Abstract:
:Normal left-right patterning in vertebrates depends on the rotational movement of nodal cilia. In order to produce this ciliary motion, the activity of axonemal dyneins must be tightly regulated in a temporal and spatial manner; the specific activation pattern of the dynein motors in the nodal cilia has not been reported. Contemporary imaging techniques cannot directly assess dynein activity in a living cilium. In this study, we establish a three-dimensional model to mimic the ciliary ultrastructure and assume that the activation of dynein proteins is related to the interdoublet distance. By employing finite-element analysis and grid deformation techniques, we simulate the mechanical function of dyneins by pairs of point loads, investigate the time-variant interdoublet distance, and simulate the dynein-triggered ciliary motion. The computational results indicate that, to produce the rotational movement of nodal cilia, the dynein activity is transferred clockwise (looking from the tip) between the nine doublet microtubules, and along each microtubule, the dynein activation should occur faster at the basal region and slower when it is close to the ciliary tip. Moreover, the time cost by all the dyneins along one microtubule to be activated can be used to deduce the dynein activation pattern; it implies that, as an alternative method, measuring this time can indirectly reveal the dynein activity. The proposed protein-structure model can simulate the ciliary motion triggered by various dynein activation patterns explicitly and may contribute to furthering the studies on axonemal dynein activity.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Chen D,Zhong Ydoi
10.1016/j.bpj.2015.05.027subject
Has Abstractpub_date
2015-07-07 00:00:00pages
35-48issue
1eissn
0006-3495issn
1542-0086pii
S0006-3495(15)00539-1journal_volume
109pub_type
杂志文章abstract::The thermophilic Bacillus caldolyticus cold shock protein (Bc-Csp) differs from the mesophilic Bacillus subtilis cold shock protein B (Bs-CspB) in 11 of the 66 residues. Stability measurements of Schmid and co-workers have implicated contributions of electrostatic interactions to the thermostability. To further elucid...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)75027-9
更新日期:2003-04-01 00:00:00
abstract::Thymine dimers were irradiated in aqueous solution with (60)Co gamma-rays in N(2) or O(2). Thymine and unidentified non-UV-absorbing products appeared. The thymine was identified by spectrophotometry, chromatography, and ability to support the growth of Escherichia coli 15 T(-). Residual dimer was determined by a UV-r...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(68)86491-4
更新日期:1968-03-01 00:00:00
abstract::Femtosecond time-resolved transient absorption spectroscopy was employed to characterize for the first time the primary photoisomerization dynamics of a bacterial phytochrome system in the two thermally stable states of the photocycle. The 85-kDa phytochrome Cph1 from the cyanobacterium Synechocystis PCC 6803 expresse...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75460-X
更新日期:2002-02-01 00:00:00
abstract::Iberiotoxin, a toxin purified from the scorpion Buthus tamulus is a 37 amino acid peptide having 68% homology with charybdotoxin. Charybdotoxin blocks large conductance Ca(2+)-activated K+ channels at nanomolar concentrations from the external side only (Miller, C., E. Moczydlowski, R. Latorre, and M. Phillips. 1985. ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81630-2
更新日期:1992-08-01 00:00:00
abstract::The strength of receptor-mediated cell adhesion is directly controlled by the mechanism of cohesive failure between the cell surface and underlying substrate. Unbinding can occur either at the locus of the specific bond or within the bilayer, which results in tearing the hydrophobic anchors from the membrane interior....
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)79990-8
更新日期:1995-09-01 00:00:00
abstract::Recently, several studies have shown that short doubled-stranded DNA (dsDNA) loops more readily than the wormlike chain model predicts. In most of these experiments, the intrinsic bendedness of dsDNA, which in theory can dramatically influence looping dynamics, was either avoided or unaccounted for. To investigate the...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.03.029
更新日期:2013-05-07 00:00:00
abstract::We have constructed a theory for diffusion through the pore of a single-ion channel by taking a limit of a random walk around a cycle of states. Similar to Levitt's theory of single-ion diffusion, one obtains boundary conditions for the Nernst-Planck equation that guarantee that the pore is occupied by at most one ion...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79374-8
更新日期:1996-10-01 00:00:00
abstract::This article describes the application of a change-point algorithm to the analysis of stochastic signals in biological systems whose underlying state dynamics consist of transitions between discrete states. Applications of this analysis include molecular-motor stepping, fluorophore bleaching, electrophysiology, partic...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.05.038
更新日期:2015-07-21 00:00:00
abstract::Directly measured forces between DNA helices in ordered arrays have been reduced to simple force coefficients and mathematical expressions for the interactions between pairs of molecules. The tabulated force parameters and mathematical expressions can be applied to parallel molecules or, by transformation, to skewed m...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80877-X
更新日期:1994-04-01 00:00:00
abstract::The conformation of ribosomal protein S4 from Escherichia coli has been studied by circular dichroism (CD) and shown to possess unique conformation free in solution. The near ultraviolet spectrum suggests the existence of unique tertiary structural environment for the aromatic amino acid residues. The far ultraviolet ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(78)85455-1
更新日期:1978-09-01 00:00:00
abstract::The retinal Na+:Ca2+, K+exchanger cDNA was transiently expressed in human embryonic kidney (HEK 293) cells by transfection with plasmid DNA. The correct targeting of the expressed protein to the plasma membrane was confirmed by immunocytochemistry. The reverse exchange offrent (Ca2+ imported per Na+ extruded) was meas...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78046-9
更新日期:1997-07-01 00:00:00
abstract::Cochlear outer hair cells undergo reversible changes in shape when externally stimulated. This response, known as OHC motility, is a central component of the cochlear amplifier, the mechanism responsible for the high sensitivity of mammalian hearing. We report that actin depolymerization, as regulated by activation/in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.08.015
更新日期:2010-10-06 00:00:00
abstract::A model for the action of vinblastine (VLB) on cells multiplying exponentially in vivo with a generation time, T(G), has been derived. It is based on the assumption that cells attempting to pass through mitosis in the presence of VLB lose their proliferative capacity and that this lethal effect occurs only when the ce...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(66)86646-8
更新日期:1966-03-01 00:00:00
abstract::Xenopus oocytes express mechanosensitive (MS(XO)) channels that can be studied in excised patches of membrane with the patch-clamp technique. This study examines the steady-state kinetic gating properties of MS(XO) channels using detailed single-channel analysis. The open and closed one-dimensional dwell-time distribu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75857-2
更新日期:2001-10-01 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::Filopodia perform cellular functions such as environmental sensing or cell motility, but they also grab for particles and withdraw them leading to an increased efficiency of phagocytic uptake. Remarkably, withdrawal of micron-sized particles is also possible without noticeable movements of the filopodia. Here, we demo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.02.029
更新日期:2015-05-05 00:00:00
abstract::The kinetics of conformational changes of P-type ATPases necessary for the occlusion or deocclusion of transported ions are known to be sensitive to the composition of the surrounding membrane, e.g., phospholipid content, mole percentage of cholesterol, and the presence of lipid-bound anions. Research has shown that m...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2015.08.022
更新日期:2015-10-20 00:00:00
abstract::Na(+) conductance through cloned K(+) channels has previously allowed characterization of inactivation and K(+) binding within the pore, and here we have used Na(+) permeation to study recovery from C-type inactivation in human Kv1.5 channels. Replacing K(+) in the solutions with Na(+) allows complete Kv1.5 inactivati...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76486-1
更新日期:2000-11-01 00:00:00
abstract::The T-cell actin cytoskeleton mediates adaptive immune system responses to peptide antigens by physically directing the motion and clustering of T-cell receptors (TCRs) on the cell surface. When TCR movement is impeded by externally applied physical barriers, the actin network exhibits transient enrichment near the tr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.06.031
更新日期:2013-08-06 00:00:00
abstract::Structural transition can be induced in charged micelles by increasing the ionic strength of the medium. We have monitored the organization and dynamics of the functionally important tryptophan residues of gramicidin in spherical and rod-shaped sodium dodecyl sulfate micelles utilizing a combination of wavelength-sele...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.060798
更新日期:2005-11-01 00:00:00
abstract::The fluorescent Mg(2+) indicator furaptra (mag-fura-2) was introduced into single ventricular myocytes by incubation with its acetoxy-methyl ester form. The ratio of furaptra's fluorescence intensity at 382 and 350 nm was used to estimate the apparent cytoplasmic [Mg(2+)] ([Mg(2+)](i)). In Ca(2+)-free extracellular co...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.055517
更新日期:2005-03-01 00:00:00
abstract::The extracellular matrix contains components with remarkable mechanical properties, including fibronectin (Fn) fibers with extensibilities of >700% strain. We utilized what we consider a novel technique to quantify the extent of molecular unfolding that contributes to Fn fiber extension, and we compared this behavior ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.08.029
更新日期:2011-10-05 00:00:00
abstract::Calculations are reported of the time-dependent Nernst-Planck equations for a thin permeable membrane between electrolytic solutions. Charge neutrality is assumed for the time-dependent case. The response of such a membrane system to step current input is measured in terms of the time and space changes in concentratio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(65)86707-8
更新日期:1965-03-01 00:00:00
abstract::Entropy Sampling Monte Carlo (ESMC) simulations were carried out to study the thermodynamics of the folding transition in the GCN4 leucine zipper (GCN4-lz) in the context of a reduced model. Using the calculated partition functions for the monomer and dimer, and taking into account the equilibrium between the monomer ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)76872-4
更新日期:1999-07-01 00:00:00
abstract::The participation of amino-terminal domains in human ether-a-go-go (eag)-related gene (HERG) K(+) channel gating was studied using deleted channel variants expressed in Xenopus oocytes. Selective deletion of the HERG-specific sequence (HERG Delta138-373) located between the conserved initial amino terminus (the eag or...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76286-2
更新日期:2000-07-01 00:00:00
abstract::Fluorescence recovery after photobleaching (FRAP) is a powerful technique to study molecular dynamics inside living cells. During the past years, several laboratories have used FRAP to image the motion of RNA-protein and other macromolecular complexes in the nucleus and cytoplasm. In the case of mRNAs, there is growin...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.096693
更新日期:2007-04-15 00:00:00
abstract::Simulations of two distinct systems, one a planar bilayer, the other the inverse hexagonal phase, indicate consistent mechanical properties and curvature preferences, with single DOPE leaflets having a spontaneous curvature, R0 = -26 Å (experimentally ~ -29.2 Å) and DOPC leaflets preferring to be approximately flat (R...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.03.048
更新日期:2013-05-21 00:00:00
abstract::Computational methods that predict three-dimensional structures from amino acid sequences have become increasingly accurate and have provided insights into structure-function relationships for proteins in the absence of structural data. However, the accuracy of computational structural models requires experimental app...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74251-4
更新日期:2004-03-01 00:00:00
abstract::Using the substituted-cysteine-accessibility method, we previously showed that a cysteine residue introduced to the Y512 position of CLC-0 was more rapidly modified by a negatively charged methanethiosulfonate (MTS) reagent, 2-sulfonatoethyl MTS (MTSES), than by the positively charged 2-(trimethylammonium)ethyl MTS (M...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.09.066
更新日期:2010-02-03 00:00:00
abstract::The suprachiasmatic nucleus governs daily variations of physiology and behavior in mammals. Within single neurons, interlocked transcriptional/translational feedback loops generate circadian rhythms on the molecular level. We present a mathematical model that reflects the essential features of the mammalian circadian ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.040824
更新日期:2004-11-01 00:00:00