Abstract:
:The single photon response in vertebrate phototransduction is highly reproducible despite a number of random components of the activation cascade, including the random activation site, the random walk of an activated receptor, and its quenching in a random number of steps. Here we use a previously generated and tested spatiotemporal mathematical and computational model to identify possible mechanisms of variability reduction. The model permits one to separate the process into modules, and to analyze their impact separately. We show that the activation cascade is responsible for generation of variability, whereas diffusion of the second messengers is responsible for its suppression. Randomness of the activation site contributes at early times to the coefficient of variation of the photoresponse, whereas the Brownian path of a photoisomerized rhodopsin (Rh*) has a negligible effect. The major driver of variability is the turnoff mechanism of Rh*, which occurs essentially within the first 2-4 phosphorylated states of Rh*. Theoretically increasing the number of steps to quenching does not significantly decrease the corresponding coefficient of variation of the effector, in agreement with the biochemical limitations on the phosphorylated states of the receptor. Diffusion of the second messengers in the cytosol acts as a suppressor of the variability generated by the activation cascade. Calcium feedback has a negligible regulatory effect on the photocurrent variability. A comparative variability analysis has been conducted for the phototransduction in mouse and salamander, including a study of the effects of their anatomical differences such as incisures and photoreceptors geometry on variability generation and suppression.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Bisegna P,Caruso G,Andreucci D,Shen L,Gurevich VV,Hamm HE,DiBenedetto Edoi
10.1529/biophysj.107.114058subject
Has Abstractpub_date
2008-05-01 00:00:00pages
3363-83issue
9eissn
0006-3495issn
1542-0086pii
94/9/3363journal_volume
94pub_type
杂志文章abstract::BP100 (KKLFKKILKYL-NH(2)) is a short cecropin A-melittin hybrid peptide, obtained through a combinatorial chemistry approach, which is highly effective in inhibiting both the in vitro and in vivo growth of economically important plant pathogenic Gram-negatives. The intrinsic Tyr fluorescence of BP100 was taken advanta...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.11.053
更新日期:2009-03-04 00:00:00
abstract::Membrane domains known as rafts are rich in cholesterol and sphingolipids, and are thought to be thicker than the surrounding membrane. If so, monolayers should elastically deform so as to avoid exposure of hydrophobic surfaces to water at the raft boundary. We calculated the energy of splay and tilt deformations nece...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.048223
更新日期:2005-02-01 00:00:00
abstract::The electric quadrupole moment of the deuterium nucleus provides a nuclear magnetic resonance (NMR) probe of electric field gradients, and thereby of organization of tissue water. 8-17% of H(2)O in rat muscle and brain was replaced by D(2)O from 50% deuterated drinking water. The peak height of the steady-state NMR sp...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(69)86388-5
更新日期:1969-03-01 00:00:00
abstract::Cyclic 3'5' adenosine monophosphate (cAMP)-dependent-protein kinase (PKA) signaling is a fundamental regulatory pathway for mediating cellular responses to hormonal stimuli. The pathway is activated by high-affinity association of cAMP with the regulatory subunit of PKA and signal termination is achieved upon cAMP dis...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.07.050
更新日期:2014-09-16 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::Previous studies have demonstrated a calcium-dependent interaction of calmodulin (CaM) and Fas that is regulated during Fas-induced apoptosis in several cell lines, including cholangiocarcinoma, Jurkat cells, and osteoclasts. The binding of CaM and Fas has been identified on residues 231-254 of Fas; the V254N point mu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.130542
更新日期:2008-12-15 00:00:00
abstract::Molecular dynamics simulations have been applied to the DNA octamer d(GCGCA-GAAC). d(GTTCGCGC), which has an adenine bulge at the center to determine the pathway for interconversion between the stacked and extended forms. These forms are known to be important in the molecular recognition of bulges. From a total of ~35...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75705-0
更新日期:2001-07-01 00:00:00
abstract::The opening and closing of the CFTR Cl- channel are regulated by ATP hydrolysis at its two nucleotide binding domains (NBDs). However, the mechanism and functional significance of ATP hydrolysis are unknown. Sequence similarity between the NBDs of CFTR and GTP-binding proteins suggested the NBDs might have a structure...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80113-X
更新日期:1995-12-01 00:00:00
abstract::Loss of myelin in the central nervous system (CNS) leads to debilitating neurological deficits. High-resolution optical imaging of myelin in the CNS of animal models is limited by a lack of in vivo myelin labeling strategies. We demonstrated that third harmonic generation (THG) microscopy-a coherent, nonlinear, dye-fr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.01.031
更新日期:2011-03-02 00:00:00
abstract::The photophysics of the complex forming reaction of Ca2+ and Fura-2 are investigated using steady-state and time-resolved fluorescence measurements. The fluorescence decay traces were analyzed with global compartmental analysis yielding the following values for the rate constants at room temperature in aqueous solutio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80285-7
更新日期:1995-03-01 00:00:00
abstract::The effect of salt and pH titration on the selectivity of spin-labeled analogues of phosphatidic acid, phosphatidylserine, phosphatidylcholine, and stearic acid for the nicotinic acetylcholine receptor (nAcChoR) reconstituted into dioleoylphosphatidylcholine was examined at 0 degrees C using electron spin resonance sp...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81422-X
更新日期:1993-03-01 00:00:00
abstract::Disruption of the integrity of the plasma membrane by amyloidogenic proteins is linked to the pathogenesis of a number of common age-related diseases. Although accumulating evidence suggests that adverse environmental stressors such as unbalanced levels of metal ions may trigger amyloid-mediated membrane damage, many ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.11.3811
更新日期:2013-01-08 00:00:00
abstract::The raft hypothesis proposes that microdomains enriched in sphingolipids, cholesterol, and specific proteins are transiently formed to accomplish important cellular tasks. Equivocally, detergent-resistant membranes were initially assumed to be identical to membrane rafts, because of similarities between their composit...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.04.039
更新日期:2014-06-03 00:00:00
abstract::We examined the effects of brief current pulses on the pacemaker oscillations of the Purkinje fiber using the model of McAllister , Noble, and Tsien (1975. J. Physiol. [Lond.]. 251:1-57). This model was used to construct phase-response curves for brief electric stimuli to find "black holes," where rhythmic activity of...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(84)84228-9
更新日期:1984-04-01 00:00:00
abstract::Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the calculation of the change in Gibbs energy of biochemical react...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.09.043
更新日期:2010-11-17 00:00:00
abstract::At low surface concentrations that permit formation of impermeable membranes, neuronal soluble N-ethyl maleimide sensitive factor attachment protein receptor (SNARE) proteins form a stable, parallel, trans complex when vesicles are brought into contact by a low concentration of poly(ethylene glycol) (PEG). Surprisingl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.069617
更新日期:2006-03-01 00:00:00
abstract::Intramolecular electron transfer between CuA and heme a in solubilized bacterial (Paracoccus denitrificans) cytochrome c oxidase was investigated by pulse radiolysis. CuA, the initial electron acceptor, was reduced by 1-methylnicotinamide radicals in a diffusion-controlled reaction, as monitored by absorption changes ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.075440
更新日期:2006-03-15 00:00:00
abstract::Phospholipids have been treated as dimers on a hexagonal lattice, and a move has been introduced that allows the dimers to move and change their orientation on the lattice. Simulations have been performed in which phospholipid chains have been treated as being either independent or infinitely coupled thermodynamically...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79261-5
更新日期:1996-08-01 00:00:00
abstract::Three features appear to characterize steady-state light adaptation in vertebrate cone photoreceptors: (a) the shape of the "log intensity-response" curve at different levels of adaptation is the same, the only change with adaptation is in the position of the point on the curve about which the cones operate; (b) at hi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(82)84502-5
更新日期:1982-08-01 00:00:00
abstract::Rearrangement of tertiary structure in response to mechanical force (termed tertiary structure elasticity) in the tandem Ig chain is the first mode of elastic response for muscle protein titin. Tertiary structure elasticity occurs at low stretching forces (few tens of pN), and was described at atomic resolution in a r...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1016/j.bpj.2011.01.019
更新日期:2011-02-16 00:00:00
abstract::In rat mesenteric arteries, smooth muscle cells exhibit intercellular calcium waves in response to local phenylephrine stimulation. These waves have a velocity of approximately 20 cells/s and a range of approximately 80 cells. We analyze these waves in a theoretical model of a population of coupled smooth muscle cells...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.04.031
更新日期:2010-07-21 00:00:00
abstract::We report detection and quantification of ultraviolet (UV) damage in DNA at a single molecule level by atomic force microscopy (AFM). By combining the supercoiled plasmid relaxation assay with AFM imaging, we find that high doses of medium wave ultraviolet (UVB) and short wave ultraviolet (UVC) light not only produce ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.108209
更新日期:2007-09-01 00:00:00
abstract::Equilibrium binding ligands usually increase protein thermal stability by an amount proportional to the concentration and affinity of the ligand. High-throughput screening for the discovery of drug-like compounds uses an assay based on thermal stabilization. The mathematical description of this stabilization is well d...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.134973
更新日期:2008-10-01 00:00:00
abstract::Nuclear transport receptors (NTRs) mediate nucleocytoplasmic transport via their affinity for unstructured proteins (polymers) in the nuclear pore complex (NPC). Here, we have modeled the effect of NTRs on polymeric structure in the nanopore confinement of the NPC central conduit. The model explicitly takes into accou...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.11.013
更新日期:2013-12-17 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::Formation of liquid-ordered domains in model membranes can be linked to raft formation in cellular membranes. The lipid stoichiometry has a governing influence on domain formation and consequently, biochemical hydrolysis of specific lipids has the potential to remodel domain features. Activation of phospholipase A(2) ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.114363
更新日期:2008-05-15 00:00:00
abstract::A recent thermodynamic model describes a reversible reaction between cholesterol (C) and phospholipid (P) to form a condensed complex C(nq)P(np). Here q and p are relatively prime integers used to define the stoichiometric composition, and n is a measure of cooperativity. The present study applies this model to the sc...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75920-6
更新日期:2001-11-01 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::Enveloped viruses must bind to a receptor on the host membrane to initiate infection. Membrane fusion is subsequently initiated by a conformational change in the viral fusion protein, triggered by receptor binding, an environmental change, or both. Here, we present a strategy to disentangle the two processes of recept...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.05.048
更新日期:2016-07-12 00:00:00
abstract::Ribosomes isolated from growing hyphae of Neurospora crassa contain 53 per cent protein and 47 per cent RNA and have a sedimentation coefficient of 81S at 20 degrees C and infinite dilution. These ribosomes are stable at pH 7.4 in the presence of 0.01 M and 0.002 M MgCl(2) but undergo a dissociation into smaller parti...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(63)86800-9
更新日期:1963-01-01 00:00:00