cAMP Modulation of the cytoplasmic domain in the HCN2 channel investigated by molecular simulations.

abstract：:Sum-frequency vibrational spectroscopy (SFVS) is used to measure the intrinsic rate of lipid flip-flop for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) in planar-supported lipid bilayers (PSs). Asymmetric P...

journal_title：Biophysical journal

authors： Liu J,Conboy JC

更新日期：2005-10-01 00:00:00

abstract：:Loss of myelin in the central nervous system (CNS) leads to debilitating neurological deficits. High-resolution optical imaging of myelin in the CNS of animal models is limited by a lack of in vivo myelin labeling strategies. We demonstrated that third harmonic generation (THG) microscopy-a coherent, nonlinear, dye-fr...

journal_title：Biophysical journal

authors： Farrar MJ,Wise FW,Fetcho JR,Schaffer CB

更新日期：2011-03-02 00:00:00

abstract：:The stability of the structure of double-stranded DNA in the salt-free solution is discussed on the basis of the polyelectrolyte theory. Assuming that DNA is an infinitely long rod, and the formation of double strands is divided into combining process and folding process, the free energy changes required in these proc...

journal_title：Biophysical journal

authors： OHNISHI T

更新日期：1963-11-01 00:00:00

abstract：:Recently, it has become clear that the influenza virus fusion protein, hemagglutinin (HA), produces membrane destabilization and fusion by a multistep process, which involves the aggregation of the HAs to form a fusion site. While the details of this process are under debate, it is important to recognize that proposin...

journal_title：Biophysical journal

authors： Bentz J

更新日期：1992-08-01 00:00:00

abstract：:To investigate the force generation properties of Chlamydomonas axonemal inner-arm dyneins in response to external force, we analyzed microtubule gliding on dynein-coated surfaces under shear flow. When inner-arm dynein c was used, microtubule translocation in the downstream direction accelerated with increasing flow ...

journal_title：Biophysical journal

authors： Kikushima K,Kamiya R

更新日期：2009-09-16 00:00:00

abstract：:Deuterium and phosphorus nuclear magnetic resonance (NMR) has been used to investigate the dynamics of slow motional processes induced in bilayer cardiolipin upon binding with cytochrome c. 31P NMR line shapes suggest that protein binding induces less restricted, isotropic-like motions in the lipid phosphates within t...

journal_title：Biophysical journal

authors： Spooner PJ,Duralski AA,Rankin SE,Pinheiro TJ,Watts A

更新日期：1993-07-01 00:00:00

abstract：:Molecular dynamics simulations supplement single-molecule pulling experiments by providing the possibility of examining the full free energy landscape using many coordinates. Here, we use an all-atom structure-based model to study the force and temperature dependence of the unfolding of the protein filamin by applying...

journal_title：Biophysical journal

authors： Sun L,Noel JK,Sulkowska JI,Levine H,Onuchic JN

更新日期：2014-12-16 00:00:00

abstract：:The tunneling transfer of electrons between two sites, appropriate to biological intermolecular electron transfer, contains physical considerations which are not important in the tunneling transfer between two metals. Analyses (such as the recent one by Hales) based on the well-known formula for the latter but applied...

journal_title：Biophysical journal

authors： Hopfield JJ

更新日期：1976-10-01 00:00:00

abstract：:Isothermal (27 degrees C) phase behavior of dimyristoyl phosphatidyl choline-cholesterol mixtures at various osmotic pressures and cholesterol contents was investigated by means of isothermal sorption microcalorimetry and (2)H-nuclear magnetic resonance. The calorimetric method allows for simultaneous measurement of t...

journal_title：Biophysical journal

authors： Sparr E,Hallin L,Markova N,Wennerström H

更新日期：2002-10-01 00:00:00

abstract：:This paper reports on a coupled approach to determining the structure of the gramicidin A ion channel, utilizing solid state nuclear magnetic resonance (NMR) of isotopically labeled gramicidin channels aligned parallel to the magnetic field direction, and molecular dynamics (MD). MD computations using an idealized rig...

journal_title：Biophysical journal

authors： Chiu SW,Nicholson LK,Brenneman MT,Subramaniam S,Teng Q,McCammon JA,Cross TA,Jakobsson E

更新日期：1991-10-01 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：:Dendritic shaft (Zd) and spine (Zsp) input impedances were computed numerically for sites on hippocampal neurons, using a segmental format of cable calculations. The Zsp values for a typical spine appended onto a dendritic shaft averaged less than 2% higher than the Zd values for the adjacent dendritic shaft. Spine sy...

journal_title：Biophysical journal

authors： Turner DA

更新日期：1984-07-01 00:00:00

abstract：:An analysis is presented of the complex anisotropy behavior of trans-parinaric acid in single component DEPC lipid bilayers. It is shown that a model involving two species with distinct lifetime and motional behavior is required, and is adequate, to explain the observed data. In particular, the observed increase in th...

journal_title：Biophysical journal

authors： Ruggiero A,Hudson B

更新日期：1989-06-01 00:00:00

abstract：:The salt dependence of the binding free energy of five protein-protein hetero-dimers and two homo-dimers/tetramers was calculated from numerical solutions to the Poisson-Boltzmann equation. Overall, the agreement with experimental values is very good. In all cases except one involving the highly charged lactoglobulin ...

journal_title：Biophysical journal

authors： Bertonati C,Honig B,Alexov E

更新日期：2007-03-15 00:00:00

abstract：:Protein conformational fluctuations modulate the catalytic powers of enzymes. The frequency of conformational fluctuations may modulate the catalytic rate at individual reaction steps. In this study, we modulated the rotary fluctuation frequency of F1-ATPase (F1) by attaching probes with different viscous drag coeffic...

journal_title：Biophysical journal

authors： Watanabe R,Hayashi K,Ueno H,Noji H

更新日期：2013-11-19 00:00:00

abstract：:The pKa values of ionizable groups that lie between the active site region of bacteriorhodopsin (bR) and the extracellular surface of the protein are reported. Glu-204 is found to have an elevated pKa in the resting state of bR, suggesting that it corresponds to the proton-releasing group in bR. Its elevated pKa is pr...

journal_title：Biophysical journal

authors： Sampogna RV,Honig B

更新日期：1996-09-01 00:00:00

abstract：:The cornea is the primary refractive lens in the eye and transmits >90% of incident visible light. It has been suggested that the development of postoperative corneal haze could be due to an increase in light scattering from activated corneal stromal cells. Quiescent keratocytes are thought to produce crystallins that...

journal_title：Biophysical journal

authors： Gardner SJ,White N,Albon J,Knupp C,Kamma-Lorger CS,Meek KM

更新日期：2015-10-20 00:00:00

abstract：:The structural dynamics of bovine erythrocyte Cu, Zn superoxide dismutase (BSOD) was studied by time-resolved fluorescence spectroscopy. BSOD is a homodimer containing a single tyrosine residue (and no tryptophan) per subunit. Frequency-domain fluorometry revealed a heterogeneous fluorescence decay that could be descr...

journal_title：Biophysical journal

authors： Ferreira ST,Stella L,Gratton E

更新日期：1994-04-01 00:00:00

abstract：:Actin is ubiquitous globular protein that polymerizes into filaments and forms networks that participate in the force generation of eukaryotic cells. Such forces are used for cell motility, cytokinesis, and tissue remodeling. Among those actin networks, we focus on the actin cortex, a dense branched network beneath th...

journal_title：Biophysical journal

authors： Bussonnier M,Carvalho K,Lemière J,Joanny JF,Sykes C,Betz T

更新日期：2014-08-19 00:00:00

abstract：:We demonstrate a novel method for stretching a long DNA molecule in agarose gel with alternating current (AC) electric fields. The molecular motion of a long DNA (T4 DNA; 165.6 kb) in agarose gel was studied using fluorescence microscopy. The effects of a wide range of field frequencies, field strengths, and gel conce...

journal_title：Biophysical journal

authors： Kaji N,Ueda M,Baba Y

更新日期：2002-01-01 00:00:00

abstract：:Molecular dynamics simulations of protein folding and unfolding are often carried out at temperatures (400-600 K) that are much higher than physiological or room temperature to speed up the (un)folding process. Use of such high temperatures changes both the protein and solvent properties considerably, compared to phys...

journal_title：Biophysical journal

authors： Walser R,Mark AE,van Gunsteren WF

更新日期：2000-06-01 00:00:00

abstract：:We describe simulations of absorption difference spectra in strongly coupled photosynthetic antennas. In the presence of large resonance couplings, distinctive features arise from excited-state absorption transitions between one- and two-exciton levels. We first outline the theory for the heterodimer and for the gener...

journal_title：Biophysical journal

authors： Buck DR,Savikhin S,Struve WS

更新日期：1997-01-01 00:00:00

abstract：:Aggregated Markov models are a widely used tool to model patch clamp data measured from single ion channels. These channels must obey the principle of detailed balance in thermodynamic equilibrium; otherwise, the channel is driven by an external source of energy. We investigate the power of a likelihood ratio test for...

journal_title：Biophysical journal

authors： Wagner M,Timmer J

更新日期：2000-12-01 00:00:00

abstract：:Diphtheria toxin (DT) contains separate domains for receptor-specific binding, translocation, and enzymatic activity. After binding to cells, DT is taken up into endosome-like acidic compartments where the translocation domain inserts into the endosomal membrane and releases the catalytic domain into the cytosol. The ...

journal_title：Biophysical journal

authors： Kent MS,Yim H,Murton JK,Satija S,Majewski J,Kuzmenko I

更新日期：2008-03-15 00:00:00

abstract：:We present a theoretical model for aqueous solutions of double-stranded (ds) DNA with explicit consideration of electrostatic interactions, excluded-volume effects, van der Waals attractions, and salt ions. With reasonable parameters estimated from the DNA structure and experimental data for electrolytes, we are able ...

journal_title：Biophysical journal

authors： Li Z,Wu J,Wang ZG

更新日期：2008-02-01 00:00:00

abstract：:The photocycle of salinarum halorhodopsin was investigated in the presence of azide. The azide binds to the halorhodopsin with 150 mM binding constant in the absence of chloride and with 250 mM binding constant in the presence of 1 M chloride. We demonstrate that the azide-binding site is different from that of chlori...

journal_title：Biophysical journal

authors： Lakatos M,Groma GI,Ganea C,Lanyi JK,Váró G

更新日期：2002-04-01 00:00:00

abstract：:We successfully demonstrate the effectiveness of two-photon fluorescence cross-correlation spectroscopy (TPCCS) to study the complex binding stoichiometry of calmodulin (CaM) and Ca(2+)/CaM-dependent protein kinase II (CaMKII). Practical considerations are made for developing an intracellular cross-correlation assay, ...

journal_title：Biophysical journal

authors： Kim SA,Heinze KG,Bacia K,Waxham MN,Schwille P

更新日期：2005-06-01 00:00:00

abstract：:The sarcoplasmic reticulum channel (ryanodine receptor) from cardiac myocytes was reconstituted into planar lipid bilayers consisting of 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) and 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) in varying ratios. The channel activity parameters, i.e., open probability an...

journal_title：Biophysical journal

authors： Cannon B,Hermansson M,Györke S,Somerharju P,Virtanen JA,Cheng KH

更新日期：2003-08-01 00:00:00

abstract：:Several investigators have demonstrated that under conditions where little or no gas exchange occurs across the alveolar capillary membrane the PCO(2) is higher in the alveolus than in the mixed venous blood, whereas there are no PO(2) differences. Gurtner et al. have explained the DeltaPCO(2) by a model in which H(+)...

journal_title：Biophysical journal

authors： Gurtner GH

更新日期：1972-06-01 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