The Role of Lipid Interactions in Simulations of the α-Hemolysin Ion-Channel-Forming Toxin.

abstract：:We study the folding of small proteins inside confining potentials. Proteins are described using an effective potential model that contains the Ramachandran angles as degrees of freedom and does not need any a priori information about the native state. Hydrogen bonds, dipole-dipole-, and hydrophobic interactions are t...

journal_title：Biophysical journal

authors： Ojeda P,Garcia ME,Londoño A,Chen NY

更新日期：2009-02-01 00:00:00

abstract：:Estimates of the free myoplasmic [Ca2+] ([Ca2+]i) with fluorescent dyes are complicated by the fact that some properties of these dyes are altered in the intracellular environment. In the present study indo-1 was used to measure [Ca2+]i in isolated muscle fibers from Xenopus frogs. Fluorescent ratio signals obtained f...

journal_title：Biophysical journal

authors： Westerblad H,Allen DG

更新日期：1996-08-01 00:00:00

abstract：:We report on the application of two photon molecular excitation to fluorescence correlation spectroscopy. We demonstrate the first fluorescence correlation spectroscopy measurements of translational mobility in the cytoplasm of living cells. Two-photon excitation inherently excites small sample volumes in three dimens...

journal_title：Biophysical journal

authors： Berland KM,So PT,Gratton E

更新日期：1995-02-01 00:00:00

abstract：:The state of photosystem II core complex (PS II CC) in monolayer at the gas-water interface was investigated using in situ polarization-modulated infrared reflection absorption spectroscopy and x-ray reflectivity techniques. Two approaches for preparing and manipulating the monolayers were examined and compared. In th...

journal_title：Biophysical journal

authors： Gallant J,Desbat B,Vaknin D,Salesse C

更新日期：1998-12-01 00:00:00

abstract：:Xenopus oocytes are widely employed for heterologous expression of cloned proteins, particularly electrogenic molecules such as ion channels and transporters. The high levels of expression readily obtained permit detailed investigations without interference from endogenous conductances. Injection of min K mRNA into Xe...

journal_title：Biophysical journal

authors： Tzounopoulos T,Maylie J,Adelman JP

更新日期：1995-09-01 00:00:00

abstract：:In an attempt to better define the parameters governing reconstitution and two-dimensional crystallization of membrane proteins, we have studied Ca2(+)-ATPase from rabbit sarcoplasmic reticulum. This ion pump forms vanadate-induced crystals in its native membrane and has previously been reconstituted at high lipid-to-...

journal_title：Biophysical journal

authors： Young HS,Rigaud JL,Lacapère JJ,Reddy LG,Stokes DL

更新日期：1997-06-01 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：:The geometry and mechanical properties of the human erythrocyte membrane cytoskeleton are investigated by a computer simulation in which the cytoskeleton is represented by a network of polymer chains. Four elastic moduli as well as the area and thickness are predicted for the chain network as a function of temperature...

journal_title：Biophysical journal

authors： Boal DH

更新日期：1994-08-01 00:00:00

abstract：:beta-Lactamase, which catalyzes beta-lactam antibiotics, is prototypical of large alpha/beta proteins with a scaffolding formed by strong noncovalent interactions. Experimentally, the enzyme is well characterized, and intermediates that are slightly less compact and having nearly the same content of secondary structur...

journal_title：Biophysical journal

authors： Vijayakumar S,Vishveshwara S,Ravishanker G,Beveridge DL

更新日期：1993-12-01 00:00:00

abstract：:Recent NMR structural characterization studies showed that a seven-residue segment (FKKGERL) from the src SH3 domain adopts the nativelike diverging type II beta-turn in aqueous solution in support of the prediction based on the I-sites library of sequence structural motifs. We study the conformational variability and...

journal_title：Biophysical journal

authors： Gnanakaran S,Garcia AE

更新日期：2003-03-01 00:00:00

abstract：:The effects of intracellular magnesium ions and extracellular calcium and magnesium ions on the delayed rectifier potassium ion channel, IK, were investigated from intracellularly perfused squid giant axons. Cao+2 and Mgo+2 both blocked IK in a voltage-independent manner with a KD of approximately 100 and 500 mM, resp...

journal_title：Biophysical journal

authors： Clay JR

更新日期：1995-11-01 00:00:00

abstract：:Impact loading of articular cartilage causes extensive chondrocyte death. Cell membranes have a limited elastic range of 3-4% strain but are protected from direct stretch during physiological loading by their membrane reservoir, an intricate pattern of membrane folds. Using a finite-element model, we suggested previou...

journal_title：Biophysical journal

authors： Moo EK,Amrein M,Epstein M,Duvall M,Abu Osman NA,Pingguan-Murphy B,Herzog W

更新日期：2013-10-01 00:00:00

abstract：:Myoplasmic free calcium transients were measured with antipyrylazo III in voltage clamped segments of frog skeletal muscle fibers and were used to calculate the rate of release (Rrel) of calcium from the sarcoplasmic reticulum. Intramembrane charge movement was measured for the same pulses in the same fibers. During a...

journal_title：Biophysical journal

authors： Simon BJ,Schneider MF

更新日期：1988-12-01 00:00:00

abstract：:The space-clamped squid axon membrane and two versions of the Hodgkin-Huxley model (the original, and a strongly adapting version) are subjected to a first order dynamic analysis. Stable, repetitive firing is induced by phase-locking nerve impulses to sinusoidal currents. The entrained impulses are then pulse position...

journal_title：Biophysical journal

authors： Fohlmeister JF,Adelman WJ Jr,Poppele RE

更新日期：1980-04-01 00:00:00

abstract：:We study dsDNA-RecA interactions by exerting forces in the pN range on single DNA molecules while the interstrand topological state is controlled owing to a magnetic tweezers setup. We show that unwinding a duplex DNA molecule induces RecA polymerization even at moderate force. Once initial polymerization has nucleate...

journal_title：Biophysical journal

authors： Fulconis R,Bancaud A,Allemand JF,Croquette V,Dutreix M,Viovy JL

更新日期：2004-10-01 00:00:00

abstract：:Thermodynamically rigorous free energy methods in principle allow the exact computation of binding free energies in biological systems. Here, we use thermodynamic integration together with molecular dynamics simulations of a DNA-protein complex to compute relative binding free energies of a series of mutants of a prot...

journal_title：Biophysical journal

authors： Beierlein FR,Kneale GG,Clark T

更新日期：2011-09-07 00:00:00

abstract：:Global analysis techniques are described for frequency domain fluorescence lifetime imaging microscopy (FLIM) data. These algorithms exploit the prior knowledge that only a limited number of fluorescent molecule species whose lifetimes do not vary spatially are present in the sample. Two approaches to implementing the...

journal_title：Biophysical journal

authors： Verveer PJ,Squire A,Bastiaens PI

更新日期：2000-04-01 00:00:00

abstract：:Quantitative characterization of protein interactions under physiological conditions is vital for systems biology. Fluorescence photobleaching/activation experiments of GFP-tagged proteins are frequently used for this purpose, but robust analysis methods to extract physicochemical parameters from such data are lacking...

journal_title：Biophysical journal

authors： Beaudouin J,Mora-Bermúdez F,Klee T,Daigle N,Ellenberg J

更新日期：2006-03-15 00:00:00

abstract：:The kinetics of oxygen geminate binding with the taxonomic substates of MbO2 are reported. The maximum entropy method was used to analyze the rebinding kinetics of MbCO and MbO2 monitored in the Soret. The resulting rate distributions were found to consist of a small number of overlapping bands. A global parametric fi...

journal_title：Biophysical journal

authors： Tetreau C,Novikov E,Tourbez M,Lavalette D

更新日期：2002-04-01 00:00:00

abstract：:X-ray fiber diffraction is one of the most useful methods for examining the structural details of live biological filaments under physiological conditions. To investigate biologically active or labile materials, it is crucial to finish fiber alignment within seconds before diffraction analysis. However, the convention...

journal_title：Biophysical journal

authors： Sugiyama T,Miyashiro D,Takao D,Iwamoto H,Sugimoto Y,Wakabayashi K,Kamimura S

更新日期：2009-12-16 00:00:00

abstract：:The light-harvesting complex I (LH-I) of Rhodobacter sphaeroides has been modeled computationally as a hexadecamer of alphabeta-heterodimers, based on a close homology of the heterodimer to that of light-harvesting complex II (LH-II) of Rhodospirillum molischianum. The resulting LH-I structure yields an electron densi...

journal_title：Biophysical journal

authors： Hu X,Schulten K

更新日期：1998-08-01 00:00:00

abstract：:Perfusion is one of the most important processes maintaining organ health. From a computational perspective, however, perfusion is among the least-studied physiological processes of the heart. The recent development of novel nanoparticle-based targeted cardiac therapy calls for novel simulation methods that can provid...

journal_title：Biophysical journal

authors： Diem AK,Valen-Sendstad K

更新日期：2019-12-17 00:00:00

abstract：:We manipulate lipid bilayer surface charge and gauge its influence on gramicidin A channel conductance by two strategies: titration of the lipid charge through bulk solution pH and dilution of a charged lipid by neutral. Using diphytanoyl phosphatidylserine (PS) bilayers with CsCl aqueous solutions, we show that the e...

journal_title：Biophysical journal

authors： Rostovtseva TK,Aguilella VM,Vodyanoy I,Bezrukov SM,Parsegian VA

更新日期：1998-10-01 00:00:00

abstract：:The effect of aggregation of gramicidin A' (GA) on the phase structure of dipalmitoylphosphatidylcholine (DPPC) multilamellar vesicles was studied by cw-ESR using a chain-labeled lipid (16PC) at temperatures between 30 degrees and 45 degreesC that span the main phase transition of DPPC. Boundary lipids were observed o...

journal_title：Biophysical journal

authors： Ge M,Freed JH

更新日期：1999-01-01 00:00:00

abstract：:The cardiac muscle protein titin, responsible for developing passive elasticity and extensibility of muscle, possesses about 40 immunoglobulin-like (Ig) domains in its I-band region. Atomic force microscopy (AFM) and steered molecular dynamics (SMD) have been successfully combined to investigate the reversible unfoldi...

journal_title：Biophysical journal

authors： Gao M,Wilmanns M,Schulten K

更新日期：2002-12-01 00:00:00

abstract：:In recent years, optical sensors for tracking neural activity have been developed and offer great utility. However, developing microscopy techniques that have several kHz bandwidth necessary to reliably capture optically reported action potentials (APs) at multiple locations in parallel remains a significant challenge...

journal_title：Biophysical journal

authors： Shtrahman M,Aharoni DB,Hardy NF,Buonomano DV,Arisaka K,Otis TS

更新日期：2015-02-03 00:00:00

abstract：:The protonation state and intracellular distribution of ellipticine were investigated in single human mammary T47D cells by confocal laser microspectrofluorimetry. In the cell nucleus, only the protonated form of ellipticine was detected as a direct consequence of its apparent pK increase upon DNA binding. Both proton...

journal_title：Biophysical journal

authors： Sureau F,Moreau F,Millot JM,Manfait M,Allard B,Aubard J,Schwaller MA

更新日期：1993-11-01 00:00:00

abstract：:Structured illumination microscopy is a method that can increase the spatial resolution of wide-field fluorescence microscopy beyond its classical limit by using spatially structured illumination light. Here we describe how this method can be applied in three dimensions to double the axial as well as the lateral resol...

journal_title：Biophysical journal

authors： Gustafsson MG,Shao L,Carlton PM,Wang CJ,Golubovskaya IN,Cande WZ,Agard DA,Sedat JW

更新日期：2008-06-01 00:00:00

abstract：:The effect of antibodies to glycophorin A on the rotational diffusion of band 3 in human erythrocyte membranes was investigated by transient dichrosim. Three antibodies that recognize different epitopes on the exofacial domain of glycophorin A all strongly reduce the rotational mobility of band 3. The effect is at mos...

journal_title：Biophysical journal

authors： Che A,Cherry RJ

更新日期：1995-05-01 00:00:00

abstract：:We have studied the atomic level structure of mineralized articular cartilage with heteronuclear solid-state NMR, our aims being to identify the inorganic species present at the surfaces of the mineral crystals which may interact with the surrounding organic matrix and to determine which components of the organic matr...

journal_title：Biophysical journal

authors： Duer MJ,Friscić T,Murray RC,Reid DG,Wise ER

更新日期：2009-04-22 00:00:00