Abstract:
:Biological systems often have to measure extremely low concentrations of chemicals with high precision. When dealing with such small numbers of molecules, the inevitable randomness of physical transport processes and binding reactions will limit the precision with which measurements can be made. An important question is what the lower bound on the noise would be in such measurements. Using the theory of diffusion-influenced reactions, we derive an analytical expression for the precision of concentration estimates that are obtained by monitoring the state of a receptor to which a diffusing ligand can bind. The variance in the estimate consists of two terms, one resulting from the intrinsic binding kinetics and the other from the diffusive arrival of ligand at the receptor. The latter term is identical to the fundamental limit derived by Berg and Purcell (Biophys. J., 1977), but disagrees with a more recent expression by Bialek and Setayeshgar. Comparing the theoretical predictions against results from particle-based simulations confirms the accuracy of the resulting expression and reaffirms the fundamental limit established by Berg and Purcell.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Kaizu K,de Ronde W,Paijmans J,Takahashi K,Tostevin F,ten Wolde PRdoi
10.1016/j.bpj.2013.12.030subject
Has Abstractpub_date
2014-02-18 00:00:00pages
976-85issue
4eissn
0006-3495issn
1542-0086pii
S0006-3495(13)05847-5journal_volume
106pub_type
杂志文章abstract::To study why pancreatic beta-cells prefer to burst as a multi-cellular complex, we have formulated a stochastic model for bursting clusters of excitable cells. Our model incorporated a delayed rectifier K+ channel, a fast voltage-gated Ca2+ channel, and a slow Cai-blockable Ca2+ channel. The fraction of ATP-sensitive ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(88)82976-X
更新日期:1988-09-01 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::Titin is a giant filamentous polypeptide of multidomain construction spanning between the Z- and M-lines of the cardiac muscle sarcomere. Extension of the I-band segment of titin gives rise to a force that underlies part of the diastolic force of cardiac muscle. Titin's force arises from its extensible I-band region, ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77149-3
更新日期:1999-12-01 00:00:00
abstract::Steady state fluorescence polarization spectra and time-resolved emission decay kinetics have been measured in vitro from malignant and normal rat kidney tissue. The degrees of polarization and emission lifetimes from the cancerous and normal systems are different. The spectroscopic differences are attributed to envir...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(86)83483-X
更新日期:1986-09-01 00:00:00
abstract::Phosphorus-31 nuclear magnetic resonance (31P-NMR) spectra were obtained from living toad retinae and toad retinal extracts at 4 degrees C. Several phosphorus metabolites--nucleoside di- and triphosphates (NTP), phosphocreatine, phosphodiesters, inorganic phosphate, and phosphomonoesters--were identified from the spec...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(89)82691-8
更新日期:1989-09-01 00:00:00
abstract::Using homonuclear (1)H NOESY spectra, with chemical shifts, (3)JH(N)H(α) scalar couplings, residual dipolar couplings, and (1)H-(15)N NOEs, we have optimized and validated the conformational ensembles of the amyloid-β 1-40 (Aβ40) and amyloid-β 1-42 (Aβ42) peptides generated by molecular dynamics simulations. We find t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.04.056
更新日期:2013-06-18 00:00:00
abstract::Ceramides have been implicated in the initiation of apoptosis by permeabilizing the mitochondrial outer membrane to small proteins, including cytochrome c. In addition, ceramides were shown to form large metastable channels in planar membranes and liposomes, indicating that these lipids permeabilize membranes directly...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.071977
更新日期:2006-04-01 00:00:00
abstract::Choice of network topology for gene regulation has been a question of interest for a long time. How do simple and more complex topologies arise? In this work, we analyze the topology of the marRAB operon in Escherichia coli, which is associated with control of expression of genes associated with conferring resistance ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.08.017
更新日期:2015-10-06 00:00:00
abstract::Receptor activity modifying proteins (RAMPs) are a family of single-pass transmembrane proteins that dimerize with G-protein-coupled receptors. They may alter the ligand recognition properties of the receptors (particularly for the calcitonin receptor-like receptor, CLR). Very little structural information is availabl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.084582
更新日期:2006-07-15 00:00:00
abstract::Single-molecule studies allow the study of subtle activity differences due to local folding in proteins, but are time consuming and difficult because only a few molecules are observed in one experiment. We developed an assay where we can simultaneously measure the activity of hundreds of individual molecules. The assa...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.055053
更新日期:2005-06-01 00:00:00
abstract::Escherichia coli B phr(-), which is not photoreactivable under certain conditions, has been shown to exhibit photoreactivation of killing in the logarithmic growth phase at 3341 A. Dependence of the reaction upon (a) wavelength, (b) dose, and (c) dose rate of the reactivating radiation, as well as upon (d) temperature...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(65)86703-0
更新日期:1965-01-01 00:00:00
abstract::Cationic lipid-DNA (CL-DNA) complexes are abundantly used in nonviral gene therapy clinical applications. Surface functionality is the next step in developing these complexes as competent, target-specific gene carriers. Poly(ethylene glycol) (PEG) is the natural choice to serve as a protective coat or act as a tether ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74190-9
更新日期:2004-02-01 00:00:00
abstract::High-resolution measurement of membrane capacitance in the whole-cell-recording configuration can be used to detect small changes in membrane surface area that accompany exocytosis and endocytosis. We have investigated the noise of membrane capacitance measurements to determine the fundamental limits of resolution in ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76464-2
更新日期:2000-10-01 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::Fluorescent proteins are often used as reporters of transcriptional activity. Here we present a mathematical characterization of a novel fluorescent reporter that was recently engineered to have a short half-life (approximately 12 min). The advantage of this destabilized protein is that it can track the transient tran...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.122200
更新日期:2008-03-15 00:00:00
abstract::The susceptibility of the Neurospora crassa (slime) cellular membrane to electroporation and electrodestruction in an alternating electric field was further investigated. The results were analyzed according to the dynamic rheological model of the cytoplasmic membrane. Based on an analytical description of membrane sus...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79647-9
更新日期:1996-02-01 00:00:00
abstract::Alterations in bone tissue composition during osteoporosis likely disrupt the mechanical environment of bone cells and may thereby initiate a mechanobiological response. It has proved challenging to characterize the mechanical environment of bone cells in vivo, and the mechanical environment of osteoporotic bone cells...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.02.031
更新日期:2015-04-07 00:00:00
abstract::The mechanical properties of living cells are a label-free biophysical marker of cell viability and health; however, their use has been greatly limited by low measurement throughput. Although examining individual cells at high rates is now commonplace with fluorescence activated cell sorters, development of comparable...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.10.003
更新日期:2013-11-19 00:00:00
abstract::Gap junctions formed of connexin46 (Cx46) and connexin50 (Cx50) in lens fiber cells are crucial for maintaining lens transparency. We determined the functional properties of homotypic Cx46, heterotypic Cx46/Cx50, and heteromeric Cx46/Cx50 channels in a communication-deficient neuroblastoma (N2A) cell line, using dual ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76444-7
更新日期:2000-10-01 00:00:00
abstract::Many essential processes in eukaryotic cells depend on regulated molecular exchange between its two major compartments, the cytoplasm and the nucleus. In general, nuclear import of macromolecular complexes is dependent on specific peptide signals and their recognition by receptors that mediate translocation through th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.060160
更新日期:2005-09-01 00:00:00
abstract::In cardiac tissue, during partial blockade of the membrane sodium channels, or at high frequencies of excitation, inexcitable obstacles with sharp edges may destabilize the propagation of electrical excitation waves, causing the formation of self-sustained vortices and turbulent cardiac electrical activity. The format...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79691-1
更新日期:1996-03-01 00:00:00
abstract::We study the folding mechanism of a triple beta-strand WW domain from the Formin binding protein 28 (FBP28) at atomic resolution with explicit water model using replica exchange molecular dynamics computer simulations. Extended sampling over a wide range of temperatures to obtain the free energy, enthalpy, and entropy...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.076406
更新日期:2006-06-01 00:00:00
abstract::Trimethylamine-N-oxide (TMAO) in the cells of sharks and rays is believed to counteract the deleterious effects of the high intracellular concentrations of urea in these animals. It has been hypothesized that TMAO has the generic ability to counteract the effects of urea on protein structure and function, regardless o...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77972-X
更新日期:1998-05-01 00:00:00
abstract::The development of scanning probe techniques has made it possible to examine protein-protein interactions at the level of individual molecular pairs. A calibrated optical tweezers, along with immunoglobulin G (IgG)-coated polystyrene microspheres, has been used to detect individual surface-linked Staphylococcus protei...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76263-7
更新日期:2001-06-01 00:00:00
abstract::The GroE chaperonin system facilitates protein folding in an ATP-dependent manner. It has remained unclear why some proteins are obligate clients of the GroE system, whereas other closely related proteins are able to fold efficiently in its absence. Factors that cause folding to be slower affect kinetic partitioning b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.11.019
更新日期:2019-01-08 00:00:00
abstract::The CLC family of chloride channels and transporters is a functionally diverse group of proteins important in a wide range of physiological processes. ClC-4 and ClC-5 are localized to endosomes and seem to play roles in the acidification of these compartments. These proteins were recently shown to function as Cl(-)/H(...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.137158
更新日期:2008-11-15 00:00:00
abstract::Cardiac transverse (T)-tubules provide a specialized structure for synchronization and stabilization of sarcoplasmic reticulum Ca(2+) release in healthy cardiomyocytes. The application of laser scanning confocal microscopy and the use of fluorescent lipophilic membrane dyes have boosted the discoveries that T-tubule r...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.05.013
更新日期:2014-06-17 00:00:00
abstract::The nuclear magnetic resonance (NMR) of water protons in live and glycerinated muscle, suspensions of glycerinated myofibrils, and solutions of several muscle proteins has been studied. T(1) and T(2), measured on partially hydrated proteins by pulsed spin-echo techniques, decreased as the ratio of water to protein dec...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(71)86274-4
更新日期:1971-12-01 00:00:00
abstract::We have attempted to link the solution actomyosin ATPase with the mechanical properties of in vitro actin filament sliding over heavy meromyosin. To accomplish this we perturbed the system by altering the substrate with various NTPs and divalent cations, and by altering ionic strength. A wide variety of enzymatic and ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76022-5
更新日期:2001-01-01 00:00:00
abstract::Cationic liposomes (CLs) are used worldwide as gene vectors (carriers) in nonviral clinical applications of gene delivery, albeit with unacceptably low transfection efficiencies (TE). We present three-dimensional laser scanning confocal microscopy studies revealing distinct interactions between CL-DNA complexes, for b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)70055-1
更新日期:2003-05-01 00:00:00