Evaluation of dynamic features of Escherichia coli 16S ribosomal RNA in homogeneous physiological solution.


:There is no methodology for the estimation of the dynamic features of large-molecular-weight RNAs in homogeneous physiological media. In this report, a luminescence anisotropy-based method using a long-lifetime luminescent oligonucleotide probe for the estimation of the dynamic features of large-molecular-weight RNA is described. As a luminescent probe, Ru(II) complex-labeled oligonucleotides, which have a complementary sequence to the single-stranded regions of Escherichia coli 16S rRNA, were synthesized. After the hybridization of the probe to single-stranded regions of 16S rRNA, the segmental motions of the regions were evaluated by time-resolved luminescence anisotropy analysis. In 16S rRNA, the L2 site (323-332 nt) was found to be the most flexible among the seven sites chosen. From a comparison between the hybridization kinetics of oligonucleotides to these single-stranded regions and the rotational correlation times, it was suggested that the flexibility of the single-stranded region was closely correlated with the hybridization kinetics. Furthermore, results of the luminescence lifetime measurement and luminescence quenching experiments suggested that the highly flexible region was located on the surface of the 16S rRNA and that the less flexible region was located in the depths of 16S rRNA.


Biophys J


Biophysical journal


Sakamoto T,Mahara A,Yamagata K,Iwase R,Yamaoka T,Murakami A




Has Abstract


2005-12-01 00:00:00














  • Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding.

    abstract::Binding of a small molecule to a macromolecular target reduces its conformational freedom, resulting in a negative entropy change that opposes the binding. The goal of this study is to estimate the configurational entropy change of two minor-groove-binding ligands, netropsin and distamycin, upon binding to the DNA dup...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Dolenc J,Baron R,Oostenbrink C,Koller J,van Gunsteren WF

    更新日期:2006-08-15 00:00:00

  • Simultaneous measurement of Ca2+ influx and reversal potentials in recombinant N-methyl-D-aspartate receptor channels.

    abstract::The Ca(2+) permeability of N-methyl-D-aspartate receptor (NMDA-R) channels was studied in human embryonic kidney cells transfected with the NR1-NR2A subunit combination. To determine the fractional Ca(2+) current (P(f)), measurements of fura-2-based Ca(2+) influx and whole-cell currents were made in symmetrical monova...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Schneggenburger R

    更新日期:1996-05-01 00:00:00

  • A quantitative approach to analyze binding diffusion kinetics by confocal FRAP.

    abstract::Most of the important types of interactions that occur in cells can be characterized as binding-diffusion type processes, and can be quantified by kinetic rate constants such as diffusion coefficients (D) and binding rate constants (k(on) and k(off)). Confocal FRAP is a potentially important tool for the quantitative ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Kang M,Day CA,DiBenedetto E,Kenworthy AK

    更新日期:2010-11-03 00:00:00

  • Stability of the heme environment of the nitric oxide synthase from Staphylococcus aureus in the absence of pterin cofactor.

    abstract::We have used resonance Raman spectroscopy to probe the heme environment of a recently discovered NOS from the pathogenic bacterium Staphylococcus aureus, named SANOS. We detect two forms of the CO complex in the absence of L-arginine, with nu(Fe-CO) at 482 and 497 cm(-1) and nu(C-O) at 1949 and 1930 cm(-1), respective...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Chartier FJ,Couture M

    更新日期:2004-09-01 00:00:00

  • Mutating three residues in the bovine rod cyclic nucleotide-activated channel can switch a nucleotide from inactive to active.

    abstract::Cyclic nucleotide-gated (CNG) channels, which were initially studied in retina and olfactory neurons, are activated by cytoplasmic cGMP or cAMP. Detailed comparisons of nucleotide-activated currents using nucleotide analogs and mutagenesis revealed channel-specific residues in the nucleotide-binding domain that regula...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Scott SP,Cummings J,Joe JC,Tanaka JC

    更新日期:2000-05-01 00:00:00

  • Kinetic analysis of protein crystal nucleation in gel matrix.

    abstract::The effect of agarose on nucleation of hen egg white lysozyme crystal was examined quantitatively using a temperature-jumping technique. For the first time, to our knowledge, the inhibition of agarose during the nucleation of lysozyme was quantified in two respects: a), the effect of increasing interfacial nucleation ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Wang L,Liu XY

    更新日期:2008-12-15 00:00:00

  • The hill coefficient for the Ca2+-activation of striated muscle contraction.

    abstract::The following arguments are presented for the observation that curves relating free Ca2+ and force development of thin filament regulated myofilaments of skinned muscle fibers have Hill coefficient (n) greater than 4, which is the number of Ca2+ binding sites on troponin: Activation of the myofilaments is a process re...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Shiner JS,Solaro RJ

    更新日期:1984-10-01 00:00:00

  • Observation volumes and {gamma}-factors in two-photon fluorescence fluctuation spectroscopy.

    abstract::Fluorescence fluctuation spectroscopy has become an important measurement tool for investigating molecular dynamics, molecular interactions, and chemical kinetics in biological systems. Although the basic theory of fluctuation spectroscopy is well established, it is not widely recognized that saturation of the fluores...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Nagy A,Wu J,Berland KM

    更新日期:2005-09-01 00:00:00

  • Conformation of DNA GG intrastrand cross-link of antitumor oxaliplatin and its enantiomeric analog.

    abstract::Downstream processes that discriminate between DNA adducts of a third generation platinum antitumor drug oxaliplatin and conventional cisplatin are believed to be responsible for the differences in their biological effects. These different biological effects are explained by the ability of oxaliplatin to form DNA addu...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Malina J,Novakova O,Vojtiskova M,Natile G,Brabec V

    更新日期:2007-12-01 00:00:00

  • The need for a kinetics for biological transport.

    abstract::The traditional theory of transport across capillary membranes via a laminar Poiseuille flow is shown to be invalid. It is demonstrated that the random, diffusive nature of the molecular flow and interactions with the "pore" walls play an important role in the transport process. Neither the continuum Navier-Stokes the...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Schindler AM,Iberall AS

    更新日期:1973-08-01 00:00:00

  • Selectivity in lipid binding to the bacterial outer membrane protein OmpF.

    abstract::The outer membrane porin OmpF from Escherichia coli has been reconstituted into lipid bilayers of defined composition, and fluorescence spectroscopy is used to characterize its interaction with the surrounding lipid. OmpF is a trimer within the membrane. It contains two Trp residues per monomer, Trp(214) at the lipid-...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: O'Keeffe AH,East JM,Lee AG

    更新日期:2000-10-01 00:00:00

  • Structural role of the conserved cysteines in the dimerization of the viral transmembrane oncoprotein E5.

    abstract::The E5 oncoprotein is the major transforming protein of bovine papillomavirus type 1. This 44-residue transmembrane protein can interact with the platelet-derived growth factor receptor β, leading to ligand-independent activation and cell transformation. For productive interaction, E5 needs to dimerize via a C-termina...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Windisch D,Hoffmann S,Afonin S,Vollmer S,Benamira S,Langer B,Bürck J,Muhle-Goll C,Ulrich AS

    更新日期:2010-09-22 00:00:00

  • Solutions to axon equations.

    abstract::The solutions to a general class of axon partial differential equations proposed by FitzHugh which includes the Hodgkin-Huxley equations are studied. It is shown that solutions to the partial differential equations are exactly the solutions to a related set of integral equations. An iterative procedure for constructin...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Evans J,Shenk N

    更新日期:1970-11-01 00:00:00

  • Unusual Isothermal Hysteresis in DNA i-Motif pH Transitions: A Study of the RAD17 Promoter Sequence.

    abstract::We have interrogated the isothermal folding behavior of the DNA i-motif of the human telomere, dC19, and a high-stability i-motif-forming sequence in the promoter of the human DNA repair gene RAD17 using human physiological solution and temperature conditions. We developed a circular-dichroism-spectroscopy-based pH ti...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Rogers RA,Fleming AM,Burrows CJ

    更新日期:2018-04-24 00:00:00

  • Exploring peptide-membrane interactions with coarse-grained MD simulations.

    abstract::The interaction of α-helical peptides with lipid bilayers is central to our understanding of the physicochemical principles of biological membrane organization and stability. Mutations that alter the position or orientation of an α-helix within a membrane, or that change the probability that the α-helix will insert in...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Hall BA,Chetwynd AP,Sansom MS

    更新日期:2011-04-20 00:00:00

  • Passive membrane potentials: a generalization of the theory of electrotonus.

    abstract::THE THEORY OF ELECTROTONUS, WHICH HAS BEEN WELL DEVELOPED FOR SMALL CYLINDERS, IS EXTENDED: the fundamental potential equations for a membrane of arbitrary shape are derived, and solutions are found for cylindrical and spherical geometries. If two purely conductive media are separated by a resistance-capacitance membr...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Hellerstein D

    更新日期:1968-03-01 00:00:00

  • Effect of fluorine substitution on the interaction of lipophilic ions with the plasma membrane of mammalian cells.

    abstract::The effects of the anionic tungsten carbonyl complex [W(CO)(5)SC(6)H(5)](-) and its fluorinated analog [W(CO)(5)SC(6)F(5)](-) on the electrical properties of the plasma membrane of mouse myeloma cells were studied by the single-cell electrorotation technique. At micromolar concentrations, both compounds gave rise to a...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Kürschner M,Nielsen K,von Langen JR,Schenk WA,Zimmermann U,Sukhorukov VL

    更新日期:2000-09-01 00:00:00

  • The role of diffusion in enzyme kinetics.

    abstract::A discussion is given of the general role of diffusion in enzyme kinetics based upon a rigorous theory for bimolecular association and dissociation steps that was presented previously, and criteria are formulated for the dependence of the over-all rate on medium viscosity. With these criteria it is possible to conclud...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Schurr JM

    更新日期:1970-08-01 00:00:00

  • Density invariance of cultured Chinese hamster cells with stage of the mitotic cycle.

    abstract::Isopycnic banding of Chinese hamster line CHO cells in Ficoll gradients shows that a population in balanced, exponential growth is very homogeneous with respect to density, the coefficient of variation of the density distribution spectrum being less than 5% of the mean reduced density (i.e. density minus one). Similar...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Anderson EC,Petersen DF,Tobey RA

    更新日期:1970-07-01 00:00:00

  • Phospholipid complexation and association with apolipoprotein C-II: insights from mass spectrometry.

    abstract::The interactions between phospholipid molecules in suspensions have been studied by using mass spectrometry. Electrospray mass spectra of homogeneous preparations formed from three different phospholipid molecules demonstrate that under certain conditions interactions between 90 and 100 lipid molecules can be preserve...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Hanson CL,Ilag LL,Malo J,Hatters DM,Howlett GJ,Robinson CV

    更新日期:2003-12-01 00:00:00

  • Temperature derivative fluorescence spectroscopy as a tool to study dynamical changes in protein crystals.

    abstract::Motions through the energy landscape of proteins lead to biological function. At temperatures below a dynamical transition (150-250 K), some of these motions are arrested and the activity of some proteins ceases. Here, we introduce the technique of temperature-derivative fluorescence microspectrophotometry to investig...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Weik M,Vernede X,Royant A,Bourgeois D

    更新日期:2004-05-01 00:00:00

  • Proton transfer dynamics on the surface of the late M state of bacteriorhodopsin.

    abstract::The cytoplasmic surface of the BR (initial) state of bacteriorhodopsin is characterized by a cluster of three carboxylates that function as a proton-collecting antenna. Systematic replacement of most of the surface carboxylates indicated that the cluster is made of D104, E161, and E234 (Checover, S., Y. Marantz, E. Na...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Nachliel E,Gutman M,Tittor J,Oesterhelt D

    更新日期:2002-07-01 00:00:00

  • Kinetics of the iodine- and bromine-mediated transport of halide ions: demonstration of an interfacial complexation mechanism.

    abstract::Stationary and kinetic experiments were performed on lipid bilayer membranes to study the mechanism of iodine- and bromine-mediated halide transport in detail. The stationary conductance data suggested that four different 1:1 complexes between I2 and Br2 and the halides I- and Br- were responsible for the observed con...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Klotz KH,Benz R

    更新日期:1993-12-01 00:00:00

  • Electrostatic contributions to the stability of a thermophilic cold shock protein.

    abstract::The thermophilic Bacillus caldolyticus cold shock protein (Bc-Csp) differs from the mesophilic Bacillus subtilis cold shock protein B (Bs-CspB) in 11 of the 66 residues. Stability measurements of Schmid and co-workers have implicated contributions of electrostatic interactions to the thermostability. To further elucid...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Zhou HX,Dong F

    更新日期:2003-04-01 00:00:00

  • Concerted gating mechanism underlying KATP channel inhibition by ATP.

    abstract::KATP channels assemble from four regulatory SUR1 and four pore-forming Kir6.2 subunits. At the single-channel current level, ATP-dependent gating transitions between the active burst and the inactive interburst conformations underlie inhibition of the KATP channel by intracellular ATP. Previously, we identified a slow...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Drain P,Geng X,Li L

    更新日期:2004-04-01 00:00:00

  • Determination of the oligomer size of amyloidogenic protein beta-amyloid(1-40) by single-molecule spectroscopy.

    abstract::Amyloid diseases are traditionally characterized by the appearance of inter- and intracellular fibrillar protein deposits, termed amyloid. Historically, these deposits have been thought to be the etiology of the disease. However, recent evidence suggests that small oligomers of the amyloidogenic protein/peptide are th...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Ding H,Wong PT,Lee EL,Gafni A,Steel DG

    更新日期:2009-08-05 00:00:00

  • Binding features of diacetylmorphine (heroin) in whole blood and in blood fractions.

    abstract::Binding features of heroin in whole blood and in blood fractions were delineated by measuring the selective spin-lattice relaxation rates of heroin protons in physiologic conditions. Interaction with some receptor located in the whole human blood or in the human plasma was detected and the apparent binding constant ca...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Barni Comparini I,Gaggelli E,Marchettini N,Valensin G

    更新日期:1985-08-01 00:00:00

  • Shear-Induced Unfolding and Enzymatic Cleavage of Full-Length VWF Multimers.

    abstract::Proteolysis of the multimeric blood coagulation protein von Willebrand Factor (VWF) by ADAMTS13 is crucial for prevention of microvascular thrombosis. ADAMTS13 cleaves VWF within the mechanosensitive A2 domain, which is believed to open under shear flow. In this study, we combine fluorescence correlation spectroscopy ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Lippok S,Radtke M,Obser T,Kleemeier L,Schneppenheim R,Budde U,Netz RR,Rädler JO

    更新日期:2016-02-02 00:00:00

  • Molecular models need to be tested: the case of a solar flares discoidal HDL model.

    abstract::In the absence of atomic structures of high-density lipoproteins in their lipid-bound states, many molecular models have been produced based on experimental data. Using molecular dynamics, we show that a recently proposed "solar-flares" model of discoidal high-density lipoprotein is implausible. Our simulations show a...

    journal_title:Biophysical journal

    pub_type: 信件


    authors: Shih AY,Sligar SG,Schulten K

    更新日期:2008-06-01 00:00:00

  • A theoretical examination of ionic interactions between neural and non-neural membranes.

    abstract::Evidence from electron microscopy indicates that the separation between adjacent membranes of the central nervous system (CNS) is less than 500 A and perhaps as small as 100-250 A. The rapid K(+) efflux associated with the neural action potential may therefore be sufficient to affect the local extracellular potassium ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Lebovitz RM

    更新日期:1970-05-01 00:00:00