Abstract:
:Autoregulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic parameters of the main biochemical steps. These models differ according to 1) which subcellular processes are explicitly modeled, 2) the modeling methodology employed (discrete, continuous, or hybrid), and 3) whether they can be analytically solved for the steady-state distribution of protein numbers. We discuss the assumptions and properties of the main models in the literature, summarize our current understanding of the relationship between them, and highlight some of the insights gained through modeling.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Holehouse J,Cao Z,Grima Rdoi
10.1016/j.bpj.2020.02.016subject
Has Abstractpub_date
2020-04-07 00:00:00pages
1517-1525issue
7eissn
0006-3495issn
1542-0086pii
S0006-3495(20)30165-Xjournal_volume
118pub_type
杂志文章,评审abstract::Immunocytochemical, biochemical, and molecular genetic studies indicate that apolipoprotein E (apoE) plays an important role in the process of amyloidogenesis-beta. However, there is still no clear translation of these data into the pathogenesis of amyloidosis-beta. Previous studies demonstrated sodium dodecyl sulfate...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76354-5
更新日期:2000-08-01 00:00:00
abstract::Dendritic shaft (Zd) and spine (Zsp) input impedances were computed numerically for sites on hippocampal neurons, using a segmental format of cable calculations. The Zsp values for a typical spine appended onto a dendritic shaft averaged less than 2% higher than the Zd values for the adjacent dendritic shaft. Spine sy...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(84)84001-1
更新日期:1984-07-01 00:00:00
abstract::The depth of insertion of an antimicrobial peptide, protegrin-1 (PG-1), in lipid bilayers is investigated using solid-state NMR. Paramagnetic Mn(2+) ions bind to the surface of lipid bilayers and induce distance-dependent dipolar relaxation of nuclear spins. By comparing the signal dephasing of the peptide with that o...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74660-8
更新日期:2003-10-01 00:00:00
abstract::We present a truly quantitative fluorescence recovery after photobleaching (FRAP) model for use with the confocal laser scanning microscope based on the photobleaching of a long line segment. The line FRAP method is developed to complement the disk FRAP method reported before. Although being more subject to the influe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.099838
更新日期:2007-03-15 00:00:00
abstract::Coat protein (COP) I and COP II complexes are involved in the transport of proteins between the endoplasmic reticulum and the Golgi apparatus in eukaryotic cells. The formation of COP I/II complexes at membrane surfaces is an early step in vesicle formation and is mastered by p24, a type I transmembrane protein. Oligo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.09.021
更新日期:2019-11-05 00:00:00
abstract::A continuum model is provided of the free energy terms that contribute to the molecular association of ricin A-chain (RTA) with the rRNA substrate and several small ligands. The model for RTA interactions with the RNA was taken from a previously proposed complex containing a 29-mer oligonucleotide hairpin (. Proteins ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77175-4
更新日期:1999-01-01 00:00:00
abstract::We have examined the kinetics and thermodynamics of the exchange of a fluorescent amphiphile derived from a phospholipid, NBD-DMPE, between serum albumin and the serum lipoproteins of high density (HDL2 and HDL3), LDL, and VLDL. Binding of the fluorescent lipid amphiphile to bovine serum albumin is characterized, at 3...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.047050
更新日期:2005-01-01 00:00:00
abstract::Understanding the information processing ability of signal transduction pathways is of great importance because of their crucial roles in triggering various cellular responses. Despite continuing theoretical investigation, some important aspects of signal transduction such as a transient response and its connection to...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.070797
更新日期:2006-09-15 00:00:00
abstract::Hair cells of the inner ear can power spontaneous oscillations of their mechanosensory hair bundle, resulting in amplification of weak inputs near the characteristic frequency of oscillation. Recently, dynamic force measurements have revealed that delayed gating of the mechanosensitive ion channels responsible for mec...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.11.019
更新日期:2018-01-23 00:00:00
abstract::We study a differential equation that models nerve impulse transmission. The nonlinearity is simplified to be piecewise linear in order to allow explicit solution. In general, two solitary impulse solutions are exhibited. The temporal stability of these solutions is analyzed by a technique that identifies the number o...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(78)85511-8
更新日期:1978-02-01 00:00:00
abstract::In isolated thick filaments from many types of muscle, the two head domains of each myosin molecule are folded back against the filament backbone in a conformation called the interacting heads motif (IHM) in which actin interaction is inhibited. This conformation is present in resting skeletal muscle, but it is not kn...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.06.038
更新日期:2015-08-18 00:00:00
abstract::The crystal structure of the Mycobacterium tuberculosis homolog of the bacterial mechanosensitive channel of large conductance (Tb-MscL) provides a unique opportunity to consider mechanosensitive signal transduction at the atomic level. Molecular dynamics simulations of the Tb-MscL channel embedded in an explicit lipi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75791-8
更新日期:2001-09-01 00:00:00
abstract::Computer simulations suggest that the translocation of arginine through the hydrocarbon core of a lipid membrane proceeds by the formation of a water-filled defect that keeps the arginine molecule hydrated even at the center of the bilayer. We show here that adding additional arginine molecules into one of these water...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.05.038
更新日期:2011-07-06 00:00:00
abstract::The clustering of ryanodine receptors (RyR2) into functional Ca2+ release units is central to current models for cardiac excitation-contraction (E-C) coupling. Using immunolabeling and confocal microscopy, we have analyzed the distribution of RyR2 clusters in rat and ventricular atrial myocytes. The resolution of the ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.077180
更新日期:2006-07-01 00:00:00
abstract::Soft x-ray tomography (SXT) is increasingly being recognized as a valuable method for visualizing and quantifying the ultrastructure of cryopreserved cells. Here, we describe the combination of SXT with cryogenic confocal fluorescence tomography (CFT). This correlative approach allows the incorporation of molecular lo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.09.011
更新日期:2014-10-21 00:00:00
abstract::Detection of the transition between the two myosin isoforms α- and β-myosin in living cardiomyocytes is essential for understanding cardiac physiology and pathology. In this study, the differences in symmetry of polarization spectra obtained from α- and β-myosin in various mammalian ventricles and propylthiouracil-tre...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.12.030
更新日期:2020-03-10 00:00:00
abstract::Fluorescent probes in biological systems are sensitive to environmental polarity by virtue of their response to the reaction field created by polarization of the dielectric medium. Classically, fluorophore solvatochromism is analyzed in terms of the Lippert equation and later variants, all of which rely upon the origi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.01.006
更新日期:2009-04-08 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::Some plant leaves display complex, orientation-dependent, proton nuclear magnetic resonance (1H NMR) spectra. The spectral patterns vary as the angle between the leaf surface and the applied magnetic field is varied. They also vary with temperature and with the quantity of absorbed manganous ions, but they are indepen...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83826-1
更新日期:1985-11-01 00:00:00
abstract::Formation of low-temperature ordered gel phases in several fully hydrated phosphatidylethanolamines (PEs) and phosphatidylcholines (PCs) with saturated chains as well as in dipalmitoylphosphatidylglycerol (DPPG) was observed by synchrotron x-ray diffraction, microcalorimetry, and densitometry. The diffraction patterns...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76157-7
更新日期:2001-04-01 00:00:00
abstract::Artificial membrane systems allow researchers to study the structure and function of membrane proteins in a matrix that approximates their natural environment and to integrate these proteins in ex vivo devices such as electronic biosensors, thin-film protein arrays, or biofuel cells. Given that most membrane proteins ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.07.043
更新日期:2013-09-17 00:00:00
abstract::We used the nonlinear Poisson-Boltzmann equation to calculate electrostatic potentials in the aqueous phase adjacent to model phospholipid bilayers containing mixtures of zwitterionic lipids (phosphatidylcholine) and acidic lipids (phosphatidylserine or phosphatidylglycerol). The aqueous phase (relative permittivity, ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80253-5
更新日期:1995-03-01 00:00:00
abstract::Computer-assisted motion analysis coupled to flash photolysis of caged chemoeffectors provides a means for time-resolved analysis of bacterial chemotaxis. Escherichia coli taxis toward the amino acid attractant L-aspartate is mediated by the Tar receptor. The physiology of this response, as well as Tar structure and b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77329-7
更新日期:1999-03-01 00:00:00
abstract::Prion diseases are infectious fatal neurodegenerative diseases including Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy in cattle. The misfolding and conversion of cellular PrP in such mammals into pathogenic PrP is believed to be the key procedure. Rabbits are among the few mammalian species...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.08.018
更新日期:2011-09-21 00:00:00
abstract::Critical to biological processes such as secretion and transport, protein-lipid interactions within the membrane and at the membrane-water interface still raise many questions. Here we examine the role of lipid headgroups in these interactions by using gramicidin A (gA) channels in planar bilayers as a probe. We show ...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1529/biophysj.107.120261
更新日期:2008-02-15 00:00:00
abstract::Topical microbicide products are being developed for the prevention of sexually transmitted infections. These include vaginally-applied gels that deliver anti-HIV molecules. Gels may also provide partial barriers that slow virion diffusion from semen to vulnerable epithelium, increasing the time during which anti-HIV ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.08.010
更新日期:2009-11-04 00:00:00
abstract::Fluorescence fluctuation spectroscopy has become an important measurement tool for investigating molecular dynamics, molecular interactions, and chemical kinetics in biological systems. Although the basic theory of fluctuation spectroscopy is well established, it is not widely recognized that saturation of the fluores...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.052779
更新日期:2005-09-01 00:00:00
abstract::This work describes the first cell-based model of tumor-induced angiogenesis. At the extracellular level, the model describes diffusion, uptake, and decay of tumor-secreted pro-angiogenic factor. At the cellular level, the model uses the cellular Potts model based on system-energy reduction to describe endothelial cel...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.101501
更新日期:2007-05-01 00:00:00
abstract::Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped by dual-beam lasers and the other was held by a micropipette. Several experimen...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.094052
更新日期:2007-05-01 00:00:00
abstract::Interpretation of fluorescence anisotropy decay for the case of restricted rotational diffusion often requires a model. To investigate the extent of model dependence, two models are compared: a strict cone model, in which a fluorescent probe wobbles uniformly within a cone, and a Gaussian model, where the stationary d...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(82)84692-4
更新日期:1982-02-01 00:00:00