Cross talk and interference enhance information capacity of a signaling pathway.


:A recurring motif in gene regulatory networks is transcription factors (TFs) that regulate each other and then bind to overlapping sites on DNA, where they interact and synergistically control transcription of a target gene. Here, we suggest that this motif maximizes information flow in a noisy network. Gene expression is an inherently noisy process due to thermal fluctuations and the small number of molecules involved. A consequence of multiple TFs interacting at overlapping binding sites is that their binding noise becomes correlated. Using concepts from information theory, we show that in general a signaling pathway transmits more information if 1), noise of one input is correlated with that of the other; and 2), input signals are not chosen independently. In the case of TFs, the latter criterion hints at upstream cross-regulation. We demonstrate these ideas for competing TFs and feed-forward gene-regulatory modules, and discuss generalizations to other signaling pathways. Our results challenge the conventional approach of treating biological noise as uncorrelated fluctuations, and present a systematic method for understanding TF cross-regulation networks either from direct measurements of binding noise or from bioinformatic analysis of overlapping binding sites.


Biophys J


Biophysical journal


Hormoz S




Has Abstract


2013-03-05 00:00:00














  • Heteropolymer collapse theory for protein folding in the pressure-temperature plane.

    abstract::We revisit a heteropolymer collapse theory originally introduced to explore how the balance between hydrophobic interactions and configurational entropy determines the thermal stability of globular proteins at ambient pressure. We generalize the theory by introducing a basic statistical mechanical treatment for how pr...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Cheung JK,Shah P,Truskett TM

    更新日期:2006-10-01 00:00:00

  • A model of phosphofructokinase and glycolytic oscillations in the pancreatic beta-cell.

    abstract::We have constructed a model of the upper part of the glycolysis in the pancreatic beta-cell. The model comprises the enzymatic reactions from glucokinase to glyceraldehyde-3-phosphate dehydrogenase (GAPD). Our results show, for a substantial part of the parameter space, an oscillatory behavior of the glycolysis for a ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Westermark PO,Lansner A

    更新日期:2003-07-01 00:00:00

  • Formation of "solvent-free" black lipid bilayer membranes from glyceryl monooleate dispersed in squalene.

    abstract::A simple technique for forming "black" lipid bilayer membranes containing negligible amounts of alkyl solvent is described. The membranes are formed by the method of Mueller et al (Circulation. 1962. 26:1167.) from glyceryl monooleate (GMO) dispersed in squalene. The squalene forms an annulus to satisfy the boundary c...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: White SH

    更新日期:1978-09-01 00:00:00

  • The mechanism of oxidation-induced low-density lipoprotein aggregation: an analogy to colloidal aggregation and beyond?

    abstract::Atherosclerosis is a disease initiated by lipoprotein aggregation and deposition in artery walls. In this study, the de novo low-density lipoprotein aggregation process was examined. Nine major intermediates were identified in two stages of the aggregation process. In the aggregation stage, low-density lipoprotein mol...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Xu S,Lin B

    更新日期:2001-10-01 00:00:00

  • Low-resolution reconstruction of a synthetic DNA holliday junction.

    abstract::We have studied the low-resolution solution conformation of a Holliday (or four-way) DNA junction by using small-angle x-ray scattering, sedimentation velocity, and computational modeling techniques. The scattering data were analyzed in two independent ways: firstly, by rigid-body modeling of the scattering data using...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Nöllmann M,Stark WM,Byron O

    更新日期:2004-05-01 00:00:00

  • Intermediates and kinetics of membrane fusion.

    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

    pub_type: 杂志文章


    authors: Bentz J

    更新日期:1992-08-01 00:00:00

  • DNA Occupancy of Polymerizing Transcription Factors: A Chemical Model of the ETS Family Factor Yan.

    abstract::Transcription factors use both protein-DNA and protein-protein interactions to assemble appropriate complexes to regulate gene expression. Although most transcription factors operate as monomers or dimers, a few, including the E26 transformation-specific family repressors Drosophila melanogaster Yan and its human homo...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Hope CM,Rebay I,Reinitz J

    更新日期:2017-01-10 00:00:00

  • Protein thermostability calculations using alchemical free energy simulations.

    abstract::Thermal stability of proteins is crucial for both biotechnological and therapeutic applications. Rational protein engineering therefore frequently aims at increasing thermal stability by introducing stabilizing mutations. The accurate prediction of the thermodynamic consequences caused by mutations, however, is highly...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Seeliger D,de Groot BL

    更新日期:2010-05-19 00:00:00

  • Measurement of local viscoelasticity and forces in living cells by magnetic tweezers.

    abstract::We measured the viscoelastic properties of the cytoplasm of J774 macrophages with a recently developed microrheometer. Ferromagnetic beads (1.3 microm in diameter) were used to determine the local viscoelastic moduli. Step-force pulses were applied to the magnetic beads and the displacement was observed by single part...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Bausch AR,Möller W,Sackmann E

    更新日期:1999-01-01 00:00:00

  • Large-scale rotational motions of proteins detected by electron paramagnetic resonance and fluorescence.

    abstract::Direct spectroscopic measurements of rotational motions of proteins and large protein segments are crucial to understanding the molecular dynamics of protein function. Fluorescent probes and spin labels attached to proteins have proved to be powerful tools in the study of large-scale protein motions. Fluorescence depo...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Thomas DD

    更新日期:1978-11-01 00:00:00

  • Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach.

    abstract::Characterizing the ionic distribution around chromatin is important for understanding the electrostatic forces governing chromatin structure and function. Here we develop an electrostatic model to handle multivalent ions and compute the ionic distribution around a mesoscale chromatin model as a function of conformatio...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Gan HH,Schlick T

    更新日期:2010-10-20 00:00:00

  • Lipid-cholesterol interactions in the P beta' phase. Application of a statistical mechanical model.

    abstract::We describe a statistical mechanical model for lipid-cholesterol mixtures in the P beta' (ripple) phase of lipid bilayers. The model is a simple extension of an earlier model for the ripple phase in pure lipid bilayers. The extension consists of adding a degree of freedom to allow for the occupation of underlying latt...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Scott HL,McCullough WS

    更新日期:1993-05-01 00:00:00

  • Smoothed acyl chain orientational order parameter profiles in dimyristoylphosphatidylcholine-distearoylphosphatidylcholine mixtures: a 2H-NMR study.

    abstract::The accommodation of chain-length mismatch in liquid crystal phase bilayers was examined by using deuterium nuclear magnetic resonance to obtain smoothed orientational order parameter profiles for acyl chains of both components in binary lipid mixture bilayers. Mixtures of dimyristoylphosphatidylcholine (DMPC) and dis...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Lu D,Vavasour I,Morrow MR

    更新日期:1995-02-01 00:00:00

  • Flash photolysis and low temperature photochemistry of bovine rhodopsin with a fixed 11-ene.

    abstract::Nonbleachable rhodopsins containing retinal moieties with fixed 11-ene structures have been prepared. When the nonbleachable rhodopsin analogue corresponding to the natural pigment was flash-photolysed at 20.8 degrees C, no absorption changes occurred at the monitoring wavelengths of 380, 480, and 580 nm for the time ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Mao B,Tsuda M,Ebrey TG,Akita H,Balogh-Nair V,Nakanishi K

    更新日期:1981-08-01 00:00:00

  • Surfing along Filopodia: A Particle Transport Revealed by Molecular-Scale Fluctuation Analyses.

    abstract::Filopodia perform cellular functions such as environmental sensing or cell motility, but they also grab for particles and withdraw them leading to an increased efficiency of phagocytic uptake. Remarkably, withdrawal of micron-sized particles is also possible without noticeable movements of the filopodia. Here, we demo...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Kohler F,Rohrbach A

    更新日期:2015-05-05 00:00:00

  • Disposition of calcium release units in agarose gel for an optimal propagation of Ca2+ signals.

    abstract::Clusters of calcium-loaded sarcoplasmic reticulum (SR) vesicles in agarose gel were previously shown to behave as an excitable medium that propagates calcium waves. In a 3D-hexagonal disposition, the distance between neighboring spheres (which may stand for SR vesicles) is constant and the relationship between distanc...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Wussling MH,Aurich I,Knauf O,Podhaisky H,Holzhausen HJ

    更新日期:2004-12-01 00:00:00

  • Late events in the photocycle of bacteriorhodopsin mutant L93A.

    abstract::In the photocycle of bacteriorhodopsin (bR) from Halobacterium salinarum mutant L93A, the O-intermediate accumulates and the cycling time is increased approximately 200 times. Nevertheless, under continuous illumination, the protein pumps protons at near wild-type rates. We excited the mutant L93A in purple membrane w...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Tóth-Boconádi R,Keszthelyi L,Stoeckenius W

    更新日期:2003-06-01 00:00:00

  • Refractive-index-based screening of membrane-protein-mediated transfer across biological membranes.

    abstract::Numerous membrane-transport proteins are major drug targets, and therefore a key ingredient in pharmaceutical development is the availability of reliable, efficient tools for membrane transport characterization and inhibition. Here, we present the use of evanescent-wave sensing for screening of membrane-protein-mediat...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Brändén M,Tabaei SR,Fischer G,Neutze R,Höök F

    更新日期:2010-07-07 00:00:00

  • Residue-specific α-helix propensities from molecular simulation.

    abstract::Formation of α-helices is a fundamental process in protein folding and assembly. By studying helix formation in molecular simulations of a series of alanine-based peptides, we obtain the temperature-dependent α-helix propensities of all 20 naturally occurring residues with two recent additive force fields, Amber ff03w...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Best RB,de Sancho D,Mittal J

    更新日期:2012-03-21 00:00:00

  • Simultaneous measurement of ciliary beating and intracellular calcium.

    abstract::A novel system for measuring, simultaneously, ciliary beating and intracellular free calcium is presented. The advantages and dynamic nature of the system are demonstrated by measuring the effects of the calcium ionophore lonomycin and of extracellular ATP on ciliated rabbit trachea. The results are discussed with reg...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Korngreen A,Priel Z

    更新日期:1994-07-01 00:00:00

  • Structural studies of synthetic filaments prepared from column-purified myosin.

    abstract::Synthetic filaments prepared from column-purified rabbit skeletal myosin by slow dialysis exhibit characteristic bipolar organization and 14-nm axial subunit spacing. Backbone substructure can be discerned in high resolution micrographs in the form of striations of 3--4-nm width and slight angular tilt from the direct...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Koretz JF

    更新日期:1979-09-01 00:00:00

  • Spectroscopy on the B850 band of individual light-harvesting 2 complexes of Rhodopseudomonas acidophila. I. Experiments and Monte Carlo simulations.

    abstract::The electronic structure of the circular aggregate of 18 bacteriochlorophyll a (BChl a) molecules responsible for the B850 absorption band of the light-harvesting 2 (LH2) complex of the photosynthetic purple bacterium Rhodopseudomonas acidophila has been studied by measuring fluorescence-excitation spectra of individu...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Ketelaars M,van Oijen AM,Matsushita M,Köhler J,Schmidt J,Aartsma TJ

    更新日期:2001-03-01 00:00:00

  • Potassium ion accumulation at the external surface of the nodal membrane in frog myelinated fibers.

    abstract::Potassium accumulation associated with outward membrane potassium current was investigated experimentally in myelinated fibers and analyzed in terms of two models-three-compartment and diffusion in an unstirred layer. In the myelinated fibers, as in squid giant axons, the three-compartment model satisfactorily describ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Moran N,Palti Y,Levitan E,Stämpfli R

    更新日期:1980-12-01 00:00:00

  • Structural characterization of apomyoglobin self-associated species in aqueous buffer and urea solution.

    abstract::The biophysical characterization of nonfunctional protein aggregates at physiologically relevant temperatures is much needed to gain deeper insights into the kinetic and thermodynamic relationships between protein folding and misfolding. Dynamic and static laser light scattering have been employed for the detection an...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Chow C,Kurt N,Murphy RM,Cavagnero S

    更新日期:2006-01-01 00:00:00

  • Mathematical analysis and quantification of fluorescent proteins as transcriptional reporters.

    abstract::Fluorescent proteins are often used as reporters of transcriptional activity. Here we present a mathematical characterization of a novel fluorescent reporter that was recently engineered to have a short half-life (approximately 12 min). The advantage of this destabilized protein is that it can track the transient tran...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Wang X,Errede B,Elston TC

    更新日期:2008-03-15 00:00:00

  • Single cell mechanotransduction and its modulation analyzed by atomic force microscope indentation.

    abstract::The skeleton adapts to its mechanical usage, although at the cellular level, the distribution and magnitude of strains generated and their detection are ill-understood. The magnitude and nature of the strains to which cells respond were investigated using an atomic force microscope (AFM) as a microindentor. A confocal...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Charras GT,Horton MA

    更新日期:2002-06-01 00:00:00

  • Constant pH molecular dynamics with proton tautomerism.

    abstract::The current article describes a new two-dimensional lambda-dynamics method to include proton tautomerism in continuous constant pH molecular dynamics (CPHMD) simulations. The two-dimensional lambda-dynamics framework is used to devise a tautomeric state titration model for the CPHMD simulations involving carboxyl and ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Khandogin J,Brooks CL 3rd

    更新日期:2005-07-01 00:00:00

  • Angular Approach Scanning Ion Conductance Microscopy.

    abstract::Scanning ion conductance microscopy (SICM) is a super-resolution live imaging technique that uses a glass nanopipette as an imaging probe to produce three-dimensional (3D) images of cell surface. SICM can be used to analyze cell morphology at nanoscale, follow membrane dynamics, precisely position an imaging nanopipet...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Shevchuk A,Tokar S,Gopal S,Sanchez-Alonso JL,Tarasov AI,Vélez-Ortega AC,Chiappini C,Rorsman P,Stevens MM,Gorelik J,Frolenkov GI,Klenerman D,Korchev YE

    更新日期:2016-05-24 00:00:00

  • The mechanics of pulling a glass micropipette.

    abstract::The pulling of micropipette electrodes from glass tubing has been treated as a problem of viscous flow coupled with the Newtonian dynamics of the pulling apparatus. Analytical solutions are given from which the taper profile, tip diameter, and pulling time can be obtained. The physical principles of operation of micro...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Purves RD

    更新日期:1980-03-01 00:00:00

  • Biophysical mechanisms of endotoxin neutralization by cationic amphiphilic peptides.

    abstract::Bacterial endotoxins (lipopolysaccharides (LPS)) are strong elicitors of the human immune system by interacting with serum and membrane proteins such as lipopolysaccharide-binding protein (LBP) and CD14 with high specificity. At LPS concentrations as low as 0.3 ng/ml, such interactions may lead to severe pathophysiolo...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Kaconis Y,Kowalski I,Howe J,Brauser A,Richter W,Razquin-Olazarán I,Iñigo-Pestaña M,Garidel P,Rössle M,Martinez de Tejada G,Gutsmann T,Brandenburg K

    更新日期:2011-06-08 00:00:00