Twisting and untwisting a single DNA molecule covered by RecA protein.


: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 nucleated, the extent of RecA coverage still depends on the degree of supercoiling: exerting a positive or negative torsional constraint on the fiber forces partial depolymerization, with a strikingly greater stability when ATPgammaS is used as a cofactor instead of ATP. This nucleofilament's sensitivity to topology might be a way for the bacterial cell to limit consumption of precious RecA monomers when DNA damage is addressed through homologous recombination repair.


Biophys J


Biophysical journal


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




Has Abstract


2004-10-01 00:00:00














  • Framework model for single proton conduction through gramicidin.

    abstract::This paper describes a framework model for proton conduction through gramicidin; a model designed to incorporate information from molecular dynamics and use this to predict conductance properties. The state diagram describes both motion of an excess proton within the pore as well as the reorientation of waters within ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Schumaker MF,Pomès R,Roux B

    更新日期:2001-01-01 00:00:00

  • Permeation in ionic channels: a statistical rate theory approach.

    abstract::A novel way to model permeation through ionic channels is formulated. Our method does not require that equilibrium exists in the channel or at the channel interfaces. In addition, the potential profile does not need to be specified and the assumption of constant field across the membrane does not need to be made. Our ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Skinner FK,Ward CA,Bardakjian BL

    更新日期:1993-08-01 00:00:00

  • The monovalent cation "leak" transport in human erythrocytes: an electroneutral exchange process.

    abstract::The mechanism of the "ground permeability" of the human erythrocyte membrane for K+ and Na+ was investigated with respect to a possible involvement of a previously unidentified specific transport pathway, because earlier studies showed that it cannot be explained on the basis of simple electrodiffusion. In particular,...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Richter S,Hamann J,Kummerow D,Bernhardt I

    更新日期:1997-08-01 00:00:00

  • Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei.

    abstract::We study a Brownian dynamics simulation model of a biopolymeric shell deformed by axial forces exerted at opposing poles. The model exhibits two distinct, linear force-extension regimes, with the response to small tensions governed by linear elasticity and the response to large tensions governed by an effective spring...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Banigan EJ,Stephens AD,Marko JF

    更新日期:2017-10-17 00:00:00

  • The standard Hodgkin-Huxley model and squid axons in reduced external Ca++ fail to accommodate to slowly rising currents.

    abstract::Accommodation may be defined as an increase in the threshold of an excitable membrane when the membrane is subjected to a sustained subthreshold depolarizing stimulus. Some excitable membranes show accommodation in response to currents which rise linearly at a very slow rate. In this report we point out a theoretical ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Jakobsson E,Guttman R

    更新日期:1980-08-01 00:00:00

  • Reconstitution of membrane proteins into giant unilamellar vesicles via peptide-induced fusion.

    abstract::In this work, we present a protocol to reconstitute membrane proteins into giant unilamellar vesicles (GUV) via peptide-induced fusion. In principle, GUV provide a well-defined lipid matrix, resembling a close-to-native state for biophysical studies, including optical microspectroscopy, of transmembrane proteins at th...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Kahya N,Pécheur EI,de Boeij WP,Wiersma DA,Hoekstra D

    更新日期:2001-09-01 00:00:00

  • Membrane tension, myosin force, and actin turnover maintain actin treadmill in the nerve growth cone.

    abstract::A growth cone is a motile structure at the tips of axons that is driven by the actin network and guides axon extension. Low actin adhesion to the substrate creates a stationary actin treadmill that allows leading-edge protrusion when adhesion increases in response to guidance cues. We use experimental measurements in ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Craig EM,Van Goor D,Forscher P,Mogilner A

    更新日期:2012-04-04 00:00:00

  • Rotation Mechanism of Molecular Motor V1-ATPase Studied by Multiscale Molecular Dynamics Simulation.

    abstract::Enterococcus hirae V1-ATPase is a molecular motor composed of the A3B3 hexamer ring and the central stalk. In association with ATP hydrolysis, three catalytic AB pairs in the A3B3 ring undergo conformational changes, which lead to a 120° rotation of the central stalk. To understand how the conformational changes of th...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Isaka Y,Ekimoto T,Kokabu Y,Yamato I,Murata T,Ikeguchi M

    更新日期:2017-03-14 00:00:00

  • The donnan equilibrium: a theoretical study of the effects of interionic forces.

    abstract::We investigate the conditions under which nonideality in solution influences the Donnan equilibrium. Of the various parameters that characterize this equilibrium, the osmotic pressure established across the Donnan membrane is found to be particularly sensitive to intermolecular interactions between the diffusible and ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Stell G,Joslin CG

    更新日期:1986-11-01 00:00:00

  • Theory for RNA folding, stretching, and melting including loops and salt.

    abstract::Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop formation, and salt effects. Using an iterative expression for the partition function ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Einert TR,Netz RR

    更新日期:2011-06-08 00:00:00

  • Free energies of molecular bound states in lipid bilayers: lethal concentrations of antimicrobial peptides.

    abstract::The lipid matrix, or the lipid bilayer, of cell membranes is a natural binding site for amphipathic molecules, including antimicrobial peptides, pore-forming proteins, and many drugs. The unique property of pore-forming antimicrobial peptides is that they exhibit a threshold concentration (called the lethal concentrat...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Huang HW

    更新日期:2009-04-22 00:00:00

  • Laser flow measurements of scattering and fluorescence from cell nuclei in the presence of increasing Mg++ concentrations.

    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

    pub_type: 杂志文章


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

    更新日期:1985-04-01 00:00:00

  • Cations as switches of amyloid-mediated membrane disruption mechanisms: calcium and IAPP.

    abstract::Disruption of the integrity of the plasma membrane by amyloidogenic proteins is linked to the pathogenesis of a number of common age-related diseases. Although accumulating evidence suggests that adverse environmental stressors such as unbalanced levels of metal ions may trigger amyloid-mediated membrane damage, many ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Sciacca MF,Milardi D,Messina GM,Marletta G,Brender JR,Ramamoorthy A,La Rosa C

    更新日期:2013-01-08 00:00:00

  • Comparison between orientational and conformational orders in fluid lipid bilayers.

    abstract::The orientational order as determined by 2H NMR and the infrared frequencies of the C--H stretching modes of the methylene groups have been measured for several systems (POPC, POPC/cholesterol and POPE), all in the fluid phase, and then were compared; this work reveals an unexpected linear correlation between them. Th...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Kodati VR,Lafleur M

    更新日期:1993-01-01 00:00:00

  • The intrinsic pKa values for phosphatidylserine and phosphatidylethanolamine in phosphatidylcholine host bilayers.

    abstract::Potentiometric titrations and surface potential measurements have been used to determine the intrinsic pKa values of both the carboxyl and amino groups of phosphatidylserine (PS) in mixed vesicles of PS and phosphatidylcholine (PC), and also of the amino group of phosphatidylethanolamine (PE) in mixed PE-PC vesicles. ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Tsui FC,Ojcius DM,Hubbell WL

    更新日期:1986-02-01 00:00:00

  • More gating charges are needed to open a Shaker K+ channel than are needed to open an rBIIA Na+ channel.

    abstract::This study presents what is, to our knowledge, a novel technique by means of which the ratio of the single gating charges of voltage-gated rat brain IIA (rBIIA) sodium and Shaker potassium ion channels was estimated. In the experiment, multiple tandems of enhanced green fluorescent protein were constructed and inserte...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Gamal El-Din TM,Grögler D,Lehmann C,Heldstab H,Greeff NG

    更新日期:2008-08-01 00:00:00

  • Link between the enzymatic kinetics and mechanical behavior in an actomyosin motor.

    abstract::We have attempted to link the solution actomyosin ATPase with the mechanical properties of in vitro actin filament sliding over heavy meromyosin. To accomplish this we perturbed the system by altering the substrate with various NTPs and divalent cations, and by altering ionic strength. A wide variety of enzymatic and ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Amitani I,Sakamoto T,Ando T

    更新日期:2001-01-01 00:00:00

  • New model of charged molecule redistribution induced in spherical vesicles by direct current electric field.

    abstract::A new electrophoresis model of charged components in a spherical phospholipid vesicle is proposed. In the new model the effective local tangential electric field is a result of the uniform external electric field modified by the electric field of redistributed charges. The modification is calculated on the basis of th...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Piasecki W,Salwiński L,Froncisz W

    更新日期:1997-02-01 00:00:00

  • A computational framework for the topological analysis and targeted disruption of signal transduction networks.

    abstract::In this article, optimization-based frameworks are introduced for elucidating the input-output structure of signaling networks and for pinpointing targeted disruptions leading to the silencing of undesirable outputs in therapeutic interventions. The frameworks are demonstrated on a large-scale reconstruction of a sign...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Dasika MS,Burgard A,Maranas CD

    更新日期:2006-07-01 00:00:00

  • Kinetics of interaction of N epsilon-fluorescein isothiocyanate-lysine-23-cobra alpha-toxin with the acetylcholine receptor.

    abstract::We have studied the kinetics of N epsilon-fluorescein isothiocyanate-lysine-23 cobra alpha-toxin (FITC-toxin) binding to the membrane-associated acetylcholine receptor from the Torpedo californica electric organ. The fluorescent toxin not only enabled us to monitor the binding reaction continuously but also to examine...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Cheung AT,Johnson DA,Taylor P

    更新日期:1984-02-01 00:00:00

  • Intrinsic electric fields and proton diffusion in immobilized protein membranes. Effects of electrolytes and buffers.

    abstract::We present a theory for proton diffusion through an immobilized protein membrane perfused with an electrolyte and a buffer. Using a Nernst-Planck equation for each species and assuming local charge neutrality, we obtain two coupled nonlinear diffusion equations with new diffusion coefficients dependent on the concentr...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Zabusky NJ,Deem GS

    更新日期:1979-01-01 00:00:00

  • Is there a conserved interaction between cardiolipin and the type II bacterial reaction center?

    abstract::In a recent publication, the structural details of an interaction between the Rhodobacter sphaeroides reaction center and the anionic phospholipid diphosphatidyl glycerol (cardiolipin) were described (K. E. McAuley, P. K. Fyfe, J. P. Ridge, N. W. Isaacs, R. J. Cogdell, and M. R. Jones, 1999, Proc. Natl. Acad. Sci. U.S...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Wakeham MC,Sessions RB,Jones MR,Fyfe PK

    更新日期:2001-03-01 00:00:00

  • Rapid Formation of Peptide/Lipid Coaggregates by the Amyloidogenic Seminal Peptide PAP248-286.

    abstract::Protein/lipid coassembly is an understudied phenomenon that is important to the function of antimicrobial peptides as well as the pathological effects of amyloid. Here, we study the coassembly process of PAP248-286, a seminal peptide that displays both amyloid-forming and antimicrobial activity. PAP248-286 is a peptid...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Vane EW,He S,Maibaum L,Nath A

    更新日期:2020-09-01 00:00:00

  • Analysis of a Functional Dimer Model of Ubiquinol Cytochrome c Oxidoreductase.

    abstract::Ubiquinol cytochrome c oxidoreductase (bc1 complex) serves as an important electron junction in many respiratory systems. It funnels electrons coming from NADH and ubiquinol to cytochrome c, but it is also capable of producing significant amounts of the free radical superoxide. In situ and in other experimental system...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Bazil JN

    更新日期:2017-10-03 00:00:00

  • Probing tubulin-blocked state of VDAC by varying membrane surface charge.

    abstract::Reversible blockage of the voltage-dependent anion channel (VDAC) of the mitochondrial outer membrane by dimeric tubulin is being recognized as a potent regulator of mitochondrial respiration. The tubulin-blocked state of VDAC is impermeant for ATP but only partially closed for small ions. This residual conductance al...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Gurnev PA,Queralt-Martin M,Aguilella VM,Rostovtseva TK,Bezrukov SM

    更新日期:2012-05-02 00:00:00

  • Regulation of calcium channel activity by lipid domain formation in planar lipid bilayers.

    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

    pub_type: 杂志文章


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

    更新日期:2003-08-01 00:00:00

  • Effect of the anesthetics benzyl alcohol and chloroform on bilayers made from monolayers.

    abstract::The neutral anesthetics chloroform and benzyl alcohol, at concentrations that block the nerve impulse, greatly modify the transport parameters of positive and negative ions in lipid bilayers made from monolayers. Both chloroform and benzyl alcohol increase the membrane permeability to these ions and increase the trans...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Reyes J,Latorre R

    更新日期:1979-11-01 00:00:00

  • Reversing nerve cell pathology by optimizing modulatory action on target ion channels.

    abstract::In diseases of the brain, the distribution and properties of ion channels display deviations from healthy control subjects. We studied three cases of ion channel alteration related to epileptogenesis. The first case of ion channel alteration represents an enhanced sodium current, the second case addresses the downregu...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Tigerholm J,Fransén E

    更新日期:2011-10-19 00:00:00

  • Electrofusion between heterogeneous-sized mammalian cells in a pellet: potential applications in drug delivery and hybridoma formation.

    abstract::High-efficiency electrofusion between cells of different sizes was achieved by application of fusing electric pulses to cells in centrifuged pellets. Larger target cells (Chinese hamster ovary or L1210 cells) were stacked among smaller human erythrocytes or erythrocyte ghosts by sequential centrifugation at 700 g to f...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Li LH,Hensen ML,Zhao YL,Hui SW

    更新日期:1996-07-01 00:00:00

  • How Hofmeister ion interactions affect protein stability.

    abstract::Model compound studies in the literature show how Hofmeister ion interactions affect protein stability. Although model compound results are typically obtained as salting-out constants, they can be used to find out how the interactions affect protein stability. The null point in the Hofmeister series, which divides pro...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Baldwin RL

    更新日期:1996-10-01 00:00:00