Roles of boundary conditions in DNA simulations: analysis of ion distributions with the finite-difference Poisson-Boltzmann method.

abstract：:X-ray edge absorption of copper and extended fine structure studies of both copper and iron centers have been made of cytochrome oxidase from beef heart, Paracoccus dentrificans, and HB-8 thermophilic bacteria (1-2.5 mM in heme). The desired redox state (fully oxidized, reduced CO, mixed valence formate and CO) in the...

journal_title：Biophysical journal

authors： Powers L,Chance B,Ching Y,Angiolillo P

更新日期：1981-06-01 00:00:00

abstract：:We report constraints on the supramolecular structure of amyloid fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (A beta(1-40)) obtained from solid-state nuclear magnetic resonance (NMR) measurements of intermolecular dipole-dipole couplings between (13)C labels at 11 carbon s...

journal_title：Biophysical journal

authors： Balbach JJ,Petkova AT,Oyler NA,Antzutkin ON,Gordon DJ,Meredith SC,Tycko R

更新日期：2002-08-01 00:00:00

abstract：:In dialyzed Myxicola axons substitution of heavy water (D2O) externally and internally slows both sodium and potassium kinetics and decreases the maximum conductances. Furthermore, this effect is strongly temperature dependent, the magnitude of the slowing produced by D2O substitution decreasing with increasing temper...

journal_title：Biophysical journal

authors： Schauf CL,Bullock JO

更新日期：1979-08-01 00:00:00

abstract：:The effects of the Ca(2+)-induced Ca2+ release blocker procaine on individual sarcoplasmic reticulum Ca2+ release channels have been examined in planar lipid bilayers. Procaine did not reduce the single channel conductance nor appreciably shorten the mean open times of the channel; rather, it increased the longest clo...

journal_title：Biophysical journal

authors： Zahradníková A,Palade P

更新日期：1993-04-01 00:00:00

abstract：:The bacterial flagellar motor (BFM) is a molecular machine that rotates the helical filaments and propels the bacteria swimming toward favorable conditions. In our previous works, we built a stochastic conformational spread model to explain the dynamic and cooperative behavior of BFM switching. Here, we extended this ...

journal_title：Biophysical journal

authors： Ma Q,Sowa Y,Baker MA,Bai F

更新日期：2016-03-29 00:00:00

abstract：:Membrane nanotubes, also known as membrane tethers, play important functional roles in many cellular processes, such as trafficking and signaling. Although considerable progresses have been made in understanding the physics regulating the mechanical behaviors of individual membrane nanotubes, relatively little is know...

journal_title：Biophysical journal

authors： Li S,Yan Z,Luo Z,Xu Y,Huang F,Zhang X,Yi X,Yue T

更新日期：2019-03-05 00:00:00

abstract：:The adult form of the nicotinic acetylcholine receptor (AChR) consists of five subunits (alpha(2)betaepsilondelta), each having four transmembrane domains (M1-M4). The atomic model of the nicotinic acetylcholine receptor shows that the pore-lining M2 domains make no extensive contacts with the rest of the transmembran...

journal_title：Biophysical journal

authors： Corradi J,Spitzmaul G,De Rosa MJ,Costabel M,Bouzat C

更新日期：2007-01-01 00:00:00

abstract：:It has long been recognized that protein dynamical processes occur over a wide temporal range. However, the functionality of this spectrum of events remains unclear. In this work, a generalized noise function analysis is applied to a collection of diverse protein dynamical systems. It is shown that a power law model w...

journal_title：Biophysical journal

authors： Dewey TG,Bann JG

更新日期：1992-08-01 00:00:00

abstract：:Cubic insulin crystals contain a binding site for monovalent cations in a cavity of the crystal dyad in which the bound cation is ligated by protein atomic dipoles and water molecules. These types of interaction are analogous to interactions that occur in small cation-selective carrier and channel molecules. X-ray dif...

journal_title：Biophysical journal

authors： Badger J,Kapulsky A,Gursky O,Bhyravbhatla B,Caspar DL

更新日期：1994-02-01 00:00:00

abstract：:The Green's function technique is applied to a study of breathing modes in a DNA double helix which contains a region of different base pairs from the rest of the double helix. The calculation is performed on a G-C helix in the B conformation with four consecutive base pairs replaced by A-T. The average stretch in hyd...

journal_title：Biophysical journal

authors： Feng Y,Prohofsky EW

更新日期：1990-03-01 00:00:00

abstract：:Evidence that the fluorophore sempervirene binds to nucleic acids is presented. The complexes were studied by fluorescence intensity, spectra, decay lifetime, and polarization methods. Both fluorescent and nonfluorescent complexes are formed. The sempervirene is rigidly fixed to DNA. If ethidium bromide and sempervire...

journal_title：Biophysical journal

authors： Burns VW

更新日期：1974-03-01 00:00:00

abstract：:Sharing of positive or negative regulators between multiple targets is frequently observed in cellular signaling cascades. For instance, phosphatase sharing between multiple kinases is ubiquitous within the MAPK pathway. Here we investigate how such phosphatase sharing could shape robustness and evolvability of the ph...

journal_title：Biophysical journal

authors： Ghosh B,Sarma U,Sourjik V,Legewie S

更新日期：2018-01-09 00:00:00

abstract：:Förster resonance energy transfer (FRET)-based biosensors for the quantitative analysis of intracellular signaling, including sensors for monitoring cyclic adenosine monophosphate (cAMP), are of increasing interest. The measurement of the donor/acceptor emission ratio in tandem biosensors excited at the donor excitati...

journal_title：Biophysical journal

authors： Salonikidis PS,Zeug A,Kobe F,Ponimaskin E,Richter DW

更新日期：2008-12-01 00:00:00

abstract：:Distinct lipid environments, including lipid rafts, are increasingly recognized as a crucial factor affecting membrane protein function in plasma membranes. Unfortunately, an understanding of their role in membrane protein activation and oligomerization has remained elusive due to the challenge of characterizing these...

journal_title：Biophysical journal

authors： Siegel AP,Kimble-Hill A,Garg S,Jordan R,Naumann CA

更新日期：2011-10-05 00:00:00

abstract：:DNA release from lipoplexes is an essential step during lipofection and is probably a result of charge neutralization by cellular anionic lipids. As a model system to test this possibility, fluorescence resonance energy transfer between DNA and lipid covalently labeled with Cy3 and BODIPY, respectively, was used to mo...

journal_title：Biophysical journal

authors： Tarahovsky YS,Koynova R,MacDonald RC

更新日期：2004-08-01 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：:A simple formula for the expansion rate U of the bilayer membrane perimeter was derived by the solution of the hydrodynamic and the Laplace equations at small rates and small contact angles: U = theta delta/6 micron ln (h/e 3/2 h0), where theta is the equilibrium contact angle between the bilayer membrane and the Plat...

journal_title：Biophysical journal

authors： Dimitrov DS

更新日期：1981-10-01 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：:Elastin-derived peptides are released from the extracellular matrix remodeling by numerous proteases and seem to regulate many biological processes, notably cancer progression. The canonical elastin peptide is VGVAPG, which harbors the XGXXPG consensus pattern, allowing interaction with the elastin receptor complex lo...

journal_title：Biophysical journal

authors： Hernández B,Crowet JM,Thiery J,Kruglik SG,Belloy N,Baud S,Dauchez M,Debelle L

更新日期：2020-06-02 00:00:00

abstract：:A number of models proposed to account for the sodium conductance changes are shown to fall into two classes. The Hodgkin-Huxley (HH) model falls into a class (I) in which the conductance depends on two or more independent variables controlled by independent processes. The Mullins, Hoyt, and Goldman models fall into c...

journal_title：Biophysical journal

authors： Hoyt RC

更新日期：1968-10-01 00:00:00

abstract：:The nature of the mechanism limiting the velocity of ATP-induced unidirectional movements of actin-myosin filaments in vitro is considered. In the sliding process two types of "cyclic" interactions between myosin heads and actin are involved, i.e., productive and nonproductive. In the productive interaction, myosin he...

journal_title：Biophysical journal

authors： Tawada K,Sekimoto K

更新日期：1991-02-01 00:00:00

abstract：:Heme proteins react inhomogeneously with ligands at cryogenic temperatures and homogeneously at room temperature. We have identified and characterized a transition from inhomogeneous to homogeneous behavior at intermediate temperatures in the time dependence of CO binding to horse myoglobin. The turnover is attributed...

journal_title：Biophysical journal

authors： Agmon N,Doster W,Post F

更新日期：1994-05-01 00:00:00

abstract：:Nisin is an antimicrobial peptide used as food preservative. To gain some insights into the hypothesis that its bactericidal activity is due to the perturbation of the lipid fraction of the bacterial plasmic membrane, we have investigated the effect of nisin on model phosphatidylcholine (PC) membranes. We show that ni...

journal_title：Biophysical journal

authors： El Jastimi R,Edwards K,Lafleur M

更新日期：1999-08-01 00:00:00

abstract：:High-affinity and cooperative binding of two Ca(2+) per ATPase (SERCA) occurs within the membrane-bound region of the enzyme. Direct measurements of binding at various Ca(2+) concentrations demonstrate that site-directed mutations within this region interfere selectively with Ca(2+) occupancy of either one or both bin...

journal_title：Biophysical journal

authors： Inesi G,Zhang Z,Lewis D

更新日期：2002-11-01 00:00:00

abstract：:Hundreds of cationic antimicrobial and cell-penetrating peptides (CPPs) form amphipathic α-helices when bound to lipid membranes. Here, we test two hypotheses for the differences in the ability of these peptides to translocate across membranes. The first, which we now call the hydrophobicity hypothesis, is that peptid...

journal_title：Biophysical journal

authors： Ablan FDO,Spaller BL,Abdo KI,Almeida PF

更新日期：2016-10-18 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：:The effect of uncharged, dipolar phloretin on anion and cation conductance through a black lipid membrane can be used to study its adsorption behavior. The adsorption of phloretin can be described by a Langmuir isotherm with weak dipole-dipole interaction. ...

journal_title：Biophysical journal

authors： de Levie R,Rangarajan SK,Seelig PF,Andersen OS

更新日期：1979-02-01 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：:The folding of short alanine-based peptides with different numbers of lysine residues is simulated at constant temperature (274 K) using the rigid-element Monte Carlo method. The solvent-referenced potential has prevented the multiple-minima problem in helix folding. From various initial structures, the peptides with ...

journal_title：Biophysical journal

authors： Sung SS

更新日期：1995-03-01 00:00:00

abstract：:Freeze-fracture electron micrographs from degranulating cells show that the lumen of the secretory granule is connected to the extracellular compartment via large (20 to 150 nm diameter) aqueous pores. These exocytotic fusion pores appear to be made up of a highly curved bilayer that spans the plasma and granule membr...

journal_title：Biophysical journal

authors： Nanavati C,Markin VS,Oberhauser AF,Fernandez JM

更新日期：1992-10-01 00:00:00