors: Zouridis H,Hatzimanikatis V

    更新日期:2007-02-01 00:00:00

  • Compressibilities and volume fluctuations of archaeal tetraether liposomes.

    abstract::Bipolar tetraether lipids (BTLs) are abundant in crenarchaeota, which thrive in both thermophilic and nonthermophilic environments, with wide-ranging growth temperatures (4-108°C). BTL liposomes can serve as membrane models to explore the role of BTLs in the thermal stability of the plasma membrane of crenarchaeota. I...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2010.09.061

    authors: Chong PL,Sulc M,Winter R

    更新日期:2010-11-17 00:00:00

  • Probing tubulin-blocked state of VDAC by varying membrane surface charge.

    abstract::Reversible blockage of the voltage-dependent anion channel (VDAC) of the mitochondrial outer membrane by dimeric tubulin is being recognized as a potent regulator of mitochondrial respiration. The tubulin-blocked state of VDAC is impermeant for ATP but only partially closed for small ions. This residual conductance al...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2012.03.058

    authors: Gurnev PA,Queralt-Martin M,Aguilella VM,Rostovtseva TK,Bezrukov SM

    更新日期:2012-05-02 00:00:00

  • Atomic detail peptide-membrane interactions: molecular dynamics simulation of gramicidin S in a DMPC bilayer.

    abstract::Molecular dynamics simulations have been performed of the sequence-symmetric cyclic decapeptide antibiotic gramicidin S (GS), in interaction with a hydrated dimyristoylphosphatidylcholine (DMPC) bilayer, and the results compared with a "control" simulation of the system in the absence of GS. Following experimental evi...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(00)76424-1

    authors: Mihailescu D,Smith JC

    更新日期:2000-10-01 00:00:00

  • Hybrid global optimization algorithms for protein structure prediction: alternating hybrids.

    abstract::Hybrid global optimization methods attempt to combine the beneficial features of two or more algorithms, and can be powerful methods for solving challenging nonconvex optimization problems. In this paper, novel classes of hybrid global optimization methods, termed alternating hybrids, are introduced for application as...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(03)74905-4

    authors: Klepeis JL,Pieja MJ,Floudas CA

    更新日期:2003-02-01 00:00:00

  • Propagation speed in myelinated nerve. I. Experimental dependence on external Na and on temperature.

    abstract::Conduction speed (theta) in single myelinated Rana pipiens sciatic nerve fibers has been precisely measured using intracellular recording and on-line digital computer techniques. The dependence of relative speed on external Na concentration at 15 degrees C has been found to be ln(theta(1)/theta(2)) = 0.524 (+/-0.018) ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(73)86045-X

    authors: Hardy WL

    更新日期:1973-10-01 00:00:00

  • A model of Na+/H+ exchanger and its central role in regulation of pH and Na+ in cardiac myocytes.

    abstract::A new kinetic model of the Na(+)/H(+) exchanger (NHE) was developed by fitting a variety of major experimental findings, such as ion-dependencies, forward/reverse mode, and the turnover rate. The role of NHE in ion homeostasis was examined by implementing the NHE model in a minimum cell model including intracellular p...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2009.08.053

    authors: Cha CY,Oka C,Earm YE,Wakabayashi S,Noma A

    更新日期:2009-11-18 00:00:00

  • Resident Calmodulin Primes NMDA Receptors for Ca2+-Dependent Inactivation.

    abstract::N-methyl-d-aspartate (NMDA) receptors are glutamate- and glycine-gated channels that flux Na+ and Ca2+ into postsynaptic neurons during synaptic transmission. The resulting intracellular Ca2+ transient is essential to physiological and pathological processes related to synaptic development, plasticity, and apoptosis. ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2017.06.035

    authors: Iacobucci GJ,Popescu GK

    更新日期:2017-11-21 00:00:00

  • Dendritic signals command firing dynamics in a mathematical model of cerebellar Purkinje cells.

    abstract::Dendrites of cerebellar Purkinje cells (PCs) respond to brief excitations from parallel fibers with lasting plateau depolarizations. It is unknown whether these plateaus are local events that boost the synaptic signals or they propagate to the soma and directly take part in setting the cell firing dynamics. To address...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2010.04.056

    authors: Genet S,Sabarly L,Guigon E,Berry H,Delord B

    更新日期:2010-07-21 00:00:00

  • Methodology for increased precision in saturation transfer electron paramagnetic resonance studies of rotational dynamics.

    abstract::Microsecond rotational motions of nitroxide spin labels are measured primarily with saturation transfer electron paramagnetic resonance (ST-EPR). In the present study we have used model system experiments to quantitatively evaluate different ST-EPR spectral parameters, both in-phase and out-of-phase, with an emphasis ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(86)83720-1

    authors: Squier TC,Thomas DD

    更新日期:1986-04-01 00:00:00

  • Applications of Results from Linear Kinetics to the Hodgkin-Huxley Equations.

    abstract::On the basis of its role in the analysis of mammillary compartmental systems, a matrix with non-zero elements in the first row, first column, and along the main diagonal and with zero elements elsewhere is called a mammillary matrix. It is pointed out that such matrices occur in a variety of biological problems includ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/s0006-3495(64)86769-2

    authors: Hearon JZ

    更新日期:1964-01-01 00:00:00

  • Molecular simulation of the binding of nerve growth factor peptide mimics to the receptor tyrosine kinase A.

    abstract::Nerve growth factor (NGF) mimics play an important role for therapies that target the receptor tyrosine kinase A (trkA). The N-terminal fragment of the NGF (N-term@NGF) was previously demonstrated to be an important determinant for affinity and specificity in the binding to trkA. Here we use a variety of computational...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.106.083519

    authors: Berrera M,Cattaneo A,Carloni P

    更新日期:2006-09-15 00:00:00

  • Dynamics-Driven Allostery Underlies Ca2+-Mediated Release of SERCA Inhibition by Phospholamban.

    abstract::Sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA) and phospholamban (PLB) are essential for intracellular Ca2+ transport in myocytes. Ca2+-dependent activation of SERCA-PLB provides a control function that regulates cytosolic and SR Ca2+ levels. Although experimental and computational studies alone have led to a greater...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2020.09.014

    authors: Raguimova ON,Aguayo-Ortiz R,Robia SL,Espinoza-Fonseca LM

    更新日期:2020-11-03 00:00:00

  • Bathoproducts of rhodopsin, isorhodopsin I, and isorhodopsin II.

    abstract::Bathorhodopsins were prepared by partially (10--15%) photoconverting bovine rhodopsin (11-cis chromophore) or isorhodopsin I (9-cis chromophore) at 77 degrees K; care was taken to avoid establishing photostationary states. The absorption spectra calculated for the bathorhodopsins derived from the two parent pigments a...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(80)85129-0

    authors: Mao B,Ebrey TG,Crouch R

    更新日期:1980-02-01 00:00:00

  • Passive tension and stiffness of vertebrate skeletal and insect flight muscles: the contribution of weak cross-bridges and elastic filaments.

    abstract::Tension and dynamic stiffness of passive rabbit psoas, rabbit semitendinosus, and waterbug indirect flight muscles were investigated to study the contribution of weak-binding cross-bridges and elastic filaments (titin and minititin) to the passive mechanical behavior of these muscles. Experimentally, a functional diss...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(93)81262-1

    authors: Granzier HL,Wang K

    更新日期:1993-11-01 00:00:00

  • Voltage-dependent gating of single gap junction channels in an insect cell line.

    abstract::De novo formation of cell pairs was used to examine the gating properties of single gap junction channels. Two separate cells of an insect cell line (clone C6/36, derived from the mosquito Aedes albopictus) were pushed against each other to provoke formation of gap junction channels. A dual voltage-clamp method was us...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(94)80521-1

    authors: Bukauskas FF,Weingart R

    更新日期:1994-08-01 00:00:00

  • Modeling of the three-dimensional structure of polypeptides in solution using potential-scaled/hot-solute molecular dynamics.

    abstract::We present here an efficient and accurate procedure for modeling of the three-dimensional structures of polypeptides in the explicit solvent water based on molecular dynamics calculations. Using the toxic domain analog of heat-stable enterotoxin as a model peptide, we examined the utilities of two molecular dynamics t...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(94)80975-0

    authors: Tsujishita H,Moriguchi I,Hirono S

    更新日期:1994-06-01 00:00:00

  • Role of the dielectric constants of membrane proteins and channel water in ion permeation.

    abstract::Using both analytical solutions obtained from simplified systems and numerical results from more realistic cases, we investigate the role played by the dielectric constant of membrane proteins epsilon(p) and pore water epsilon(w) in permeation of ions across channels. We show that the boundary and its curvature are th...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(03)70015-0

    authors: Baştuğ T,Kuyucak S

    更新日期:2003-05-01 00:00:00

  • Electrostatic free energy of lysozyme.

    abstract::The electrostatic free energies of native and acetylated lysozymes were computed by the fixed charge model (Tanford, C., and J. G. Kirkwood, 1957, J. Am. Chem. Soc., 79:5333-5339). For each computation, the charges were transformed into a sphere of fixed radius without changing their depths or the distance between cha...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(83)84302-1

    authors: Imoto T

    更新日期:1983-12-01 00:00:00

  • Cavity as a source of conformational fluctuation and high-energy state: high-pressure NMR study of a cavity-enlarged mutant of T4 lysozyme.

    abstract::Although the structure, function, conformational dynamics, and controlled thermodynamics of proteins are manifested by their corresponding amino acid sequences, the natural rules for molecular design and their corresponding interplay remain obscure. In this study, we focused on the role of internal cavities of protein...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2014.11.012

    authors: Maeno A,Sindhikara D,Hirata F,Otten R,Dahlquist FW,Yokoyama S,Akasaka K,Mulder FA,Kitahara R

    更新日期:2015-01-06 00:00:00

  • Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment.

    abstract::Molecular dynamics (MD) simulations of the DNA duplex d(CCAACGTTGG)(2) were used to study the relationship between DNA sequence and structure. Two crystal simulations were carried out; one consisted of one unit cell containing two duplexes, and the other of two unit cells containing four duplexes. Two solution simulat...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(00)76625-2

    authors: Bevan DR,Li L,Pedersen LG,Darden TA

    更新日期:2000-02-01 00:00:00

  • Action of ionizing radiation on sensitive strains of Escherichia coli B.

    abstract::Strain B(8-11) has been found to be very sensitive to postirradiation DNA degradation. Up to 98% of the DNA is degraded at optimum doses. The amount of residual DNA correlates with the retention of colony-forming ability (CFA). Studies of rates of degradation as a function of dose agree with the concept that a degradi...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(72)86076-4

    authors: Pollard EC,Tilberg A

    更新日期:1972-02-01 00:00:00

  • Elasticity and phase behavior of DPPC membrane modulated by cholesterol, ergosterol, and ethanol.

    abstract::Giant vesicles formed of 1,2-dipalmitoylphosphatidylcholine (DPPC) and sterols (cholesterol or ergosterol) in water and water/ethanol solutions have been used to examine the effect of sterol composition and ethanol concentration on the area compressibility modulus (K(a)), overall mechanical behavior, vesicle morpholog...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.104.057943

    authors: Tierney KJ,Block DE,Longo ML

    更新日期:2005-10-01 00:00:00

  • Cation concentrations in the hemolymph of Loligo pealei.

    abstract::Hemolymph and protein-free hemolymph obtained from Loligo pealei were analyzed for cation concentration by the method of atomic absorption spectroscopy, for the following ions: Na+, K+, Ca++, and Mg++. No significant differences were seen in ion concentration between hemolymph and protein-free hemolymph. Of particular...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(77)85609-9

    authors: Shoukimas J,Adelman WJ Jr,Sege V

    更新日期:1977-05-01 00:00:00

  • Asymmetric modulation and blockade of the delayed rectifier in squid giant axons by divalent cations.

    abstract::The effects of intracellular magnesium ions and extracellular calcium and magnesium ions on the delayed rectifier potassium ion channel, IK, were investigated from intracellularly perfused squid giant axons. Cao+2 and Mgo+2 both blocked IK in a voltage-independent manner with a KD of approximately 100 and 500 mM, resp...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(95)80047-0

    authors: Clay JR

    更新日期:1995-11-01 00:00:00

  • Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration.

    abstract::Thermodynamically rigorous free energy methods in principle allow the exact computation of binding free energies in biological systems. Here, we use thermodynamic integration together with molecular dynamics simulations of a DNA-protein complex to compute relative binding free energies of a series of mutants of a prot...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2011.07.003

    authors: Beierlein FR,Kneale GG,Clark T

    更新日期:2011-09-07 00:00:00

  • Two conserved residues are important for inducing highly ordered membrane domains by the transmembrane domain of influenza hemagglutinin.

    abstract::The interaction with lipids of a synthetic peptide corresponding to the transmembrane domain of influenza hemagglutinin was investigated by means of electron spin resonance. A detailed analysis of the electron spin resonance spectra from spin-labeled phospholipids revealed that the major effect of the peptide on the d...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2010.11.014

    authors: Ge M,Freed JH

    更新日期:2011-01-05 00:00:00

  • Robust entrainment of circadian oscillators requires specific phase response curves.

    abstract::The circadian clocks keeping time in many living organisms rely on self-sustained biochemical oscillations entrained by external cues, such as light, to the 24-h cycle induced by Earth's rotation. However, environmental cues are unreliable due to the variability of habitats, weather conditions, or cue-sensing mechanis...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2011.04.043

    authors: Pfeuty B,Thommen Q,Lefranc M

    更新日期:2011-06-08 00:00:00

  • Characterization of biomimetic surfaces formed from cell membranes.

    abstract::A method for fabricating biomimetic surfaces from intact cell membranes is described. A monolayer of alkanethiol on gold is covered by a second layer derived from the components of erythrocyte membranes either by self-assembly or by Langmuir-Blodgett methods. The resulting asymmetric hybrid layer was characterized by ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(97)78334-6

    authors: Rao NM,Plant AL,Silin V,Wight S,Hui SW

    更新日期:1997-12-01 00:00:00

  • Reversible surface aggregation in pore formation by pardaxin.

    abstract::The mechanism of leakage induced by surface active peptides is not yet fully understood. To gain insight into the molecular events underlying this process, the leakage induced by the peptide pardaxin from phosphatidylcholine/ phosphatidylserine/cholesterol large unilamellar vesicles was studied by monitoring the rate ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(96)79822-3

    authors: Rapaport D,Peled R,Nir S,Shai Y

    更新日期:1996-06-01 00:00:00