Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.

abstract：:We have used the elastic neutron scattering technique to investigate the dynamics of the two main saccharidic components of starch: amylose and amylopectin. The measurements were carried out in the temperature range of 20 to 320 K and at different hydration levels from the dry state up to 0.47 g saccharide/g D(2)O. In...

journal_title：Biophysical journal

authors： Di Bari M,Cavatorta F,Deriu A,Albanese G

更新日期：2001-08-01 00:00:00

abstract：:The Ciona intestinalis voltage-sensitive phosphatase (Ci-VSP) represents the first discovered member of enzymes regulated by a voltage-sensor domain (VSD) related to the VSD found in voltage-gated ion channels. Although the VSD operation in Ci-VSP exhibits original voltage dependence and kinetics compared to ion chann...

journal_title：Biophysical journal

authors： Lacroix JJ,Bezanilla F

更新日期：2012-08-08 00:00:00

abstract：:We measured the exocytotic response induced by flash photolysis of caged compounds in isolated mast cells and chromaffin cells. Vesicle fusion was measured by monitoring the cell membrane capacitance. The release of vesicular contents was followed by amperometry. In response to a GTP gamma S stimulus we found that the...

journal_title：Biophysical journal

authors： Oberhauser AF,Robinson IM,Fernandez JM

更新日期：1996-08-01 00:00:00

abstract：:Inositol 1,4,5-trisphosphate (InsP(3)) receptors (InsP(3)Rs) are intracellular Ca(2+) channels gated by the second messenger InsP(3). Here we describe a novel approach for recording single-channel currents through recombinant InsP(3)Rs in mammalian cells that applies patch-clamp electrophysiology to nuclei isolated fr...

journal_title：Biophysical journal

authors： Boehning D,Joseph SK,Mak DO,Foskett JK

更新日期：2001-07-01 00:00:00

abstract：:Cells in a cloned population of coliform bacteria exhibit a wide range of swimming behaviors--a form of non-genetic individuality. We used computer models to examine the proposition that these variations are due to differences in the number of chemotaxis signaling molecules from one cell to the next. Simulations were ...

journal_title：Biophysical journal

authors： Levin MD,Morton-Firth CJ,Abouhamad WN,Bourret RB,Bray D

更新日期：1998-01-01 00:00:00

abstract：:Many proteins "bind" DNA through positively charged amino acids on their surfaces. However, to overcome significant energetic and topological obstacles, proteins that bend or package DNA might also modulate the stiffness that is generated by repulsions between phosphates within DNA. Much previous work describes how io...

journal_title：Biophysical journal

authors： Podestà A,Indrieri M,Brogioli D,Manning GS,Milani P,Guerra R,Finzi L,Dunlap D

更新日期：2005-10-01 00:00:00

abstract：:Interactions between the graft copolymer poly(L-lysine)-g-poly(ethylene glycol), PLL-g-PEG, and two kinds of surface-supported lipidic systems (supported phospholipid bilayers and supported vesicular layers) were investigated by a combination of microscopic and spectroscopic techniques. It was found that the applicati...

journal_title：Biophysical journal

authors： Rossetti FF,Reviakine I,Csúcs G,Assi F,Vörös J,Textor M

更新日期：2004-09-01 00:00:00

abstract：:With a view to determine the configuration and regularity of plectonemically supercoiled DNA, we have measured the small angle neutron scattering from pUC18 plasmid in saline solutions. Furthermore, we have derived the mathematical expression for the single chain scattering function (form factor) of a superhelical str...

journal_title：Biophysical journal

authors： Zakharova SS,Jesse W,Backendorf C,Egelhaaf SU,Lapp A,van der Maarel JR

更新日期：2002-08-01 00:00:00

abstract：:Video-based particle tracking monitors the microscopic movement of labeled biomolecules and fluorescent probes within a complex cellular environment. Information gained from this technique enables us to extract the dynamic behavior of biomolecules and the local mechanical properties inside the cell from a tracked part...

journal_title：Biophysical journal

authors： Wu PH,Arce SH,Burney PR,Tseng Y

更新日期：2009-06-17 00:00:00

abstract：:We examined the state-, voltage-, and time dependences of interaction between 4-AP and a mammalian A-type K channel clone (rKv1.4) expressed in Xenopus oocytes using whole-cell and single-channel recordings. 4-AP blocked rKv1.4 from the cytoplasmic side of the membrane. The development of block required channel openin...

journal_title：Biophysical journal

authors： Yao JA,Tseng GN

更新日期：1994-07-01 00:00:00

abstract：:The photoelectron quantum yields of 21 common amino acids and 15 polyamino acids were measured in the 180-240 nm wavelength region. On the average, the quantum yields of these two groups exhibit quite similar wavelength dependence. For lambda > 220 nm all amino acid and polyamino acid quantum yields are

journal_title：Biophysical journal

authors： Dam RJ,Burke CA,Griffith OH

更新日期：1974-06-01 00:00:00

abstract：:The effects of Mg++ on the spatial organization of nuclei from rat hepatocytes are analyzed in the range 0-60 mM, in the presence of suitable concentrations of KCl to reproduce physiological conditions. It is shown that the scatter-signal distribution measured by means of a flow microfluorimeter is greatly affected by...

journal_title：Biophysical journal

authors： Grattarola M,Carlo P,Giannetti G,Finollo R,Viviani R,Chiabrera A

更新日期：1985-04-01 00:00:00

abstract：:To explain the effect of profilin on actin critical concentration in a manner consistent with thermodynamic constraints and available experimental data, we built a thermodynamically rigorous model of actin steady-state dynamics in the presence of profilin. We analyzed previously published mechanisms theoretically and ...

journal_title：Biophysical journal

authors： Yarmola EG,Dranishnikov DA,Bubb MR

更新日期：2008-12-15 00:00:00

abstract：:An understanding of the structure-dynamics relationship is essential for understanding how a protein works. Prior research has shown that the activity of a protein correlates with intradomain dynamics occurring at picosecond to millisecond timescales. However, the correlation between interdomain dynamics and the funct...

journal_title：Biophysical journal

authors： Kumar L,Nash A,Harms C,Planas-Iglesias J,Wright D,Klein-Seetharaman J,Sarkar SK

更新日期：2020-07-21 00:00:00

abstract：:The kinetics of redistribution of lipid-like molecules between the membranes of two fused spherical vesicles is studied by solving the time-dependent diffusion equation of the system. The effects on the probe redistribution rate of pore size at the fusion junction and the relative sizes of the vesicles are examined. I...

journal_title：Biophysical journal

authors： Rubin RJ,Chen YD

更新日期：1990-11-01 00:00:00

abstract：:The switch 1 region of myosin forms a lid over the nucleotide phosphates as part of a structure known as the phosphate-tube. The homologous region in kinesin-family motors is more open, not interacting with the nucleotide. We used molecular dynamics (MD) simulations to examine a possible displacement of switch 1 of th...

journal_title：Biophysical journal

authors： Minehardt TJ,Cooke R,Pate E,Kollman PA

更新日期：2001-03-01 00:00:00

abstract：:Understanding exposure thresholds for the response of biological systems to extremely low frequency (ELF) electric and magnetic fields is a fundamental problem of long-standing interest. We consider a two-state model for voltage-gated channels in the membrane of an isolated elongated cell (Lcell = 1 mm; rcell = 25 mic...

journal_title：Biophysical journal

authors： Weaver JC,Vaughan TE,Adair RK,Astumian RD

更新日期：1998-11-01 00:00:00

abstract：:Interactions between proteins are often sufficiently weak that their study through the use of conventional structural techniques becomes problematic. Of the few techniques capable of providing experimental measures of weak protein-protein interactions, perhaps the most useful is the second virial coefficient, B(22), w...

journal_title：Biophysical journal

authors： Elcock AH,McCammon JA

更新日期：2001-02-01 00:00:00

abstract：:Knowledge about the influenza fusion peptide (FP) membrane insertion mode is crucial for understanding its fusogenic mechanism. NMR and electron paramagnetic resonance experiments showed that in micelles, the FP inserted as a fixed-angle inverted V. In membranes, however, it was shown to insert as a straight α-helix (...

journal_title：Biophysical journal

authors： Légaré S,Lagüe P

更新日期：2012-05-16 00:00:00

abstract：:Each myosin molecule contains two heavy chains and a total of four low-molecular weight light chain subunits, two "essential" and two "regulatory" light chains (RLCs). Although the roles of myosin light chains in vertebrate striated muscle are poorly understood at present, recent studies on the RLC have suggested that...

journal_title：Biophysical journal

authors： Diffee GM,Greaser ML,Reinach FC,Moss RL

更新日期：1995-04-01 00:00:00

abstract：:A simulation of the function of the human heart and heart muscle has been developed in the form of a digital computer code. For a given set of values for the input variables, realistic values of the cardiac output variables are predicted. A detailed discussion of the simulation and some results obtained from its appli...

journal_title：Biophysical journal

authors： Hanna WT

更新日期：1973-07-01 00:00:00

abstract：:Widely disparate viruses enter the host cell through an endocytic pathway and travel the cytoplasm inside an endosome. For the viral genetic material to be delivered into the cytoplasm, these viruses have to escape the endosomal compartment, an event triggered by the conformational changes of viral endosomolytic prote...

journal_title：Biophysical journal

authors： Lagache T,Danos O,Holcman D

更新日期：2012-03-07 00:00:00

abstract：:Multiphasic kinetics are often observed in stopped-flow investigations. To characterize further these kinetic phases, we have developed a methodology whereby fluorescence total intensity and anisotropy stopped-flow data can be combined in a single analysis. Fluorescence total intensity and anisotropy are highly interr...

journal_title：Biophysical journal

authors： Otto MR,Lillo MP,Beechem JM

更新日期：1994-12-01 00:00:00

abstract：:We study theoretically the feasibility of using transverse electronic transport within a nanopore for rapid DNA sequencing. Specifically, we examine the effects of the environment and detection probes on the distinguishability of the DNA bases. We find that the intrinsic measurement bandwidth of the electrodes helps t...

journal_title：Biophysical journal

authors： Lagerqvist J,Zwolak M,Di Ventra M

更新日期：2007-10-01 00:00:00

abstract：:Neuronal synapses are highly specialized structures for communication between nerve cells. Knowledge about their molecular organization and dynamics is still incomplete. The large multidomain protein Bassoon plays a major role in scaffolding and organizing the cytomatrix at the active zone of neurotransmitter release ...

journal_title：Biophysical journal

authors： Jose M,Nair DK,Altrock WD,Dresbach T,Gundelfinger ED,Zuschratter W

更新日期：2008-02-15 00:00:00

abstract：:The microsecond folding and unfolding kinetics of ovine prion proteins (ovPrP) were measured under various solution conditions. A fragment comprising residues 94-233 of the full-length ovPrP was studied for four variants with differing susceptibilities to classical scrapie in sheep. The observed biexponential unfoldin...

journal_title：Biophysical journal

authors： Chen KC,Xu M,Wedemeyer WJ,Roder H

更新日期：2011-09-07 00:00:00

abstract：:Neutron scattering and nuclear magnetic resonance relaxation experiments are combined with molecular dynamics (MD) simulations in a novel, to our knowledge, approach to investigate the change in internal dynamics on substrate (camphor) binding to a protein (cytochrome P450cam). The MD simulations agree well with both ...

journal_title：Biophysical journal

authors： Miao Y,Yi Z,Cantrell C,Glass DC,Baudry J,Jain N,Smith JC

更新日期：2012-11-21 00:00:00

abstract：:Nanodiscs are an example of discoidal nanoscale self-assembled lipid/protein particles similar to nascent high-density lipoproteins, which reduce the risk of coronary artery disease. The major protein component of high-density lipoproteins is human apolipoprotein A-I, and the corresponding protein component of Nanodis...

journal_title：Biophysical journal

authors： Li Y,Kijac AZ,Sligar SG,Rienstra CM

更新日期：2006-11-15 00:00:00

abstract：:In this article, we explore the information content of molecular force-field calculations. We make use of exhaustive lattice models of molecular conformations and reduced alphabet sequences to determine the relative resolving power of pairwise interaction-based force fields. We find that sequence-specific interactions...

journal_title：Biophysical journal

authors： Aynechi T,Kuntz ID

更新日期：2005-11-01 00:00:00

abstract：:Halorhodopsin (HR), the light-driven chloride transport pigment of Halobacterium halobium, was bleached and reconstituted with retinal analogues with the pi electron system interrupted at different locations (dihydroretinals). The absorption maxima of the artificial pigments formed with the dihydroretinals are found t...

journal_title：Biophysical journal

authors： Lanyi JK,Zimányi L,Nakanishi K,Derguini F,Okabe M,Honig B

更新日期：1988-02-01 00:00:00