Abstract:
:A model is presented for the steric interaction between a plasma membrane protein and the membrane cytoskeleton in the human erythrocyte. The cytoskeleton is treated as a network of polymer chains attached to a flat bilayer, and the membrane protein is a hemisphere of effective radius R(e) with center on the bilayer edge. The simulation is used to investigate the barrier-free path L for linear guided motion of a protein in the bilayer plane. It is shown that the barrier-free paths of small proteins can be used to extract the effective in-plane diameter of cytoskeletal components. For example, the in-plane diameter of an ankyrin attachment site is found to be approximately 12 nm in the simulation, or twice the computational spectrin diameter. The barrier-free paths of large proteins (R(e) > 23 nm) vanish when the proteins are corralled by the cytoskeleton. For intermediate size proteins, L decreases approximately as L is directly proportional to S-1.4 where S is proportional to the sum of the protein and cytoskeleton chain radii.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Boal DH,Boey SKdoi
10.1016/S0006-3495(95)79909-Xsubject
Has Abstractpub_date
1995-08-01 00:00:00pages
372-9issue
2eissn
0006-3495issn
1542-0086pii
S0006-3495(95)79909-Xjournal_volume
69pub_type
杂志文章abstract::At present, fluorescence recovery after photobleaching (FRAP) data are interpreted using various types of reaction-diffusion (RD) models: the model type is usually fixed first, and corresponding model parameters are inferred subsequently. In this article, we describe what we believe to be a novel approach for RD model...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.01.041
更新日期:2011-03-02 00:00:00
abstract::It has been shown in previous studies that cell poration (i.e., reversible permeabilization of cell membrane) and cell fusion can be induced by applying a pulse (or pulses) of high-intensity DC (direct current) electric field. Recently we suggested that such electro-poration or electro-fusion can also be accomplished ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(89)82711-0
更新日期:1989-10-01 00:00:00
abstract::This paper describes an analysis of microscopic models for the coupling between ion flow and rotation of bacterial flagella. In model I it is assumed that intersecting half-channels exist on the rotor and the stator and that the driving ion is constrained to move together with the intersection site. Model II is based ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(88)83065-0
更新日期:1988-01-01 00:00:00
abstract::Molecular chaperones are large proteins or protein complexes from which many proteins require assistance in order to fold. One unique property of molecular chaperones is the cavity they provide in which proteins fold. The interior surface residues which make up the cavities of molecular chaperone complexes from differ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.10.040
更新日期:2012-12-19 00:00:00
abstract::Fusion of a vesicle with its target membrane is preceded by tethering or docking. However, the physical mechanism of vesicle-tethering is unknown. To study this mechanism, we used eosinophil secretory granules, which undergo stimulated homotypic fusion events inside the cell during degranulation. Using a dual optical ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.132670
更新日期:2008-11-15 00:00:00
abstract::The stoichiometric matrix, S, represents a mapping of reaction rate vectors into a space of concentration time derivatives. The left null space of the stoichiometric matrix contains the dynamic invariants: a combination of concentration variables, referred to as metabolic pools, whose total concentration does not chan...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74450-6
更新日期:2003-07-01 00:00:00
abstract::Biological membranes composed of lipids and proteins are in contact with electrolytes like aqueous NaCl solutions. Based on molecular dynamics studies it is widely believed that Na(+) ions specifically bind to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes, whereas Cl(-) ions stay in solution. Here,...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.12.056
更新日期:2013-02-19 00:00:00
abstract::The effect of antibodies to glycophorin A on the rotational diffusion of band 3 in human erythrocyte membranes was investigated by transient dichrosim. Three antibodies that recognize different epitopes on the exofacial domain of glycophorin A all strongly reduce the rotational mobility of band 3. The effect is at mos...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80365-6
更新日期:1995-05-01 00:00:00
abstract::We have used magnetic relaxation dispersion to study bovine pancreatic trypsin inhibitor (BPTI) self-association as a function of pH, salt type and concentration, and temperature. The magnetic relaxation dispersion method sensitively detects stable oligomers without being affected by other interactions. We find that B...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)75122-4
更新日期:2003-06-01 00:00:00
abstract::We have monitored the organization and dynamics of the hemolytic peptide melittin in membranes containing cholesterol by utilizing the intrinsic fluorescence properties of its functionally important sole tryptophan residue and circular dichroism spectroscopy. The significance of this study is based on the fact that th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.043596
更新日期:2004-10-01 00:00:00
abstract::A general analytical description of the equilibrium and reaction kinetics of DNA multiplex hybridization has been developed. In this approach, multiplex hybridization is considered to be a competitive multichannel reaction process: a system wherein many species can react both specifically and nonspecifically with one ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.090662
更新日期:2006-12-01 00:00:00
abstract::A major challenge in synthetic gene delivery is to quantitatively predict the optimal design of polymer-based gene carriers (polyplexes). Here, we report a consistent, integrated, and fundamentally grounded computational methodology to address this challenge. This is achieved by accurately representing the spatio-temp...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.095521
更新日期:2007-02-01 00:00:00
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
更新日期:2009-02-18 00:00:00
abstract::Protein-mediated DNA looping, such as that induced by the lactose repressor (LacI) of Escherichia coli, is a well-known gene regulation mechanism. Although researchers have given considerable attention to DNA looping by LacI, many unanswered questions about this mechanism, including the role of protein flexibility, re...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.06.040
更新日期:2011-08-03 00:00:00
abstract::Many signaling pathways act through shared components, where different ligand molecules bind the same receptors or activate overlapping sets of response regulators downstream. Nevertheless, different ligands acting through cross-wired pathways often lead to different outcomes in terms of the target cell behavior and f...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1016/j.bpj.2016.07.029
更新日期:2016-09-06 00:00:00
abstract::The effect of Ca ion concentration on cross-bridge kinetics in a small bundle (one to three fibers) of chemically skinned rabbit psoas muscle is studied. The length of the muscle is oscillated in small amplitude sine waves (0.2% L0 peak-to-peak) at varying frequencies (0.125 -- 167 Hz), and the resulting amplitude and...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(81)84796-0
更新日期:1981-08-01 00:00:00
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
更新日期:2003-02-01 00:00:00
abstract::Catch bonds are characterized by average lifetimes that initially increase with increasing tensile force. Recently, they have been implicated in T cell activation, where small numbers of antigenic receptor-ligand bonds at a cell-cell interface can stimulate a T cell. Here, we use computational methods to investigate s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.05.023
更新日期:2017-07-11 00:00:00
abstract::Several biologically important protein structures give rise to strong second-harmonic generation (SHG) in their native context. In addition to high-contrast optical sections of cells and tissues, SHG imaging can provide detailed structural information based on the physical constraints of the optical effect. In this st...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.071555
更新日期:2006-01-15 00:00:00
abstract::A model for the Na-K exchange pump was applied to data on Na(+)-loaded frog sartorius muscle, and was used to relate the rate of adenosine triphosphate (ATP) hydrolysis to the electrical properties of the cell membrane. Membrane hyperpolarization was considered to arise from an electrical current which was produced by...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(71)86243-4
更新日期:1971-08-01 00:00:00
abstract::The statistical mechanics of cross-bridge action is considered in order to develop constitutive equations that express fiber tension as a function of degree of activation and time history of speed of contraction. The kinetic equation of A.F. Huxley (1) is generalized to apply to the partially activated state. The rate...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(85)83895-9
更新日期:1985-02-01 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::We investigate the validity of continuum electrostatics in the gramicidin A channel using a recently determined high-resolution structure. The potential and electric field acting on ions in and around the channel are computed by solving Poisson's equation. These are then used in Brownian dynamics simulations to obtain...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)73905-2
更新日期:2002-09-01 00:00:00
abstract::Ion channels and transporters are membrane proteins whose functions are driven by conformational changes. Classical biophysical techniques provide insight into either the structure or the function of these proteins, but a full understanding of their behavior requires a correlation of both these aspects in time. Patch-...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2014.02.006
更新日期:2014-03-18 00:00:00
abstract::A variety of amphiphilic helical peptides have been shown to exhibit a transition from adsorbing parallel to a membrane surface at low concentrations to inserting perpendicularly into the membrane at high concentrations. Furthermore, this transition has been correlated to the peptides' cytolytic activities. X-ray lame...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80418-2
更新日期:1995-06-01 00:00:00
abstract::We have used the elastic neutron scattering technique to investigate the dynamics of the two main saccharidic components of starch: amylose and amylopectin. The measurements were carried out in the temperature range of 20 to 320 K and at different hydration levels from the dry state up to 0.47 g saccharide/g D(2)O. In...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75776-1
更新日期:2001-08-01 00:00:00
abstract::The functional diversity of gap junction intercellular channels arising from the large number of connexin isoforms is significantly increased by heterotypic interactions between members of this family. This is particularly evident in the rectifying behavior of Cx26/Cx32 heterotypic channels (. Proc. Natl. Acad. Sci. U...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77129-8
更新日期:1999-12-01 00:00:00
abstract::The power spectrum of current fluctuations and the complex admittance of squid axon were determined in the frequency range 12.5 to 5,000 Hx during membrane voltage clamps to the same potentials in the same axon during internal perfusion with cesium. The complex admittance was determined rapidly and with high resolutio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(83)84353-7
更新日期:1983-09-01 00:00:00
abstract::We developed a multicellular model characterized by a high degree of heterogeneity to investigate possible mechanisms that underlie circadian network synchronization and rhythmicity in the suprachiasmatic nucleus (SCN). We populated a two-dimensional grid with 400 model neurons coupled via γ-aminobutyric acid (GABA) a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.04.051
更新日期:2011-07-06 00:00:00
abstract::Phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) are the main lipid components of the inner bacterial membrane. A computer model for such a membrane was built of palmitoyloleoyl PE (POPE) and palmitoyloleoyl PG (POPG) in the proportion 3:1, and sodium ions (Na+) to neutralize the net negative charge on each...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.048835
更新日期:2005-02-01 00:00:00