Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains.

abstract：:The coupling between the mechanical properties of enzymes and their biological activity is a well-established feature that has been the object of numerous experimental and theoretical works. In particular, recent experiments show that enzymatic function can be modulated anisotropically by mechanical stress. We study s...

journal_title：Biophysical journal

authors： Sacquin-Mora S,Delalande O,Baaden M

更新日期：2010-11-17 00:00:00

abstract：:An interactive program is described for calculating the second virial coefficient contribution to the thermodynamic nonideality of solutions of rigid macromolecules based on their triaxial dimensions. The FORTRAN-77 program, available in precompiled form for the PC, is based on theory for the covolume of triaxial elli...

journal_title：Biophysical journal

authors： Harding SE,Horton JC,Jones S,Thornton JM,Winzor DJ

更新日期：1999-05-01 00:00:00

abstract：:To investigate the properties of a pure liquid ordered (Lo) phase in a model membrane system, a series of saturated phosphatidylcholines combined with cholesterol were examined by variable temperature multinuclear (1H, 2H, 13C, 31P) solid-state NMR spectroscopy and x-ray scattering. Compositions with cholesterol conce...

journal_title：Biophysical journal

authors： Clarke JA,Heron AJ,Seddon JM,Law RV

更新日期：2006-04-01 00:00:00

abstract：:Crystals have been grown of "sperm whale" myoglobin produced in Escherichia coli from a synthetic gene and the structure has been solved to 1.9 A resolution. Because of a remaining initiator methionine, this protein crystallizes in a different space group from native sperm whale myoglobin. The three-dimensional struct...

journal_title：Biophysical journal

authors： Phillips GN Jr

更新日期：1990-02-01 00:00:00

abstract：:A block normal mode (BNM) algorithm, originally proposed by Tama et al., (Proteins Struct. Func. Genet. 41:1-7, 2000) was implemented into the simulation program CHARMM. The BNM approach projects the hessian matrix into local translation/rotation basis vectors and, therefore, dramatically reduces the size of the matri...

journal_title：Biophysical journal

authors： Li G,Cui Q

更新日期：2002-11-01 00:00:00

abstract：:Hypothetical hydroxide and proton migration along the linear water chain in Aquaporin GlpF from Escherichia coli are studied by ab initio Car-Parrinello molecular dynamics simulations. It is found that the protein stabilizes a bipolar single file of water. The single file features a contiguous set of water-water hydro...

journal_title：Biophysical journal

authors： Jensen MØ,Röthlisberger U,Rovira C

更新日期：2005-09-01 00:00:00

abstract：:The role of cholesterol in the regulation of endosome motility was investigated by monitoring the intracellular trafficking of endocytosed folate receptors (FRs) labeled with fluorescent folate conjugates. Real-time fluorescence imaging of HeLa cells transfected with green fluorescent protein-tubulin revealed that FR-...

journal_title：Biophysical journal

authors： Chen H,Yang J,Low PS,Cheng JX

更新日期：2008-02-15 00:00:00

abstract：:Cysteine residues introduced by site-directed mutagenesis have been used to probe the conformation and dynamics of two receptors in the E. coli chemotaxis pathway. (a) Thermal motions of the polypeptide backbone were investigated in the periplasmic D-galactose and D-glucose receptor, a globular protein of known struct...

journal_title：Biophysical journal

authors： Careaga CL,Falke JJ

更新日期：1992-04-01 00:00:00

abstract：:Despite the enormous interest that has been devoted to the study of farnesyltransferase, many questions concerning its catalytic mechanism remain unanswered. In particular, several doubts exist on the structure of the active-site zinc coordination sphere, more precisely on the nature of the fourth ligand, which is dis...

journal_title：Biophysical journal

authors： Sousa SF,Fernandes PA,Ramos MJ

更新日期：2005-01-01 00:00:00

abstract：:Synthetic filaments prepared from column-purified rabbit skeletal myosin by slow dialysis exhibit characteristic bipolar organization and 14-nm axial subunit spacing. Backbone substructure can be discerned in high resolution micrographs in the form of striations of 3--4-nm width and slight angular tilt from the direct...

journal_title：Biophysical journal

authors： Koretz JF

更新日期：1979-09-01 00:00:00

abstract：:Small RNA-mRNA binding is an essential step in RNA interference, an important cellular regulatory process. Calculations of binding free energy have been used in binding site prediction, but the cost of stretching the mRNA loop when the small RNA-mRNA duplex forms requires further exploration. Here, using both polymer ...

journal_title：Biophysical journal

authors： Meng Y,Aalberts DP

更新日期：2013-01-22 00:00:00

abstract：:A kinetic analysis of membrane conductance under conditions of stationary flow is presented. The semipermeable membrane is idealized as a homogeneous laminar phase separating ionic solutions on either side. It is assumed, without consideration of the mechanisms involved, that some ion species permeate the membrane whi...

journal_title：Biophysical journal

authors： Bruner LJ

更新日期：1965-11-01 00:00:00

abstract：:Studies have been performed on erythrocytes that have been subjected to a low shear stress of less than 100 dyn/cm(2) in a cone-and-plate viscometer. Alterations that were observed included decreased red cell survival, increased osmotic fragility, changes in the cation permeability of the red cell membrane, and a redu...

journal_title：Biophysical journal

authors： Nanjappa BN,Chang HK,Glomski CA

更新日期：1973-11-01 00:00:00

abstract：:In previous in vivo studies, amyloid fibers formed from a peptide ubiquitous in human seminal fluid (semen-derived enhancer of viral infection (SEVI)) were found to dramatically enhance the infectivity of the HIV virus (3-5 orders of magnitude by some measures). To complement those studies, we performed in vitro assay...

journal_title：Biophysical journal

authors： Brender JR,Hartman K,Gottler LM,Cavitt ME,Youngstrom DW,Ramamoorthy A

更新日期：2009-11-04 00:00:00

abstract：:Cholesterol is a key component of eukaryotic membranes, but its role in cellular biology in general and in lipid rafts in particular remains controversial. Model membranes are used extensively to determine the phase behavior of ternary mixtures of cholesterol, a saturated lipid, and an unsaturated lipid with liquid-or...

journal_title：Biophysical journal

authors： Bennett WFD,Shea JE,Tieleman DP

更新日期：2018-06-05 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

authors： Lin AJ,Slack NL,Ahmad A,George CX,Samuel CE,Safinya CR

更新日期：2003-05-01 00:00:00

abstract：:We have developed a saturation transfer EPR (ST-EPR) method to measure selectively the rotational dynamics of those lipids that are motionally restricted by integral membrane proteins and have applied this methodology to measure lipid-protein interactions in native sarcoplasmic reticulum (SR) membranes. This analysis ...

journal_title：Biophysical journal

authors： Squier TC,Thomas DD

更新日期：1989-10-01 00:00:00

abstract：:Bioluminescence rhythms from cellular reporters have become the most common method used to quantify oscillations in circadian gene expression. These experimental systems can reveal phase and amplitude change resulting from circadian disturbances, and can be used in conjunction with mathematical models to lend further ...

journal_title：Biophysical journal

authors： St John PC,Taylor SR,Abel JH,Doyle FJ 3rd

更新日期：2014-12-02 00:00:00

abstract：:The results of variable dielectric coefficient Poisson-Boltzmann calculations of the counter-ion concentration in the vicinity of an all-atom model of the B-form of DNA are presented with an emphasis on the importance of spatial variations in the dielectric properties of the solvent, particularly at the macro-ion-solv...

journal_title：Biophysical journal

authors： Pack GR,Garrett GA,Wong L,Lamm G

更新日期：1993-10-01 00:00:00

abstract：:Entropy Sampling Monte Carlo (ESMC) simulations were carried out to study the thermodynamics of the folding transition in the GCN4 leucine zipper (GCN4-lz) in the context of a reduced model. Using the calculated partition functions for the monomer and dimer, and taking into account the equilibrium between the monomer ...

journal_title：Biophysical journal

authors： Mohanty D,Kolinski A,Skolnick J

更新日期：1999-07-01 00:00:00

abstract：:Cardiomyocytes have intracellular diffusion restrictions, which spatially compartmentalize ADP and ATP. However, the models that predict diffusion restrictions have used data sets generated in rat heart permeabilized fibers, where diffusion distances may be heterogeneous. This is avoided by using isolated, permeabiliz...

journal_title：Biophysical journal

authors： Sepp M,Vendelin M,Vija H,Birkedal R

更新日期：2010-06-16 00:00:00

abstract：:Morphine spin labeled on the phenolic hydroxy group has been prepared using commercially available reagents and characterized by thin layer chromatography, mass spectroscopy, and electron spin resonance spectroscopy. It has been shown that morphine modified in this way retains some opiate activity, does not pass throu...

journal_title：Biophysical journal

authors： Copeland ES,Boykin ME,Kelley JA,Kullberg MP

更新日期：1975-11-01 00:00:00

abstract：:A dissipative system is approximated by a nonlinear rate equation: Z congruent to K1Z - K2Z3 (K2 greater than 0), in which the right side is derived from -delta G/delta Z of Taylor's series of the thermodynamic potential given by Gibbs' function G(Tc, Pc) (Z) at about the critical point C(Tc, Pc) of the control variab...

journal_title：Biophysical journal

authors： Shirane K,Tokimoto T,Yamaguchi Y

更新日期：1990-01-01 00:00:00

abstract：:In a pure fluid-phase lipid, the dependence of the lateral diffusion coefficient on the size of the diffusing particle may be obtained from the Saffman-Delbrück equation or the free-volume model. When diffusion is obstructed by immobile proteins or domains of gel-phase lipids, the obstacles yield an additional contrib...

journal_title：Biophysical journal

authors： Saxton MJ

更新日期：1993-04-01 00:00:00

abstract：:In most environments, such as natural aquatic systems, bacteria are found predominantly in self-organized sessile communities known as biofilms. In the presence of a significant flow, mature multispecies biofilms often develop into long filamentous structures called streamers, which can greatly influence ecosystem pro...

journal_title：Biophysical journal

authors： Rusconi R,Lecuyer S,Autrusson N,Guglielmini L,Stone HA

更新日期：2011-03-16 00:00:00

abstract：:Chimeras consisting of the homologous skeletal dihydropyridine receptor (DHPR) beta1a subunit and the heterologous cardiac/brain beta2a subunit were used to determine which regions of beta1a were responsible for the skeletal-type excitation-contraction (EC) coupling phenotype. Chimeras were transiently transfected in ...

journal_title：Biophysical journal

authors： Sheridan DC,Cheng W,Carbonneau L,Ahern CA,Coronado R

更新日期：2004-08-01 00:00:00

abstract：:The crystal structure and a 96-ps molecular dynamics simulation used to analyze structural and motional contributions to spin-lattice (T1) relaxation times of phenylalanine and tyrosine C gamma carbons of the pancreatic trypsin inhibitor. The H beta and H delta protons geminal to C gamma are calculated to account for ...

journal_title：Biophysical journal

authors： Levy RM,Dobson CM,Karplus M

更新日期：1982-07-01 00:00:00

abstract：:Previous mathematical modeling of beta cell electrical activity has involved single cells or, recently, clusters of identical cells. Here we model clusters of heterogeneous cells that differ in size, channel density, and other parameters. We use gap-junctional electrical coupling, with conductances determined by an ex...

journal_title：Biophysical journal

authors： Smolen P,Rinzel J,Sherman A

更新日期：1993-06-01 00:00:00

abstract：:Fluorescence cross-correlation spectroscopy (FCCS) is used to determine interactions and dissociation constants (K(d)s) of biomolecules. The determination of a K(d) depends on the accurate measurement of the auto- and cross-correlation function (ACF and CCF) amplitudes. In the case of complete binding, the ratio of th...

journal_title：Biophysical journal

authors： Foo YH,Naredi-Rainer N,Lamb DC,Ahmed S,Wohland T

更新日期：2012-03-07 00:00:00

abstract：:We investigated the accessibility to protons and thiol-directed reagents of a cysteine substituted at position 338 in transmembrane segment 6 (TM6) of CFTR to test the hypothesis that T338 resides in the pore. Xenopus oocytes expressing T338C CFTR exhibited pH-dependent changes in gCl and I-V shape that were specific ...

journal_title：Biophysical journal

authors： Liu X,Zhang ZR,Fuller MD,Billingsley J,McCarty NA,Dawson DC

更新日期：2004-12-01 00:00:00