Analytic binding isotherms describing competitive interactions of a protein ligand with specific and nonspecific sites on the same DNA oligomer.

Abstract:

:Many studies of specific protein-nucleic acid binding use short oligonucleotides or restriction fragments, in part to minimize the potential for nonspecific binding of the protein. However, when the specificity ratio is low, multiple nonspecifically bound proteins may occupy the region of DNA corresponding to one specific site; this situation was encountered in our recent calorimetric study of binding of integration host factor (IHF) protein to its specific 34-bp H' DNA site. Here, beginning from the analytical McGhee and von Hippel infinite-lattice nonspecific binding isotherm, we derive a novel analytic isotherm for nonspecific binding of a ligand to a finite lattice. This isotherm is an excellent approximation to the exact factorial-based Epstein finite lattice isotherm even for short lattices and therefore is of great practical significance for analysis of experimental data and for analytic theory. Using this isotherm, we develop an analytic treatment of the competition between specific and nonspecific binding of a large ligand to the same finite lattice (i.e., DNA oligomer) containing one specific and multiple overlapping nonspecific binding sites. Analysis of calorimetric data for IHF-H' DNA binding using this treatment yields enthalpies and binding constants for both specific and nonspecific binding and the nonspecific site size. This novel analysis demonstrates the potential contribution of nonspecific binding to the observed thermodynamics of specific binding, even with very short DNA oligomers, and the need for reverse (constant protein) titrations or titrations with nonspecific DNA to resolve specific and nonspecific contributions. The competition treatment is useful in analyzing low-specificity systems, including those where specificity is weakened by mutations or the absence of specificity factors.

journal_name

Biophys J

journal_title

Biophysical journal

authors

Tsodikov OV,Holbrook JA,Shkel IA,Record MT Jr

doi

10.1016/S0006-3495(01)75847-X

subject

Has Abstract

pub_date

2001-10-01 00:00:00

pages

1960-9

issue

4

eissn

0006-3495

issn

1542-0086

pii

S0006-3495(01)75847-X

journal_volume

81

pub_type

杂志文章
  • Bending resistance and chemically induced moments in membrane bilayers.

    abstract::Pure bending of a membrane bilayer is developed including different properties for each membrane half. Both connected and unconnected bilayer surfaces are treated. The bilayer bending resistance is the resultant of parallel surface compression "resistances." The neutral surface is a function of the upper and lower sur...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(74)85959-X

    authors: Evans EA

    更新日期:1974-12-01 00:00:00

  • A virial expansion for discrete charges buried in a membrane.

    abstract::Recent experiments (1,2) have shown that hydrophobic ions adsorbed to lipid membranes repel each other significantly at densities as low as one charge every few tens of square nanometers. This paper shows how to calculate the mutual repulsion of a population of such ions, assumed to be discrete but free to diffuse lat...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(78)85402-2

    authors: Tsien RY

    更新日期:1978-11-01 00:00:00

  • Secondary structure and lipid contact of a peptide antibiotic in phospholipid bilayers by REDOR.

    abstract::The chemical shifts of specific (13)C and (15)N labels distributed throughout KIAGKIA-KIAGKIA-KIAGKIA (K3), an amphiphilic 21-residue antimicrobial peptide, prove that the peptide is in an all alpha-helical conformation in the bilayers of multilamellar vesicles (MLVs) containing dipalmitoylphosphatidylcholine and dipa...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.103.032706

    authors: Toke O,Maloy WL,Kim SJ,Blazyk J,Schaefer J

    更新日期:2004-07-01 00:00:00

  • TEM-1 backbone dynamics-insights from combined molecular dynamics and nuclear magnetic resonance.

    abstract::Dynamic properties of class A beta-lactamase TEM-1 are investigated from molecular dynamics (MD) simulations. Comparison of MD-derived order parameters with those obtained from model-free analysis of nuclear magnetic resonance (NMR) relaxation data shows high agreement for N-H moieties within alpha- and beta-secondary...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2009.08.061

    authors: Fisette O,Morin S,Savard PY,Lagüe P,Gagné SM

    更新日期:2010-02-17 00:00:00

  • "Resonances" in the dielectric absorption of DNA?

    abstract::An attempt was made to confirm previous reports of resonant-like dielectric absorption of plasmid DNA in aqueous solutions at 1-10 GHz. The dielectric properties of the sample were measured using an automatic network analyzer with two different techniques. One technique used an open-ended coaxial probe immersed in the...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(87)83231-9

    authors: Foster KR,Epstein BR,Gealt MA

    更新日期:1987-09-01 00:00:00

  • Prediction of protein solubility from calculation of transfer free energy.

    abstract::Solubility plays a major role in protein purification, and has serious implications in many diseases. We studied the effects of pH and mutations on protein solubility by calculating the transfer free energy from the condensed phase to the solution phase. The condensed phase was modeled as an implicit solvent, with a d...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.127746

    authors: Tjong H,Zhou HX

    更新日期:2008-09-15 00:00:00

  • Individual activity of calcium ions in pure solutions of CaCl2 and in mixtures.

    abstract::Individual ion activities were calculated for Ca(2+) in pure solutions of CaCl(2) and in mixtures of CaCl(2) with MgCl(2) and with NaCl, using different conventions to obtain gamma(Ca2+). The results were compared with potentiometric measurements, using calcium specific electrodes. It is found that significant differe...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(68)86528-2

    authors: Shatkay A

    更新日期:1968-08-01 00:00:00

  • Water dynamics in glycosphingolipid aggregates studied by LAURDAN fluorescence.

    abstract::We have characterized the fluorescence properties of 6-dodecanoyl-2-dimethylamine-naphthalene (LAURDAN) in pure interfaces formed by sphingomyelin and 10 chemically related glycosphingolipids (GSLs).1 The GSLs contain neutral and anionic carbohydrate residues in their oligosaccharide chain. These systems were studied ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(98)77517-4

    authors: Bagatolli LA,Gratton E,Fidelio GD

    更新日期:1998-07-01 00:00:00

  • The molecular basis of the solution properties of hyaluronan investigated by confocal fluorescence recovery after photobleaching.

    abstract::Hyaluronan (HA) is a highly hydrated polyanion, which is a network-forming and space-filling component in the extracellular matrix of animal tissues. Confocal fluorescence recovery after photobleaching (confocal-FRAP) was used to investigate intramolecular hydrogen bonding and electrostatic interactions in hyaluronan ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(99)77061-X

    authors: Gribbon P,Heng BC,Hardingham TE

    更新日期:1999-10-01 00:00:00

  • The fastest contracting muscles of nonmammalian vertebrates express only one isoform of the ryanodine receptor.

    abstract::The skeletal muscles of chickens, frogs, and fish have been reported to express two isoforms (alpha and beta) of the sarcoplasmic reticulum calcium release channel (ryanodine receptor or RYR), while mammals express only one. We have studied patterns of RYR isoform expression in skeletal muscles from a variety of fish,...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(93)81303-1

    authors: O'Brien J,Meissner G,Block BA

    更新日期:1993-12-01 00:00:00

  • Lipid Droplets Can Spontaneously Bud Off from a Symmetric Bilayer.

    abstract::Lipid droplets (LDs) are cytosolic organelles that protrude from the endoplasmic reticulum membrane under energy-rich conditions. How an LD buds off from the endoplasmic reticulum bilayer is still elusive. By using a continuous media description, we computed the morphology of a lipid droplet embedded in between two id...

    journal_title:Biophysical journal

    pub_type: 信件

    doi:10.1016/j.bpj.2017.05.045

    authors: Deslandes F,Thiam AR,Forêt L

    更新日期:2017-07-11 00:00:00

  • Disparate fluorescence properties of 2-[4'-(iodoacetamido)anilino]-naphthalene-6-sulfonic acid attached to Cys-84 and Cys-35 of troponin C in cardiac muscle troponin.

    abstract::Two monocysteine mutants of cardiac muscle troponin C, cTnC(C35S) and cTnC(C84S), were genetically generated and labeled with the fluorescent probe 2-[4'-(iodoacetamido)anilino]naphthalene-6-sulfonic acid (IAANS) at Cys-84 and Cys-35, respectively. Cys-84 is located on helix D in the regulatory N-domain, and Cys-35 is...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/s0006-3495(97)78719-8

    authors: Dong WJ,Wang CK,Gordon AM,Cheung HC

    更新日期:1997-02-01 00:00:00

  • Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation.

    abstract::Cholesterol is essential to the formation of phase-separated lipid domains in membranes. Lipid domains can exist in different thermodynamic phases depending on the molecular composition and play significant roles in determining structure and function of membrane proteins. We investigate the role of cholesterol in the ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2018.10.011

    authors: Pantelopulos GA,Straub JE

    更新日期:2018-12-04 00:00:00

  • Cooperativity in F-actin: chemical modifications of actin monomers affect the functional interactions of myosin with unmodified monomers in the same actin filament.

    abstract::We have chemically modified a fraction of the monomers in actin filaments, and then measured the effects on the functional interaction of myosin with unmodified monomers within the same filament. Two modifications were used: (a) covalent attachment of various amounts of myosin subfragment-1 (S1) with the bifunctional ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(93)81057-9

    authors: Prochniewicz E,Katayama E,Yanagida T,Thomas DD

    更新日期:1993-07-01 00:00:00

  • Superresolution imaging of dynamic MreB filaments in B. subtilis--a multiple-motor-driven transport?

    abstract::The cytoskeletal protein MreB is an essential component of the bacterial cell-shape generation system. Using a superresolution variant of total internal reflection microscopy with structured illumination, as well as three-dimensional stacks of deconvolved epifluorescence microscopy, we found that inside living Bacillu...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2013.07.038

    authors: Olshausen PV,Defeu Soufo HJ,Wicker K,Heintzmann R,Graumann PL,Rohrbach A

    更新日期:2013-09-03 00:00:00

  • Time course of activation of calcium release from sarcoplasmic reticulum in skeletal muscle.

    abstract::Myoplasmic free calcium transients were measured with antipyrylazo III in voltage clamped segments of frog skeletal muscle fibers and were used to calculate the rate of release (Rrel) of calcium from the sarcoplasmic reticulum. Intramembrane charge movement was measured for the same pulses in the same fibers. During a...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(88)83050-9

    authors: Simon BJ,Schneider MF

    更新日期:1988-12-01 00:00:00

  • Modulation of 4-AP block of a mammalian A-type K channel clone by channel gating and membrane voltage.

    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

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(94)80462-X

    authors: Yao JA,Tseng GN

    更新日期:1994-07-01 00:00:00

  • Constant helical pitch of the gramicidin channel in phospholipid bilayers.

    abstract::X-ray diffraction has been applied in measuring the helical pitch of the gramicidin channel in oriented bilayers of dilauroylphosphatidylcholine (DLPC) and dimyristoylphosphatidylcholine (DMPC) at a polypeptide concentration of 9.1 mol %. The diffraction data show the helical pitch of gramicidin to be 4.7 +/- 0.2 A in...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(92)81888-X

    authors: Katsaras J,Prosser RS,Stinson RH,Davis JH

    更新日期:1992-03-01 00:00:00

  • Deuterium solid-state NMR investigations of exchange labeled oriented purple membranes at different hydration levels.

    abstract::Oriented purple membranes were equilibrated under controlled (2)H(2)O relative humidity ranging from 15% to 93% and introduced into the magnetic field of an NMR spectrometer with the membrane normal parallel to the magnetic field direction. Deuterium solid-state NMR spectra of these samples resolved four deuteron popu...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(03)74480-4

    authors: Bechinger B,Weik M

    更新日期:2003-07-01 00:00:00

  • Coding design of positional information for robust morphogenesis.

    abstract::Robust positioning of cells in a tissue against unavoidable noises is important for achieving normal and reproducible morphogenesis. The position in a tissue is represented by morphogen concentrations, and cells read them to recognize their spatial coordinates. From the engineering viewpoint, these positioning process...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2011.09.048

    authors: Morishita Y,Iwasa Y

    更新日期:2011-11-16 00:00:00

  • Switch II mutants reveal coupling between the nucleotide- and actin-binding regions in myosin V.

    abstract::Conserved active-site elements in myosins and other P-loop NTPases play critical roles in nucleotide binding and hydrolysis; however, the mechanisms of allosteric communication among these mechanoenzymes remain unresolved. In this work we introduced the E442A mutation, which abrogates a salt-bridge between switch I an...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2012.04.025

    authors: Trivedi DV,David C,Jacobs DJ,Yengo CM

    更新日期:2012-06-06 00:00:00

  • Laser light-scattering studies of bull spermatozoa. I. Orientational effects.

    abstract::Calculations based on the known dimensions of bull spermatozoa show that the scattered light intensity is strongly dependent upon the relative orientation of the particle to the incident beam. The magnitude of this effect of apparently much greater than for other systems where motility has been investigated by dynamic...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(80)85046-6

    authors: Harvey JD,Woolford MW

    更新日期:1980-07-01 00:00:00

  • Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes.

    abstract::Plant light-harvesting complex II (LHCII) is the key antenna complex for plant photosynthesis. We present coarse-grained molecular dynamics simulations of monomeric and trimeric LHCII in a realistic thylakoid membrane environment based on the Martini force field. The coarse-grained protein model has been optimized wit...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2019.03.009

    authors: Thallmair S,Vainikka PA,Marrink SJ

    更新日期:2019-04-23 00:00:00

  • A Coiled-Coil Peptide Shaping Lipid Bilayers upon Fusion.

    abstract::A system based on two designed peptides, namely the cationic peptide K, (KIAALKE)3, and its complementary anionic counterpart called peptide E, (EIAALEK)3, has been used as a minimal model for membrane fusion, inspired by SNARE proteins. Although the fact that docking of separate vesicle populations via the formation ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2016.10.010

    authors: Rabe M,Aisenbrey C,Pluhackova K,de Wert V,Boyle AL,Bruggeman DF,Kirsch SA,Böckmann RA,Kros A,Raap J,Bechinger B

    更新日期:2016-11-15 00:00:00

  • Preformed oligomeric epidermal growth factor receptors undergo an ectodomain structure change during signaling.

    abstract::Fluorescence resonance energy transfer (FRET) was used to reveal aspects of the mechanism of signal transduction by epidermal growth factor receptors (EGFR). The superpositions of epidermal growth factor (EGF), transforming growth factor-alpha (TGFalpha) and an antibody fragment (29.1) to the carbohydrate extremity of...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(02)75585-9

    authors: Martin-Fernandez M,Clarke DT,Tobin MJ,Jones SV,Jones GR

    更新日期:2002-05-01 00:00:00

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

    abstract::The hyperpolarization-activated cyclic nucleotide-modulated (HCN) cation channels are opened by membrane hyperpolarization, while their activation is modulated by the binding of cyclic adenosine monophosphate (cAMP) in the cytoplasm. Here we investigate the molecular basis of cAMP channel modulation by performing mole...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.105.071621

    authors: Berrera M,Pantano S,Carloni P

    更新日期:2006-05-15 00:00:00

  • Protein Partitioning into Ordered Membrane Domains: Insights from Simulations.

    abstract::Cellular membranes are laterally organized into domains of distinct structures and compositions by the differential interaction affinities between various membrane lipids and proteins. A prominent example of such structures are lipid rafts, which are ordered, tightly packed domains that have been widely implicated in ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2018.03.020

    authors: Lin X,Gorfe AA,Levental I

    更新日期:2018-04-24 00:00:00

  • Electrophysiological characterization of ionic transport by the retinal exchanger expressed in human embryonic kidney cells.

    abstract::The retinal Na+:Ca2+, K+exchanger cDNA was transiently expressed in human embryonic kidney (HEK 293) cells by transfection with plasmid DNA. The correct targeting of the expressed protein to the plasma membrane was confirmed by immunocytochemistry. The reverse exchange offrent (Ca2+ imported per Na+ extruded) was meas...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(97)78046-9

    authors: Navanglone A,Rispoli G,Gabellini N,Carafoli E

    更新日期:1997-07-01 00:00:00

  • Cell growth and division. I. A mathematical model with applications to cell volume distributions in mammalian suspension cultures.

    abstract::A mathematical model is formulated for the development of a population of cells in which the individual members may grow and divide or die. A given cell is characterized by its age and volume, and these parameters are assumed to determine the rate of volume growth and the probability per unit time of division or death...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(67)86592-5

    authors: Bell GI,Anderson EC

    更新日期:1967-07-01 00:00:00

  • Coupled flexibility change in cytochrome P450cam substrate binding determined by neutron scattering, NMR, and molecular dynamics simulation.

    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

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2012.10.013

    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