Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations.

abstract：:A mode of internal motion of single tryptophan, Trp 86, of Streptomyces subtilisin inhibitor, was analyzed from its time-resolved fluorescence. The intensity and anisotropy decays of Trp 86 were measured in the picosecond range. These decays were analyzed with theoretical expressions derived assuming that the indole r...

journal_title：Biophysical journal

authors： Tanaka F,Tamai N,Mataga N,Tonomura B,Hiromi K

更新日期：1994-08-01 00:00:00

abstract：:The photocycle of the photophobic receptor sensory rhodopsin II from N. pharaonis was analyzed by varying measuring wavelengths, temperature, and pH, and by exchanging H2O with D2O. The data can be satisfactorily modeled by eight exponents over the whole range of modified parameters. The kinetic data support a model s...

journal_title：Biophysical journal

authors： Chizhov I,Schmies G,Seidel R,Sydor JR,Lüttenberg B,Engelhard M

更新日期：1998-08-01 00:00:00

abstract：:We used optical tweezers to analyze the effect of jasplakinolide and cyclodextrin on the force exerted by lamellipodia from developing growth cones (GCs) of isolated dorsal root ganglia (DRG) neurons. We found that 25 nM of jasplakinolide, which is known to inhibit actin filament turnover, reduced both the maximal exe...

journal_title：Biophysical journal

authors： Amin L,Ercolini E,Shahapure R,Migliorini E,Torre V

更新日期：2012-06-06 00:00:00

abstract：:We have used magnetic relaxation dispersion to study bovine pancreatic trypsin inhibitor (BPTI) self-association as a function of pH, salt type and concentration, and temperature. The magnetic relaxation dispersion method sensitively detects stable oligomers without being affected by other interactions. We find that B...

journal_title：Biophysical journal

authors： Gottschalk M,Venu K,Halle B

更新日期：2003-06-01 00:00:00

abstract：:A one-dimensional kinetic Ising model is developed to describe the binding of myosin subfragment 1 (SF-1) to regulated actin. The model allows for cooperative interactions between individual actin sites with bound SF-1 ligands rather than assuming that groups of actin monomer sites change their state in a cooperative ...

journal_title：Biophysical journal

authors： Balazs AC,Epstein IR

更新日期：1983-11-01 00:00:00

abstract：:As double-stranded DNA is stretched to its B-form contour length, models of polymer elasticity can describe the dramatic increase in measured force. When the molecule is stretched beyond this contour length, it shows a highly cooperative overstretching transition. We have measured the elasticity and overstretching tra...

journal_title：Biophysical journal

authors： Wenner JR,Williams MC,Rouzina I,Bloomfield VA

更新日期：2002-06-01 00:00:00

abstract：:Deuterium magnetic resonance is applied to the study of the liquid crystalline and gel phases, and of the phase transition, of a multilamellar dispersion of chain perdeuterated (d62)-dipalmitoyl phosphatidylcholine/H2O. Analysis of the deuterium spectra in terms of the moments of the spectra allows one to make quantit...

journal_title：Biophysical journal

authors： Davis JH

更新日期：1979-09-01 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

authors： Krishnamurthy S,Moorthy BS,Xin Xiang L,Xin Shan L,Bharatham K,Tulsian NK,Mihalek I,Anand GS

更新日期：2014-09-16 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

authors： Elmore DE,Dougherty DA

更新日期：2001-09-01 00:00:00

abstract：:Although ubiquitous, the processes by which bacteria colonize surfaces remain poorly understood. Here we report results for the influence of the wall shear stress on the early-stage adhesion of Pseudomonas aeruginosa PA14 on glass and polydimethylsiloxane surfaces. We use image analysis to measure the residence time o...

journal_title：Biophysical journal

authors： Lecuyer S,Rusconi R,Shen Y,Forsyth A,Vlamakis H,Kolter R,Stone HA

更新日期：2011-01-19 00:00:00

abstract：:Properties of filamentous acetamidofluorescein-labeled actin and acetamidotetramethylrhodamine-labeled actin (AF and ATR-actin, respectively) were examined to resolve discrepancies in the reported translational diffusion coefficients of F-actin measured in vitro by FPR and other techniques. Using falling-ball viscomet...

journal_title：Biophysical journal

authors： Simon JR,Gough A,Urbanik E,Wang F,Lanni F,Ware BR,Taylor DL

更新日期：1988-11-01 00:00:00

abstract：:Atrial fibrosis has been implicated in the development and maintenance of atrial arrhythmias, and is characterized by expansion of the extracellular matrix and an increased number of fibroblasts (Fbs). Electrotonic coupling between atrial myocytes and Fbs may contribute to the formation of an arrhythmogenic substrate....

journal_title：Biophysical journal

authors： Maleckar MM,Greenstein JL,Giles WR,Trayanova NA

更新日期：2009-10-21 00:00:00

abstract：:Influenza A virus M2 protein is known to form acid-activated, proton-selective, amantadine-sensitive channels. We directly measured proton uptake in vesicles containing reconstituted M2 by monitoring external pH after addition of valinomycin to vesicles with 100-fold-diluted external [K(+)]. External pH typically incr...

journal_title：Biophysical journal

authors： Moffat JC,Vijayvergiya V,Gao PF,Cross TA,Woodbury DJ,Busath DD

更新日期：2008-01-15 00:00:00

abstract：:Catch bonds are characterized by average lifetimes that initially increase with increasing tensile force. Recently, they have been implicated in T cell activation, where small numbers of antigenic receptor-ligand bonds at a cell-cell interface can stimulate a T cell. Here, we use computational methods to investigate s...

journal_title：Biophysical journal

authors： Pullen RH 3rd,Abel SM

更新日期：2017-07-11 00:00:00

abstract：:The detection of the 1H NMR signal of myoglobin (Mb) in tissue opens an opportunity to examine its cellular diffusion property, which is central to its purported role in facilitating oxygen transport. In perfused myocardium the field-dependent transverse relaxation analysis of the deoxy Mb proximal histidyl NdeltaH in...

journal_title：Biophysical journal

authors： Wang D,Kreutzer U,Chung Y,Jue T

更新日期：1997-11-01 00:00:00

abstract：:Monolayers prepared from myelin conserve all the compositional complexity of the natural membrane when spread at the air-water interface. They show a complex pressure-dependent surface pattern that, on compression, changes from the coexistence of two liquid phases to a viscous fractal phase embedded in a liquid phase....

journal_title：Biophysical journal

authors： Rosetti CM,Maggio B

更新日期：2007-12-15 00:00:00

abstract：:Despite growing interest in light-driven ion pumps for use in optogenetics, current estimates of their transport rates span two orders of magnitude due to challenges in measuring slow transport processes and determining protein concentration and/or orientation in membranes in vitro. In this study, we report, to our kn...

journal_title：Biophysical journal

authors： Feroz H,Ferlez B,Lefoulon C,Ren T,Baker CS,Gajewski JP,Lugar DJ,Gaudana SB,Butler PJ,Hühn J,Lamping M,Parak WJ,Hibberd JM,Kerfeld CA,Smirnoff N,Blatt MR,Golbeck JH,Kumar M

更新日期：2018-07-17 00:00:00

abstract：:We describe Franck-Condon simulations of vibrational cooling effects on absorption difference spectra in chlorophyll a (Chl a). The relative contributions of vibrational equilibration in the electronic ground and excited states depend on the pump and probe wavelengths. For Franck-Condon-active vibrational modes exhibi...

journal_title：Biophysical journal

authors： Struve WS

更新日期：1995-12-01 00:00:00

abstract：:Analyses of receptor-ligand interactions are important to the understanding of cellular adhesion. Traditional methods of measuring the three-dimensional (3D) dissociation constant (Kd) require at least one of the molecular species in solution and hence cannot be directly applied to the case of cell adhesion. We descri...

journal_title：Biophysical journal

authors： Piper JW,Swerlick RA,Zhu C

更新日期：1998-01-01 00:00:00

abstract：:For many cell types, growth, differentiation, and motility are dependent on receptor-mediated adhesion to ligand-coated surfaces. Focal contacts are strong, specialized, adhesive connections between cell and substrate in which receptors aggregate and connect extracellular ligand to intracellular cytoskeletal molecules...

journal_title：Biophysical journal

authors： Ward MD,Hammer DA

更新日期：1993-03-01 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

authors： Rostovtseva TK,Petrache HI,Kazemi N,Hassanzadeh E,Bezrukov SM

更新日期：2008-02-15 00:00:00

abstract：:We measured the influence of alternative versions of the Drosophila melanogaster myosin heavy chain relay domain on muscle mechanical properties. We exchanged relay domain regions (encoded by alternative versions of exon 9) between an embryonic (EMB) isoform and the indirect flight muscle isoform (IFI) of myosin. Prev...

journal_title：Biophysical journal

authors： Yang C,Ramanath S,Kronert WA,Bernstein SI,Maughan DW,Swank DM

更新日期：2008-12-01 00:00:00

abstract：:Information processing and decision-making is based upon logic operations, which in cellular networks has been well characterized at the level of transcription. In recent years, however, both experimentalists and theorists have begun to appreciate that cellular decision-making can also be performed at the level of a s...

journal_title：Biophysical journal

authors： de Ronde W,Rein ten Wolde P,Mugler A

更新日期：2012-09-05 00:00:00

abstract：:Photosystem II catalyzes photosynthetic water oxidation in plants, green algae, and cyanobacteria. The manganese-containing active site cycles through a series of five oxidation states, S(n), where n refers to the number of oxidizing equivalents stored. In this report, reaction-induced Fourier transform infrared and e...

journal_title：Biophysical journal

authors： Halverson KM,Barry BA

更新日期：2003-10-01 00:00:00

abstract：:The mating pathway in Saccharomyces cerevisiae is one of the best understood signal transduction pathways in eukaryotes. It transmits the mating signal from plasma membrane into the nucleus through the G-protein coupled receptor and the mitogen-activated protein kinase (MAPK) cascade. According to current understandin...

journal_title：Biophysical journal

authors： Shao D,Zheng W,Qiu W,Ouyang Q,Tang C

更新日期：2006-12-01 00:00:00

abstract：:Comparison of the electron spin resonance spectra of phosphatidylcholines spin-labeled in the sn-2 chain at a position close to the polar region and close to the methyl terminus indicate that symmetrical saturated diacyl phosphatidylcholines with odd and even chain lengths from 13 to 20 C-atoms (and probably also 12 C...

journal_title：Biophysical journal

authors： Swamy MJ,Marsh D

更新日期：1995-10-01 00:00:00

abstract：:Proteins must be stable to accomplish their biological function and to avoid enzymatic degradation. Constitutive proteolysis, however, is the main source of free amino acids used for de novo protein synthesis. In this paper the delicate balance of protein stability and degradability is discussed in the context of func...

journal_title：Biophysical journal

authors： Simon A,Dosztányi Zs,Rajnavölgyi E,Simon I

更新日期：2000-11-01 00:00:00

abstract：:A nitroxide spin label attached to the C-terminus of the channel forming peptide alamethicin produces an enhancement of the nuclear spin-lattice relaxation rates of peptide protons as a result of both intermolecular and intramolecular magnetic dipole-dipole interactions. The intermolecular contribution provides eviden...

journal_title：Biophysical journal

authors： North CL,Franklin JC,Bryant RG,Cafiso DS

更新日期：1994-11-01 00:00:00

abstract：:The antifungal polyene antibiotic amphotericin B forms channels in lipid membranes that are permeable to ions, water, and nonelectrolytes. Anion, cation, and ion pair coordination in the water-filled pore of the "barrel" unit of the channels was studied by molecular dynamics simulations. Unlike the case of the gramici...

journal_title：Biophysical journal

authors： Khutorsky V

更新日期：1996-12-01 00:00:00

abstract：:A simple method of simulating cell kinetics experiments, suitable for use on small generally available computers and capable of any degree of accuracy without increase of store required, is described. No assumption is necessary as to cycle-time distribution; the computer program, after being adjusted to generate perce...

journal_title：Biophysical journal

authors： Eaves G

更新日期：1972-11-01 00:00:00