Abstract:
:We present a two-component coarse-grained molecular-dynamics model for simulating the erythrocyte membrane. The proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton, thus showing both the fluidic behavior of the lipid bilayer and the elastic properties of the erythrocyte cytoskeleton. In this model, three types of coarse-grained particles are introduced to represent clusters of lipid molecules, actin junctions, and band-3 complexes, respectively. The proposed model facilitates simulations that span large length scales (approximately micrometers) and timescales (approximately milliseconds). By tuning the interaction potential parameters, we were able to control the diffusivity and bending rigidity of the membrane model. We studied the membrane under shearing and found that at a low shear strain rate, the developed shear stress was due mainly to the spectrin network, whereas the viscosity of the lipid bilayer contributed to the resulting shear stress at higher strain rates. In addition, we investigated the effects of a reduced spectrin network connectivity on the shear modulus of the membrane.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Li H,Lykotrafitis Gdoi
10.1016/j.bpj.2011.11.4012subject
Has Abstractpub_date
2012-01-04 00:00:00pages
75-84issue
1eissn
0006-3495issn
1542-0086pii
S0006-3495(11)05363-Xjournal_volume
102pub_type
杂志文章abstract::The membrane protein bacteriorhodopsin (BR) can be kept soluble in its native state for months in the absence of detergent by amphipol (APol) A8-35, an amphiphilic polymer. After an actinic flash, A8-35-complexed BR undergoes a complete photocycle, with kinetics intermediate between that in detergent solution and that...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.121848
更新日期:2008-05-01 00:00:00
abstract::Epithelial injury induces rapid recruitment of antimicrobial leukocytes to the wound site. In zebrafish larvae, activation of the epithelial NADPH oxidase Duox at the wound margin is required early during this response. Before injury, leukocytes are near the vascular region, that is, ∼100-300 μm away from the injury s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.03.021
更新日期:2017-05-09 00:00:00
abstract::Using CD spectroscopy, guanine tetraplex formation was studied with short DNA fragments in which cytosine residues were systematically added to runs of guanine either at the 5' or 3' ends. Potassium cations induced the G-tetraplex more easily with fragments having the guanine run at the 5' end, which is just an opposi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78235-3
更新日期:1997-10-01 00:00:00
abstract::Annexins, found in most eukaryotic species, are cytosolic proteins that are able to bind negatively-charged phospholipids in a calcium-dependent manner. Annexin A4 (AnxA4) has been implicated in diverse cellular processes, including the regulation of exocytosis and ion-transport; however, its precise mechanistic role ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.02.057
更新日期:2013-05-07 00:00:00
abstract::We previously used an orthogonal high-throughput screen to select peptides that spontaneously cross synthetic lipid bilayers without bilayer disruption. Many of the 12-residue spontaneous membrane translocating peptides (SMTPs) selected from the library contained a 5-residue consensus motif, LRLLR in positions 5-9. We...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.06.070
更新日期:2017-08-22 00:00:00
abstract::The structure of the Bowman-Birk inhibitor from Vigna unguiculata seeds (BTCI) in complex with beta-trypsin was solved and refined at 1.55 A to a crystallographic R(factor) of 0.154 and R(free) of 0.169, and represents the highest resolution for a Bowman-Birk inhibitor structure to date. The BTCI-trypsin interface is ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.090555
更新日期:2007-03-01 00:00:00
abstract::The relevance of various residue positions for the stability and the folding characteristics of the prion protein in its normal cellular form are investigated by using molecular dynamics simulations of models exploiting the topology of the native state. These models allow for reproducing the experimentally validated t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75353-8
更新日期:2002-12-01 00:00:00
abstract::Polypeptide toxins isolated from the venom of cone snails, known as μ-conotoxins, block voltage-gated sodium channels by physically occluding the ion-conducting pathway. Using molecular dynamics, we show that one subtype of μ-conotoxins, PIIIA, effectively blocks the bacterial voltage-gated sodium channel Na(V)Ab, who...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.12.041
更新日期:2012-02-08 00:00:00
abstract::When a dissolved macromolecule is in chemical equilibrium with a free ionic species, the charge configuration, and hence the dipole vector, of the macromolecule is fluctuating. Expressions for the static dielectric constant and the relaxation spectrum of such a mixture are here derived in terms of the components of th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(65)86740-6
更新日期:1965-09-01 00:00:00
abstract::Equations are derived describing the dispersion of a permeable solute during Poiseuille flow in a capillary model. It is shown that for the normal range of physiological parameters such as capillary radius, capillary length, blood flow, permeability coefficients, and diffusion constants, the center of mass of a bolus ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(66)86637-7
更新日期:1966-01-01 00:00:00
abstract::The primary drivers of yeast endocytosis are actin polymerization and curvature-generating proteins, such as clathrin and BAR domain proteins. Previous work has indicated that these factors may not be capable of generating the forces necessary to overcome turgor pressure. Thus local reduction of the turgor pressure, v...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.10.040
更新日期:2016-12-20 00:00:00
abstract::The equation of motion for sperm flagella, in which the elastic bending moment and the active contractile moment are balanced by the moment from the viscous resistance of the surrounding fluid, is solved for a wave solution that superimposes partial solutions. Substitution of the expression for the wave solution into ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(78)85442-3
更新日期:1978-08-01 00:00:00
abstract::Endothelin-1 (ET-1) mediates physiological responses via endothelin A (ET(A)) and B (ET(B)) receptors, which may form homo- and heterodimers with unknown function. Here, we investigated ET-receptor dimerization using fluorescence resonance energy transfer (FRET) between receptors tagged with CFP (donor) and receptors ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.119206
更新日期:2008-07-01 00:00:00
abstract::To map the binding sites involved in channel formation, synthetic peptides representing sequences of connexin 32 were tested for their ability to inhibit cell-cell channel formation. Both large peptides representing most of the two presumed extracellular loops of connexin32 and shorter peptides representing subsets of...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80663-0
更新日期:1994-11-01 00:00:00
abstract::Little attention has been given to how the asymmetric lipid distribution of the plasma membrane might facilitate fusion pore formation during exocytosis. Phosphatidylethanolamine (PE), a cone-shaped phospholipid, is predominantly located in the inner leaflet of the plasma membrane and has been proposed to promote memb...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.09.014
更新日期:2017-11-07 00:00:00
abstract::Protein-mediated membrane remodeling is a ubiquitous and critical process for proper cellular function. Inverse Bin/Amphiphysin/Rvs (I-BAR) domains drive local membrane deformation as a precursor to large-scale membrane remodeling. We employ a multiscale approach to provide the molecular mechanism of unusual I-BAR dom...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.06.025
更新日期:2019-08-06 00:00:00
abstract::Calmodulin (CaM) is a highly flexible calcium-binding protein that mediates signal transduction through an ability to differentially bind to highly variable binding sequences in target proteins. To identify how binding affects CaM motions, and its relationship to conformational entropy and target peptide sequence, we ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.08.037
更新日期:2012-10-03 00:00:00
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
更新日期:1994-02-01 00:00:00
abstract::We describe simulations of absorption difference spectra in strongly coupled photosynthetic antennas. In the presence of large resonance couplings, distinctive features arise from excited-state absorption transitions between one- and two-exciton levels. We first outline the theory for the heterodimer and for the gener...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78644-2
更新日期:1997-01-01 00:00:00
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
更新日期:1986-04-01 00:00:00
abstract::Single-molecule imaging analysis of chemotactic response in eukaryotic cells has revealed a stochastic nature in the input signals and the signal transduction processes. This leads to a fundamental question about the signaling processes: how does the signaling system operate under stochastic fluctuations or noise? Her...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.100263
更新日期:2007-07-01 00:00:00
abstract::We characterized the effect of the first basepair on the conformational dynamics of the fluorescent dye Cy3 attached to the 5' end of double-stranded DNA using gaussian-mixture adaptive umbrella sampling simulations. In the simulations, the sampling of all five dihedral angles along the linker was enhanced, so that bo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.01.014
更新日期:2011-02-16 00:00:00
abstract::The development of strategies to measure plasma membrane osmotic water permeability (Pf) in epithelial cells has been motivated by the identification of a family of molecular water channels. A general approach utilizing interferometry to measure cell shape and volume was developed and applied to measure Pf in cell lay...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79546-2
更新日期:1996-12-01 00:00:00
abstract::Most of the cellular ATP in living organisms is synthesized by the enzyme F(1)F(o)-ATP synthase. The water soluble F(1) part of the enzyme can also work in reverse and utilize the chemical energy released during ATP hydrolysis to generate mechanical motion. Despite the availability of a large amount of biochemical dat...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74650-5
更新日期:2003-10-01 00:00:00
abstract::Intracellular reactions are carried out in a crowded medium where the macromolecules occupy ∼40% of the total volume. This decrease in the available volume affects the activity of the reactants. Scaled particle theory is used for the estimation of the activity coefficients of the metabolites, and thereby for the asses...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.09.030
更新日期:2015-12-01 00:00:00
abstract::FKBP12 was removed from ryanodine receptors (RyRs) by incubation of rabbit skeletal muscle terminal cisternae membranes with rapamycin. The extent of FKBP12 removal was estimated by immunostaining Western blots of terminal cisternae proteins. Single FKBP12-depleted RyR channels, incorporated into planar lipid bilayers...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78654-5
更新日期:1997-01-01 00:00:00
abstract::Calmodulin (CaM) is an intracellular cooperative calcium-binding protein essential for activating many diverse target proteins. Biophysical studies of the calcium-induced conformational changes of CaM disagree on the structure of the linker between domains and possible orientations of the domains. Molecular dynamics s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79535-8
更新日期:1996-12-01 00:00:00
abstract::We carried out experiments on single isolated myofibrils in which thin filaments had been functionally removed, leaving the connecting (titin) filaments as the sole agent taking up the length change. With technical advances that gave sub-nanometer detectability we examined the time course of single sarcomere-length ch...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75766-9
更新日期:2001-08-01 00:00:00
abstract::Mammalian sperm traverse several layers of egg vestments before fertilization can occur. The innermost vestment, the zona pellucida, is a glycoprotein shell, which captures and tethers the sperm before they penetrate it. We report here direct measurements of the force required to tether a motile human sperm as well as...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(88)83000-5
更新日期:1988-10-01 00:00:00
abstract::The photocycle of the photophobic receptor sensory rhodopsin II from N. pharaonis was analyzed by varying measuring wavelengths, temperature, and pH, and by exchanging H2O with D2O. The data can be satisfactorily modeled by eight exponents over the whole range of modified parameters. The kinetic data support a model s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77588-5
更新日期:1998-08-01 00:00:00