Abstract:
:Aggregated Markov models are a widely used tool to model patch clamp data measured from single ion channels. These channels must obey the principle of detailed balance in thermodynamic equilibrium; otherwise, the channel is driven by an external source of energy. We investigate the power of a likelihood ratio test for detailed balance for a number of data points which is in the order of magnitude of patch clamp experiments. We show that for certain models with nearly equal dwell times, a test for detailed balance suffers from a loss of power to detect violations of detailed balance which is due to the non-identifiability of the transition rates for models with equal dwell times.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Wagner M,Timmer Jdoi
10.1016/S0006-3495(00)76529-5subject
Has Abstractpub_date
2000-12-01 00:00:00pages
2918-24issue
6eissn
0006-3495issn
1542-0086pii
S0006-3495(00)76529-5journal_volume
79pub_type
杂志文章abstract::A significant amount of work has been devoted to obtaining a detailed atomistic knowledge of the human hemoglobin mechanism. Despite this impressive research, to date, the ligand diffusion processes remain unclear and controversial. Using recently developed computational techniques, PELE, we are capable of addressing ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.01.011
更新日期:2012-02-22 00:00:00
abstract::In this article, optimization-based frameworks are introduced for elucidating the input-output structure of signaling networks and for pinpointing targeted disruptions leading to the silencing of undesirable outputs in therapeutic interventions. The frameworks are demonstrated on a large-scale reconstruction of a sign...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.069724
更新日期:2006-07-01 00:00:00
abstract::We present the results of a detailed molecular dynamics study of the closed form of the P2X4 receptor. The fluctuations observed in the simulations were compared with the changes that occur in the transition from the closed to the open structure. To get further insight on the opening mechanism, the actual displacement...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.10.027
更新日期:2016-12-20 00:00:00
abstract::Maintenance of paroxysmal atrial fibrillation (AF) by fast rotors in the left atrium (LA) or at the pulmonary veins (PVs) is not fully understood. To gain insight into this dynamic and complex process, we studied the role of the heterogeneous distribution of transmembrane currents in the PVs and LA junction (PV-LAJ) i...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.02.030
更新日期:2014-04-15 00:00:00
abstract::Synchronous neurotransmitter release is mediated by the opening of voltage-gated Ca(2+) channels and the build-up of submembrane Ca(2+) microdomains. Previous models of Ca(2+) microdomains have neglected possible electrostatic interactions between Ca(2+) ions and negative surface charges on the inner leaflet of the pl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.124909
更新日期:2008-09-01 00:00:00
abstract::Biological spread cells exist in a perpetually fluctuating state and therefore cannot be described in terms of a unique deterministic system. For modeling approaches to provide novel insight and uncover new mechanisms that drive cell behavior, a framework is required that progresses from traditional deterministic meth...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.11.007
更新日期:2018-12-18 00:00:00
abstract::Rhodobacter sphaeroides can swim toward a wide range of attractants (a process known as taxis), propelled by a single rotating flagellum. The reversals of motor direction that cause tumbles in Eschericia coli taxis are replaced by brief motor stops, and taxis is controlled by a complex sensory system with multiple hom...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76678-1
更新日期:2000-03-01 00:00:00
abstract::Ca2+ release from the endoplasmic reticulum (ER) contributes to Ca2+ transients in frog sympathetic ganglion neurons. Here we use video-rate confocal fluo-4 fluorescence imaging to show that single action potentials reproducibly trigger rapidly rising Ca2+ transients at 1-3 local hot spots within the peripheral ER-ric...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74094-1
更新日期:2004-01-01 00:00:00
abstract::We have formulated a kinetic model for the primary steps that occur at the cell membrane during receptor-mediated endocytosis. This model includes the diffusion of receptor molecules, the binding of receptors to coated pits, the loss of coated pits by invagination, and random reinsertion of receptors and coated pits. ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83879-0
更新日期:1985-01-01 00:00:00
abstract::An alternative theoretical approach to enzyme kinetics that is particularly applicable to single-molecule enzymology is presented. The theory, originated by Van Slyke and Cullen in 1914, develops enzyme kinetics from a "time perspective" rather than the traditional "rate perspective" and emphasizes the nonequilibrium ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.131771
更新日期:2008-07-01 00:00:00
abstract::Molecular dynamics simulations have been performed of the sequence-symmetric cyclic decapeptide antibiotic gramicidin S (GS), in interaction with a hydrated dimyristoylphosphatidylcholine (DMPC) bilayer, and the results compared with a "control" simulation of the system in the absence of GS. Following experimental evi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76424-1
更新日期:2000-10-01 00:00:00
abstract::Ataxin-1 is a human protein responsible for spinocerebellar ataxia type 1, a hereditary disease associated with protein aggregation and misfolding. Essential for ataxin-1 aggregation is the anomalous expansion of a polyglutamine tract near the protein N-terminus, but the sequence-wise distant AXH domain modulates and ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.01.048
更新日期:2013-03-19 00:00:00
abstract::Photosystem II contains two well-characterized tyrosine radicals, D(.) and Z(.). Z is an electron carrier between the primary chlorophyll donor and the manganese catalytic site and is essential for enzymatic function. On the other hand, D forms a stable radical with no known role in oxygen evolution. D(.) and Z(.) giv...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79394-3
更新日期:1996-10-01 00:00:00
abstract::EmrE is a small multidrug resistance transporter that has been well studied as a model for secondary active transport. Because transport requires the protein to convert between at least two states open to opposite sides of the membrane, it is expected that blocking these conformational transitions will prevent transpo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.06.030
更新日期:2014-08-05 00:00:00
abstract::Amantadine is known to block the M2 proton channel of the Influenza A virus. Here, we present a structure of the M2 trans-membrane domain blocked with amantadine, built using orientational constraints obtained from solid-state NMR polarization-inversion-spin-exchange-at-the-magic-angle experiments. The data indicates ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.090183
更新日期:2007-06-15 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::The cytoskeletal protein MreB is an essential component of the bacterial cell-shape generation system. Using a superresolution variant of total internal reflection microscopy with structured illumination, as well as three-dimensional stacks of deconvolved epifluorescence microscopy, we found that inside living Bacillu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.07.038
更新日期:2013-09-03 00:00:00
abstract::Protein conformational fluctuations modulate the catalytic powers of enzymes. The frequency of conformational fluctuations may modulate the catalytic rate at individual reaction steps. In this study, we modulated the rotary fluctuation frequency of F1-ATPase (F1) by attaching probes with different viscous drag coeffic...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.09.050
更新日期:2013-11-19 00:00:00
abstract::The triplet state absorption and phosphorescence of Zn and Pd derivatives of myoglobin were compared. Both metal derivatives exhibit long triplet state lifetimes at room temperature, but whereas the Pd derivative showed exponential decay and an isosbestic point in the transient absorption spectra, the decay of the Zn ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82363-8
更新日期:1990-07-01 00:00:00
abstract::A Green's function approach is used in constructing a dynamic model of a semi-infinite length of the DNA homopolymer B poly(d) . poly(d). Considerable attention is focused on the hydrogen bond stretching close to the terminus. A melting (or breathing) coordinate (M) is defined as an average over the three linking hydr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(81)84789-3
更新日期:1981-08-01 00:00:00
abstract::The goal of this paper is to examine the origins and relative importance of primary and secondary sources of electric and magnetic fields for excitable tissue. It is shown that for axonal and cardiac tissue a comparison of the relative field strength from both primary and secondary sources shows only the latter to be ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(82)84521-9
更新日期:1982-09-01 00:00:00
abstract::The primary processes of the photochemical cycle of light-adapted bacteriorhodopsin (BR) were studied by various experimental techniques with a time resolution of 5 x 10(-13) s. The following results were obtained. (a) After optical excitation the first excited singlet state S(1) of bacteriorhodopsin is observed via i...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(86)83692-X
更新日期:1986-03-01 00:00:00
abstract::Cellular membranes are laterally organized into domains of distinct structures and compositions by the differential interaction affinities between various membrane lipids and proteins. A prominent example of such structures are lipid rafts, which are ordered, tightly packed domains that have been widely implicated in ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.03.020
更新日期:2018-04-24 00:00:00
abstract::The early events in halorhodopsin after light excitation are studied with picosecond time resolution. Absorption and fluorescence measurements show that the electronically excited state of the incorporated retinal has a lifetime of 5 ps. Within that time a red-shifted photoproduct is formed that remains stable for at ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83876-5
更新日期:1985-01-01 00:00:00
abstract::The Ca(2+) permeability of N-methyl-D-aspartate receptor (NMDA-R) channels was studied in human embryonic kidney cells transfected with the NR1-NR2A subunit combination. To determine the fractional Ca(2+) current (P(f)), measurements of fura-2-based Ca(2+) influx and whole-cell currents were made in symmetrical monova...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79782-5
更新日期:1996-05-01 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::We successfully demonstrate the effectiveness of two-photon fluorescence cross-correlation spectroscopy (TPCCS) to study the complex binding stoichiometry of calmodulin (CaM) and Ca(2+)/CaM-dependent protein kinase II (CaMKII). Practical considerations are made for developing an intracellular cross-correlation assay, ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.055319
更新日期:2005-06-01 00:00:00
abstract::The well-characterized integral membrane protein lactose (lac) permease from Escherichia coli was reconstituted together with trace amounts (molar fraction X = 0.005 of the total phospholipid) of different pyrene-labeled phospholipid analogs into 1-palmitoyl-2-oleoyl-sn-glycero-3-sn-glycero-3-phospho-rac'-glycerol (PO...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78771-X
更新日期:1997-03-01 00:00:00
abstract::The biophysical characterization of nonfunctional protein aggregates at physiologically relevant temperatures is much needed to gain deeper insights into the kinetic and thermodynamic relationships between protein folding and misfolding. Dynamic and static laser light scattering have been employed for the detection an...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.070227
更新日期:2006-01-01 00:00:00
abstract::Frog skeletal muscle fibers, mechanically skinned under water-saturated silicone oil, swell upon transfer to aqueous relaxing medium (60 mM KCl; 3 mM MgCl(2); 3 mM ATP; 4 mM EGTA; 20 mM Tris maleate; pH = 7.0; ionic strength 0.15 M). Their cross-sectional areas, estimated with an elliptical approximation, increase 2.3...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(77)85573-2
更新日期:1977-08-01 00:00:00