Abstract:
:Using molecular dynamics simulations, we examine the behavior of lipids whose preferred curvature can be systematically varied. This curvature is imposed by controlling the headgroup size of a coarse-grained lipid model recently developed by us. To validate this approach, we examine self-assembly of each individual lipid type and observe the complete range of expected bilayer and micelle phases. We then examine binary systems consisting of lipids with positive and negative preferred curvature and find a definite sorting effect. Lipids with positive preferred curvature are found in greater proportions in outer monolayers with the opposite observed for lipids with negative preferred curvature. We also observe a similar, but slightly stronger effect for lipids in a developing spherical bud formed by adhesion to a colloid (e.g., a viral capsid). Importantly, the magnitude of this effect in both cases was large only for regions with strong mean curvature (radii of curvature <10 nm). Our results suggest that lipid shape must act in concert with other physico-chemical effects such as phase transitions or interactions with proteins to produce strong sorting in cellular pathways.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Cooke IR,Deserno Mdoi
10.1529/biophysj.105.078683subject
Has Abstractpub_date
2006-07-15 00:00:00pages
487-95issue
2eissn
0006-3495issn
1542-0086pii
S0006-3495(06)71749-0journal_volume
91pub_type
杂志文章abstract::Purple membranes were adsorbed on freestanding lipid bilayers, termed nano-black lipid membranes (nano-BLMs), suspending the pores of porous alumina substrates with average pore diameters of 280 nm. Nano-BLMs were obtained by first coating the upper surface of the highly ordered porous alumina substrates with a thin g...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.059550
更新日期:2005-08-01 00:00:00
abstract::Mathematical models are increasingly important in biology, and testability is becoming a critical issue. One limitation is that one model simulation tests a parameter set representing one instance of the biological counterpart, whereas biological systems are heterogeneous in their properties and behavior, and a model ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.09.034
更新日期:2012-11-07 00:00:00
abstract::Total internal reflection (TIR) microfluorimetry was established as a method to measure continuously the volume of adherent cells and applied to measure membrane permeabilities in cells transfected with water channel homologs. Cytosol was labeled with the membrane-impermeant fluorophore calcein. Fluorescence was excit...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80335-8
更新日期:1995-04-01 00:00:00
abstract::In the plant blue-light sensor phototropin, illumination of the chromophoric LOV domains causes activation of the serine/threonine kinase domain. Flavin mononucleotide (FMN) is a chromophore molecule in the two LOV domains (LOV1 and LOV2), but only LOV2 is responsible for kinase activation. Previous studies reported a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.12.3924
更新日期:2009-04-08 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::The mechanisms that limit the speed at which striated muscles relax are poorly understood. This work presents, to our knowledge, novel simulations that show that the time course of relaxation is accelerated by interfilamentary movement resulting from series compliance; force drops faster when myosin heads move relativ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.12.024
更新日期:2016-02-02 00:00:00
abstract::The structural dynamics of bovine erythrocyte Cu, Zn superoxide dismutase (BSOD) was studied by time-resolved fluorescence spectroscopy. BSOD is a homodimer containing a single tyrosine residue (and no tryptophan) per subunit. Frequency-domain fluorometry revealed a heterogeneous fluorescence decay that could be descr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80901-4
更新日期:1994-04-01 00:00:00
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
更新日期:2011-09-07 00:00:00
abstract::This paper describes a framework model for proton conduction through gramicidin; a model designed to incorporate information from molecular dynamics and use this to predict conductance properties. The state diagram describes both motion of an excess proton within the pore as well as the reorientation of waters within ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75992-9
更新日期:2001-01-01 00:00:00
abstract::We use fluorescence correlation spectroscopy and fluorescence recovery after photobleaching to study vesicle dynamics inside the synapses of cultured hippocampal neurons labeled with the fluorescent vesicle marker FM 1-43. These studies show that when the cell is electrically at rest, only a small population of vesicl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.059295
更新日期:2005-11-01 00:00:00
abstract::Clathrin-coated membranes are precursors to coated vesicles in the receptor-mediated endocytic pathway. In this paper we present a physical model for the first steps of the transformation of a clathrin-coated membrane into a coated vesicle. The theory is based on in vitro cytoplasmic acidification experiments of Heuse...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77993-7
更新日期:1998-06-01 00:00:00
abstract::The adsorption of hydrophobic ions such as tetraphenylborate to thin lipid membranes is known to saturate at approximately 0.1 ion/(nm)2. This saturation can be quantitatively explained by electrostatic repulsion between the ions if they are treated as discrete, mobile particles that adsorb within the lipid at least p...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(82)84489-5
更新日期:1982-07-01 00:00:00
abstract::The propagation of sounds and pulse waves within the cardiovascular system is subject to strong dissipative mechanisms. To investigate the effects of blood viscosity on dissipation as well as dispersion of small waves in arteries and veins, a parametric study has been carried out. A linearized analysis of axisymmetric...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(71)86279-3
更新日期:1971-12-01 00:00:00
abstract::Cholesterol, due to its condensing effect, is considered an important regulator of membrane thickness. Other sterols, due to their structural similarities to cholesterol, are often assumed to have a universal effect on membrane properties similar to the condensing effect of cholesterol, albeit possibly to different de...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.04.003
更新日期:2016-05-10 00:00:00
abstract::Genetically identical cells exhibit diverse phenotypes even when experiencing the same environment. This phenomenon in part originates from cell-to-cell variability (noise) in protein expression. Although various kinetic schemes of stochastic transcription initiation are known to affect gene expression noise, how post...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.02.010
更新日期:2018-04-10 00:00:00
abstract::The structural features of SPM that control the transbilayer distribution of beta-GalCer in POPC vesicles were investigated by (13)C- and (31)P-NMR spectroscopy using lipid analogs that share physical similarities with GalCer or SPM. The SPM analogs included N-palmitoyl-4,5-dihydro-SPM, 3-deoxy-SPM, 1-alkyl-2-amidopho...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.057059
更新日期:2005-04-01 00:00:00
abstract::The resonance Raman spectrum of the second intermediate in the bacteriorhodopsin cycle, bL550, is obtained by a simple flow technique. The Schiff base linkage in this intermediate appears to be protonated, contrary to previous suggestion. The fingerprint region of the spectrum of bL550 does not closely match those of ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(79)85269-8
更新日期:1979-06-01 00:00:00
abstract::We have used anomalous small-angle x-ray scattering as a structural probe for solutions of rabbit parvalbumin labeled with terbium. This technique makes use of the large changes in the terbium scattering factor that occur when the x-ray energy is tuned around an L3 absorption edge of this heavy-atom label. These chang...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(83)84440-3
更新日期:1983-03-01 00:00:00
abstract::The selective permeability to monovalent metal cations, as well as the relationship between cation permeation and gating kinetics, was investigated for native tetrodotoxin-insensitive Na-channels in guinea pig ventricular myocytes using the whole-cell patch clamp technique. By the measurement of inward unidirectional ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77031-1
更新日期:1999-10-01 00:00:00
abstract::This study presents a simplified version of the quasi-one-dimensional theory (Wu, J., E. A. Johnson, and J. M. Kootsey. 1996. A quasi-one-dimensional theory for anisotropic propagation of excitation in cardiac muscle. Biophys. J. 71:2427-2439) with two components of the extracellular current, along and perpendicular t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78265-1
更新日期:1997-11-01 00:00:00
abstract::We measured the exocytotic response induced by flash photolysis of caged compounds in isolated mast cells and chromaffin cells. Vesicle fusion was measured by monitoring the cell membrane capacitance. The release of vesicular contents was followed by amperometry. In response to a GTP gamma S stimulus we found that the...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79315-3
更新日期:1996-08-01 00:00:00
abstract::The enzyme F1-adenosine triphosphatase (ATPase) is a molecular motor that converts the chemical energy stored in the molecule adenosine triphosphate (ATP) into mechanical rotation of its gamma-subunit. During steady-state catalysis, the three catalytic sites of F1 operate in a cooperative fashion such that at every in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.046128
更新日期:2004-11-01 00:00:00
abstract::In adherent and motile neutrophils NAD(P)H concentration, flavoprotein redox potential, and production of reactive oxygen species and nitric oxide, are all periodic and exhibit defined phase relationships to an underlying metabolic oscillation of approximately 20 s. Utilizing fluorescence microscopy, we have shown in ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.056663
更新日期:2005-05-01 00:00:00
abstract::In the rabbit corneal stroma, the swelling pressure, P, has been reported to have an anomalous (negative) temperature coefficient, alpha P, contradicting traditional Donnan swelling theory. A parallel-plate, diffuse double layer Gouy-Chapman model was used to resolve this discrepancy. The present model incorporates th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82584-4
更新日期:1990-03-01 00:00:00
abstract::Differential scanning calorimetry provides a new window into the plasma proteome. Plasma from normal individuals yields a characteristic, reproducible thermogram that appears to represent the weighted sum of denaturation profiles of the most abundant constituent plasma proteins. Plasma from diseased individuals yields...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.119453
更新日期:2008-02-15 00:00:00
abstract::Molecular dynamics simulations of RNA-protein complex between Escherichia coli loop E/helix IV (LE/HeIV) rRNA and L25 protein reveal a qualitative agreement between the experimental and simulated structures. The major groove of LE is a prominent rRNA cation-binding site. Divalent cations rigidify the LE major groove g...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.047126
更新日期:2004-11-01 00:00:00
abstract::The continuum and single jump treatments of ion transport through black lipid membranes predict experimentally distinguishable results, even when the same mechanistic assumptions are made and the same potential-distance profile is used. On the basis of steady-state current-voltage curves for nonactin-mediated transpor...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83766-8
更新日期:1985-07-01 00:00:00
abstract::A master equation theory is formulated to describe the dependence of the fluorescence yield (phi) in photosynthetic systems on the number of photons (Y) absorbed per photosynthetic unit (or domain). This theory is applied to the calculation of the dependence of the fluorescence yield on Y in (a) fluorescence induction...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(83)84278-7
更新日期:1983-10-01 00:00:00
abstract::A new method of fluorescence microscopy for cell imaging has been developed that takes advantage of the spatial variations of fluorescence lifetimes in single cells as a source of image contrast, and thus it is named "fluorescence lifetime imaging microscopy (flimscopy)". Since time-resolved fluorescence measurements ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81427-9
更新日期:1993-03-01 00:00:00
abstract::Experiments have shown that the ability of the HIV-1 virus to infect cells can be greatly diminished by deactivation of the N-terminal (fusion) peptide of its glycoprotein gp41. Deactivation can be achieved by the deletion of several amino acid residues, or replacement of a hydrophobic residue with a polar residue, to...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75313-7
更新日期:2002-12-01 00:00:00