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    94 results match your criteria BMC Biophysics [Journal]

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    Kinetic and thermodynamic studies reveal chemokine homologues CC11 and CC24 with an almost identical tertiary structure have different folding pathways.
    BMC Biophys 2017 12;10. Epub 2017 Sep 12.
    Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580 People's Republic of China.
    Background: Proteins with low sequence identity but almost identical tertiary structure and function have been valuable to uncover the relationship between sequence, tertiary structure, folding mechanism and functions. Two homologous chemokines, CCL11 and CCL24, with low sequence identity but similar tertiary structure and function, provide an excellent model system for respective studies.

    Results: The kinetics and thermodynamics of the two homologous chemokines were systematically characterized. Read More

    Modeling of RAS complexes supports roles in cancer for less studied partners.
    BMC Biophys 2017 11;10(Suppl 1). Epub 2017 Aug 11.
    Division of Medical Genetics, Department of Medicine, Universsity of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093 USA.
    Background: RAS protein interactions have predominantly been studied in the context of the RAF and PI3kinase oncogenic pathways. Structural modeling and X-ray crystallography have demonstrated that RAS isoforms bind to canonical downstream effector proteins in these pathways using the highly conserved switch I and II regions. Other non-canonical RAS protein interactions have been experimentally identified, however it is not clear whether these proteins also interact with RAS via the switch regions. Read More

    DNA secondary structure formation by DNA shuffling of the conserved domains of the Cry protein of Bacillus thuringiensis.
    BMC Biophys 2017 22;10. Epub 2017 May 22.
    Laboratory of Biotechnology and Molecular Biology, MASIRA Institute, School of Health, University of Santander, UDES, Bucaramanga, Colombia.
    Background: The Cry toxins, or δ-endotoxins, are a diverse group of proteins produced by Bacillus thuringiensis. While DNA secondary structures are biologically relevant, it is unknown if such structures are formed in regions encoding conserved domains of Cry toxins under shuffling conditions. We analyzed 5 holotypes that encode Cry toxins and that grouped into 4 clusters according to their phylogenetic closeness. Read More

    Accuracy of the detection of binding events using 3D single particle tracking.
    BMC Biophys 2017 23;10. Epub 2017 Mar 23.
    Huygens-Kamerlingh Onnes Laboratory, Leiden University, Postbus 9504, Leiden, 2300RA Netherlands.
    Background: Nanoparticles can be used as markers to track the position of biomolecules, such as single proteins, inside living cells. The activity of a protein can sometimes be inferred from changes in the mobility of the attached particle. Mean Square Displacement analysis is the most common method to obtain mobility information from trajectories of tracked particles, such as the diffusion coefficient D. Read More

    BFPTool: a software tool for analysis of Biomembrane Force Probe experiments.
    BMC Biophys 2017 13;10. Epub 2017 Feb 13.
    Institute of Physiology, Czech Academy of Sciences, Vídeňská 1083, Prague, 14220 Czech Republic.
    Background: The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Read More

    Native flexibility of structurally homologous proteins: insights from anisotropic network model.
    BMC Biophys 2017 31;10. Epub 2017 Jan 31.
    School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110 067 India.
    Background: Single-molecule microscopic experiments can measure the mechanical response of proteins to pulling forces applied externally along different directions (inducing different residue pairs in the proteins by uniaxial tension). This response to external forces away from equilibrium should in principle, correlate with the flexibility or stiffness of proteins in their folded states. Here, a simple topology-based atomistic anisotropic network model (ANM) is shown which captures the protein flexibility as a fundamental property that determines the collective dynamics and hence, the protein conformations in native state. Read More

    Structure and domain dynamics of human lactoferrin in solution and the influence of Fe(III)-ion ligand binding.
    BMC Biophys 2016 4;9. Epub 2016 Nov 4.
    JCNS-1 & ICS-1, Forschungszentrum Jülich GmbH, Leo-Brandt Strasse, 52425 Jülich, Germany.
    Background: Human lactoferrin is an iron-binding protein of the innate immune system consisting of two connected lobes, each with a binding site located in a cleft. The clefts in each lobe undergo a hinge movement from open to close when Fe(3+) is present in the solution and can be bound. The binding mechanism was assumed to relate on thermal domain fluctuations of the cleft domains prior to binding. Read More

    Exploring in vivo cholesterol-mediated interactions between activated EGF receptors in plasma membrane with single-molecule optical tracking.
    BMC Biophys 2016 24;9. Epub 2016 Jun 24.
    Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, 35, Keyan Road, Zhunan, Taiwan.
    Background: The first step in many cellular signaling processes occurs at various types of receptors in the plasma membrane. Membrane cholesterol can alter these signaling pathways of living cells. However, the process in which the interaction of activated receptors is modulated by cholesterol remains unclear. Read More

    Rheological properties of cells measured by optical tweezers.
    BMC Biophys 2016 22;9. Epub 2016 Jun 22.
    LPO-COPEA, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro 21941-902 Brazil.
    Background: The viscoelastic properties of cells have been investigated by a variety of techniques. However, the experimental data reported in literature for viscoelastic moduli differ by up to three orders of magnitude. This has been attributed to differences in techniques and models for cell response as well as to the natural variability of cells. Read More

    Evaluation of the coarse-grained OPEP force field for protein-protein docking.
    BMC Biophys 2016 21;9. Epub 2016 Apr 21.
    Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, 52425 Germany ; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf, 40225 Germany.
    Background: Knowing the binding site of protein-protein complexes helps understand their function and shows possible regulation sites. The ultimate goal of protein-protein docking is the prediction of the three-dimensional structure of a protein-protein complex. Docking itself only produces plausible candidate structures, which must be ranked using scoring functions to identify the structures that are most likely to occur in nature. Read More

    A biophysical model of supercoiling dependent transcription predicts a structural aspect to gene regulation.
    BMC Biophys 2015 6;9. Epub 2016 Feb 6.
    Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, USA.
    Background: Transcription in Escherichia coli generates positive supercoiling in the DNA, which is relieved by the enzymatic activity of gyrase. Recently published experimental evidence suggests that transcription initiation and elongation are inhibited by the buildup of positive supercoiling. It has therefore been proposed that intermittent binding of gyrase plays a role in transcriptional bursting. Read More

    α-synuclein-lanthanide metal ions interaction: binding sites, conformation and fibrillation.
    BMC Biophys 2015 3;9. Epub 2016 Feb 3.
    Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center of Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071 P.R. China.
    Background: The pathological hallmark of Parkinson's disease is the deposition of cytoplasmic neuronal inclusions termed Lewy bodies. The major component of Lewy bodies is amyloid fibrils of α-synuclein. To investigate what causes α-synuclein aggregation is essential to understand its pathological roles in Parkinson's disease. Read More

    Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA.
    BMC Biophys 2015 1;8:11. Epub 2015 Dec 1.
    Departamento de Química Física, Universidad de Murcia, Murcia, 30100 Spain.
    Background: The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational scheme for predicting global properties and mimicking the internal dynamics of RNA molecules in solution. A simple coarse-grained model with one bead per nucleotide and two types of intra-molecular interactions (elastic interactions and excluded volume interactions) is used to represent the RNA chain. Read More

    PDE/ODE modeling and simulation to determine the role of diffusion in long-term and -range cellular signaling.
    BMC Biophys 2015 14;8:10. Epub 2015 Oct 14.
    Department of Applied Mathematics, Im Neuenheimer Feld 294, Heidelberg, Germany.
    Background: We study the relevance of diffusion for the dynamics of signaling pathways. Mathematical modeling of cellular diffusion leads to a coupled system of differential equations with Robin boundary conditions which requires a substantial knowledge in mathematical theory. Using our new developed analytical and numerical techniques together with modern experiments, we analyze and quantify various types of diffusive effects in intra- and inter-cellular signaling. Read More

    Copper-free click chemistry for attachment of biomolecules in magnetic tweezers.
    BMC Biophys 2015 25;8. Epub 2015 Sep 25.
    Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft, Delft, The Netherlands.
    Background: Single-molecule techniques have proven to be an excellent approach for quantitatively studying DNA-protein interactions at the single-molecule level. In magnetic tweezers, a force is applied to a biopolymer that is anchored between a glass surface and a magnetic bead. Whereas the relevant force regime for many biological processes is above 20pN, problems arise at these higher forces, since the molecule of interest can detach from the attachment points at the surface or the bead. Read More

    The biophysical nature of cells: potential cell behaviours revealed by analytical and computational studies of cell surface mechanics.
    BMC Biophys 2015 12;8. Epub 2015 May 12.
    Computational and Systems Biology, John Innes Centre,, Norwich Research Park, NR4 7UH, Norwich, UK.
    Background: The biophysical characteristics of cells determine their shape in isolation and when packed within tissues. Cells can form regular or irregular epithelial structures, round up and form clusters, or deform and attach to substrates. The acquired shape of cells and tissues is a consequence of (i) internal cytoskeletal processes, such as actin polymerisation and cortical myosin contraction, (ii) adhesion molecules within the cell membrane that interact with substrates and neighbouring cells, and (iii) processes that regulate cell volume. Read More

    Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics.
    BMC Biophys 2015 7;8. Epub 2015 May 7.
    Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, MSID K7-20, 99352, Richland, PO Box 999 WA USA.
    Background: The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors.

    Methods: We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) BC, is considered on the reactive boundaries. Read More

    A nucleotide-independent cyclic nitroxide label for monitoring segmental motions in nucleic acids.
    BMC Biophys 2015 9;8. Epub 2015 Apr 9.
    Department of Chemistry, University of Southern California, 840 Downey Way, Los Angeles, CA 90089-0744 USA.
    Background: Spin labels, which are chemically stable radicals attached at specific sites of a bio-molecule, enable investigations on structure and dynamics of proteins and nucleic acids using techniques such as site-directed spin labeling and paramagnetic NMR. Among spin labels developed, the class of rigid labels have limited or no independent motions between the radical bearing moiety and the target, and afford a number of advantages in measuring distances and monitoring local dynamics within the parent bio-molecule. However, a general method for attaching a rigid label to nucleic acids in a nucleotide-independent manner has not been reported. Read More

    A flexible approach to assess fluorescence decay functions in complex energy transfer systems.
    BMC Biophys 2015 3;8. Epub 2015 Apr 3.
    Biochemistry and Biology, University of Potsdam, Potsdam, Germany ; Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
    Background: Time-correlated Förster resonance energy transfer (FRET) probes molecular distances with greater accuracy than intensity-based calculation of FRET efficiency and provides a powerful tool to study biomolecular structure and dynamics. Moreover, time-correlated photon count measurements bear additional information on the variety of donor surroundings allowing more detailed differentiation between distinct structural geometries which are typically inaccessible to general fitting solutions.

    Results: Here we develop a new approach based on Monte Carlo simulations of time-correlated FRET events to estimate the time-correlated single photon counts (TCSPC) histograms in complex systems. Read More

    Life at the mesoscale: the self-organised cytoplasm and nucleoplasm.
    BMC Biophys 2015 25;8. Epub 2015 Feb 25.
    Centre for Chromosome Biology, School of Life Sciences, National University of Ireland Galway, Galway, Ireland.
    The cell contains highly dynamic structures exploiting physical principles of self-organisation at the mesoscale (100 nm to 10 μm). Examples include non-membrane bound cytoplasmic bodies, cytoskeleton-based motor networks and multi-scale chromatin organisation. The challenges of mesoscale self-organisation were discussed at a CECAM workshop in July 2014. Read More

    Vesicle biomechanics in a time-varying magnetic field.
    BMC Biophys 2015 21;8(1). Epub 2015 Jan 21.
    Departments of Physics, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660 USA.
    Background: Cells exhibit distortion when exposed to a strong electric field, suggesting that the field imposes control over cellular biomechanics. Closed pure lipid bilayer membranes (vesicles) have been widely used for the experimental and theoretical studies of cellular biomechanics under this electrodeformation. An alternative method used to generate an electric field is by electromagnetic induction with a time-varying magnetic field. Read More

    Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric.
    BMC Biophys 2015 13;8(1). Epub 2015 Jan 13.
    Key Lab of Intelligent Information Processing and Advanced Computing Research Lab, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China.
    Background: The recent developments of far-field optical microscopy (single molecule imaging techniques) have overcome the diffraction barrier of light and improve image resolution by a factor of ten compared with conventional light microscopy. These techniques utilize the stochastic switching of probe molecules to overcome the diffraction limit and determine the precise localizations of molecules, which often requires a long image acquisition time. However, long acquisition times increase the risk of sample drift. Read More

    A novel delta current method for transport stoichiometry estimation.
    BMC Biophys 2014 11;7(1):14. Epub 2014 Dec 11.
    Division of Nephrology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 USA ; Brain Research Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 USA.
    Background: The ion transport stoichiometry (q) of electrogenic transporters is an important determinant of their function. q can be determined by the reversal potential (Erev) if the transporter under study is the only electrogenic transport mechanism or a specific inhibitor is available. An alternative approach is to calculate delta reversal potential (ΔErev) by altering the concentrations of the transported substrates. Read More

    The glassy state of crambin and the THz time scale protein-solvent fluctuations possibly related to protein function.
    BMC Biophys 2014 16;7. Epub 2014 Aug 16.
    Physics Department, Carnegie Mellon University, Pittsburgh 15213, PA, USA.
    Background: THz experiments have been used to characterize the picosecond time scale fluctuations taking place in the model, globular protein crambin.

    Results: Using both hydration and temperature as an experimental parameter, we have identified collective fluctuations (<= 200 cm(-1)) in the protein. Observation of the protein dynamics in the THz spectrum from both below and above the glass transition temperature (Tg) has provided unique insight into the microscopic interactions and modes that permit the solvent to effectively couple to the protein thermal fluctuations. Read More

    Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking.
    BMC Biophys 2014 12;7. Epub 2014 Aug 12.
    Department of Physics, University of Cyprus, PO 20537, CY1678 Nicosia, Cyprus.
    Background: The complement protein C5a acts by primarily binding and activating the G-protein coupled C5a receptor C5aR (CD88), and is implicated in many inflammatory diseases. The cyclic hexapeptide PMX53 (sequence Ace-Phe-[Orn-Pro-dCha-Trp-Arg]) is a full C5aR antagonist of nanomolar potency, and is widely used to study C5aR function in disease.

    Results: We construct for the first time molecular models for the C5aR:PMX53 complex without the a priori use of experimental constraints, via a computational framework of molecular dynamics (MD) simulations, docking, conformational clustering and free energy filtering. Read More

    Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology.
    BMC Biophys 2014 5;7. Epub 2014 Aug 5.
    Graduate Program in Molecular Biophysics and Structural Biology, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, PA 15260, USA ; Department of Structural Biology, University of Pittsburgh, Pittsburgh, USA ; Presently at: Department of Biomedicine and Systems Biology, Division of Metabolic and Vascular Health, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK.
    Background: A key challenge in interdisciplinary research is choosing the best approach from a large number of techniques derived from different disciplines and their interfaces.

    Results: To address this challenge in the area of Biophysics and Structural Biology, we have designed a graduate level course to teach students insightful use of experimental biophysical approaches in relationship to addressing biological questions related to biomolecular interactions and dynamics. A weekly seminar and data and literature club are used to compliment the training in class. Read More

    Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules.
    BMC Biophys 2014 17;7. Epub 2014 Jun 17.
    Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany ; Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
    Background: Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to contain the computational costs, especially for the computation of interaction forces and energies. A common approach is to compute interaction forces between macromolecules by precomputing their interaction potentials on three-dimensional discretized grids. Read More

    Diffusion-controlled reaction rates for two active sites on a sphere.
    BMC Biophys 2014 4;7. Epub 2014 Jun 4.
    Mathematics and Science Department, Lincoln Land Community College, 5250 Shepherd Rd, P.O. Box 19256, Springfield, IL 62794, USA.
    Background: The diffusion-limited reaction rate of a uniform spherical reactant is generalized to anisotropic reactivity. Previous work has shown that the protein model of a uniform sphere is unsatisfactory in many cases. Competition of ligands binding to two active sites, on a spherical enzyme or cell is studied analytically. Read More

    Raman characterization of Avocado Sunblotch viroid and its response to external perturbations and self-cleavage.
    BMC Biophys 2014 Mar 21;7(1). Epub 2014 Mar 21.
    Unité 779, INSERM, 78 rue du Général Leclerc, 94276 Le Kremlin Bicêtre, France.
    Background: Viroids are the smallest pathogens of plants. To date the structural and conformational details of the cleavage of Avocado sunblotch viroid (ASBVd) and the catalytic role of Mg2+ ions in efficient self-cleavage are of crucial interest.

    Results: We report the first Raman characterization of the structure and activity of ASBVd, for plus and minus viroid strands. Read More

    Investigation of nanoscale structural alterations of cell nucleus as an early sign of cancer.
    BMC Biophys 2014 Feb 10;7(1). Epub 2014 Feb 10.
    Biomedical Optical Imaging Laboratory, Department of Medicine, Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
    Background: The cell and tissue structural properties assessed with a conventional bright-field light microscope play a key role in cancer diagnosis, but they sometimes have limited accuracy in detecting early-stage cancers or predicting future risk of cancer progression for individual patients (i.e., prognosis) if no frank cancer is found. Read More

    Time-resolved force distribution analysis.
    BMC Biophys 2013 May 1;6(1). Epub 2013 May 1.
    Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
    Background: Biomolecules or other complex macromolecules undergo conformational transitions upon exposure to an external perturbation such as ligand binding or mechanical force. To follow fluctuations in pairwise forces between atoms or residues during such conformational changes as observed in Molecular Dynamics (MD) simulations, we developed Time-Resolved Force Distribution Analysis (TRFDA).

    Results: The implementation focuses on computational efficiency and low-memory usage and, along with the wide range of output options, makes possible time series analysis of pairwise forces variation in long MD simulations and for large molecular systems. Read More

    Improving accuracy of cell and chromophore concentration measurements using optical density.
    BMC Biophys 2013 Apr 22;6(1). Epub 2013 Apr 22.
    Department of Chemical Engineering, Fenske Laboratory, The Pennsylvania State University, University Park 16802, PA.
    Background: UV-vis spectrophotometric optical density (OD) is the most commonly-used technique for estimating chromophore formation and cell concentration in liquid culture. OD wavelength is often chosen with little thought given to its effect on the quality of the measurement. Analysis of the contributions of absorption and scattering to the measured optical density provides a basis for understanding variability among spectrophotometers and enables a quantitative evaluation of the applicability of the Beer-Lambert law. Read More

    Mathematical modelling of the automated FADU assay for the quantification of DNA strand breaks and their repair in human peripheral mononuclear blood cells.
    BMC Biophys 2014 9;7. Epub 2014 Sep 9.
    Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, D-78457, Germany.
    Background: Cells continuously undergo DNA damage from exogenous agents like irradiation or genotoxic chemicals or from endogenous radicals produced by normal cellular metabolic activities. DNA strand breaks are one of the most common genotoxic lesions and they can also arise as intermediates of DNA repair activity. Unrepaired DNA damage can lead to genomic instability, which can massively compromise the health status of organisms. Read More

    Langevin dynamics simulations of charged model phosphatidylinositol lipids in the presence of diffusion barriers: toward an atomic level understanding of corralling of PIP2 by protein fences in biological membranes.
    BMC Biophys 2014 26;7:13. Epub 2014 Nov 26.
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA.
    Background: The polyvalent acidic lipid phosphatidylinositol, 4,5-bisphosphate (PIP2) is important for many cellular functions. It has been suggested that different pools of PIP2 exist in the cytoplasmic leaflet of the plasma membrane, and that such pooling could play a role in the regulation of PIP2. The mechanism of fencing, however, is not understood. Read More

    Simulation tools for particle-based reaction-diffusion dynamics in continuous space.
    BMC Biophys 2014 24;7:11. Epub 2014 Oct 24.
    Department of Mathematics, Computer Science and Bioinformatics, Free University Berlin, Arnimallee 6 14195, Berlin, Germany.
    Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, depending on the system at hand and the questions asked, would require different levels of modeling detail such as particle diffusion, geometrical confinement, particle volume exclusion or particle-particle interaction potentials. Higher levels of detail usually correspond to increased number of parameters and higher computational cost. Read More

    Analytical model for macromolecular partitioning during yeast cell division.
    BMC Biophys 2014 23;7:10. Epub 2014 Sep 23.
    Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) and Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH-Allianz, Im Neuenheimer Feld 282, Heidelberg 69120, Germany.
    Background: Asymmetric cell division, whereby a parent cell generates two sibling cells with unequal content and thereby distinct fates, is central to cell differentiation, organism development and ageing. Unequal partitioning of the macromolecular content of the parent cell - which includes proteins, DNA, RNA, large proteinaceous assemblies and organelles - can be achieved by both passive (e.g. Read More

    Molecular dynamics simulations indicate an induced-fit mechanism for LSD1/CoREST-H3-histone molecular recognition.
    BMC Biophys 2013 Nov 25;6(1):15. Epub 2013 Nov 25.
    Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA.
    Background: Lysine Specific Demethylase (LSD1 or KDM1A) in complex with its co-repressor protein CoREST catalyzes the demethylation of the H3 histone N-terminal tail and is currently one of the most promising epigenetic targets for drug discovery against cancer and neurodegenerative diseases. Models of non-covalent binding, such as lock and key, induced-fit, and conformational selection could help explaining the molecular mechanism of LSD1/CoREST-H3-histone association, thus guiding drug discovery and design efforts. Here, we quantify the extent to which LSD1/CoREST substrate binding is consistent with these hypothetical models using LSD1/CoREST conformational ensembles obtained through extensive explicit solvent molecular dynamics (MD) simulations. Read More

    An exact approach for studying cargo transport by an ensemble of molecular motors.
    BMC Biophys 2013 Nov 16;6(1):14. Epub 2013 Nov 16.
    Laboratory for Information and Decision Systems, Massachussets Institute of Technology, 77 Massachusetts Avenue Cambridge, MA 02139, USA.
    Background: Intracellular transport is crucial for many cellular processes where a large fraction of the cargo is transferred by motor-proteins over a network of microtubules. Malfunctions in the transport mechanism underlie a number of medical maladies.Existing methods for studying how motor-proteins coordinate the transfer of a shared cargo over a microtubule are either analytical or are based on Monte-Carlo simulations. Read More

    A comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly.
    BMC Biophys 2013 Oct 23;6(1):13. Epub 2013 Oct 23.
    Department of Chemistry, The University of Memphis, 38152 Memphis TN, USA.
    Background: Assembly of the ribosome from its protein and RNA constituents must occur quickly and efficiently in order to synthesize the proteins necessary for all cellular activity. Since the early 1960's, certain characteristics of possible assembly pathways have been elucidated, yet the mechanisms that govern the precise recognition events remain unclear.We utilize a comparative analysis to investigate the amino acid composition of ribosomal proteins (r-proteins) with respect to their role in the assembly process. Read More

    Self-consistent field theory for the interactions between keratin intermediate filaments.
    BMC Biophys 2013 Sep 5;6(1):12. Epub 2013 Sep 5.
    Unilever R&D Port Sunlight, Quarry Road East, Bebington, Wirral, CH63 3JW, UK.
    Background: Keratins are important structural proteins found in skin, hair and nails. Keratin Intermediate Filaments are major components of corneocytes, nonviable horny cells of the Stratum Corneum, the outermost layer of skin. It is considered that interactions between unstructured domains of Keratin Intermediate Filaments are the key factor in maintaining the elasticity of the skin. Read More

    Kinetic effects of TiO2 fine particles and nanoparticles aggregates on the nanomechanical properties of human neutrophils assessed by force spectroscopy.
    BMC Biophys 2013 Aug 19;6(1):11. Epub 2013 Aug 19.
    Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia, Campus Darcy Ribeiro, Brasilia 70910-900, Brazil.
    Background: Increasing applications of titanium dioxide (TiO2) fine particles (FPs) and nanoparticles (NPs) require coupled knowledge improvement concerning their biokinetic effects. Neutrophils are quickly recruited to titanium implantation areas. Neutrophils mechanical properties display a crucial role on cell physiology and immune responsive functions. Read More

    Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies.
    BMC Biophys 2013 Aug 1;6(1):10. Epub 2013 Aug 1.
    Helmholtz-Institute for Pharmaceutical Research Saarland, Campus C2.3, 66123, Saarbrücken, Germany.
    Background: PQS (PseudomonasQuinolone Signal) and its precursor HHQ are signal molecules of the P. aeruginosa quorum sensing system. They explicate their role in mammalian pathogenicity by binding to the receptor PqsR that induces virulence factor production and biofilm formation. Read More

    Interactions of the amphiphiles arbutin and tryptophan with phosphatidylcholine and phosphatidylethanolamine bilayers in the dry state.
    BMC Biophys 2013 Jul 24;6(1). Epub 2013 Jul 24.
    Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany.
    Background: Water is essential for life, but some organisms can survive complete desiccation, while many more survive partial dehydration during drying or freezing. The function of some protective molecules, such as sugars, has been extensively studied, but much less is known about the effects of amphiphiles such as flavonoids and other aromatic compounds. Amphiphiles may be largely soluble under fully hydrated conditions, but will partition into membranes upon removal of water. Read More

    Drop drying on surfaces determines chemical reactivity - the specific case of immobilization of oligonucleotides on microarrays.
    BMC Biophys 2013 Jun 12;6. Epub 2013 Jun 12.
    Functional Genomics Center Zurich, ETH Zurich/ University of Zurich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland.
    Background: Drop drying is a key factor in a wide range of technical applications, including spotted microarrays. The applied nL liquid volume provides specific reaction conditions for the immobilization of probe molecules to a chemically modified surface.

    Results: We investigated the influence of nL and μL liquid drop volumes on the process of probe immobilization and compare the results obtained to the situation in liquid solution. Read More

    Activation of signaling receptors: do ligands bind to receptor monomer, dimer, or both?
    BMC Biophys 2013 Jun 3;6. Epub 2013 Jun 3.
    Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
    A recent study by Dietz et al. using single-molecule fluorescence microscopy techniques demonstrates that, in the absence of the ligand InlB, the MET receptor exists as both a monomer and a dimer on the cell membrane, and addition of the ligand leads to increased MET dimerization. Under the crowded conditions of the cell membrane, dimer formation may be a common phenomenon for cell surface receptors. Read More

    Single-molecule photobleaching reveals increased MET receptor dimerization upon ligand binding in intact cells.
    BMC Biophys 2013 Jun 3;6(1). Epub 2013 Jun 3.
    Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str, 7, 60438 Frankfurt, Germany.
    Background: The human receptor tyrosine kinase MET and its ligand hepatocyte growth factor/scatter factor are essential during embryonic development and play an important role during cancer metastasis and tissue regeneration. In addition, it was found that MET is also relevant for infectious diseases and is the target of different bacteria, amongst them Listeria monocytogenes that induces bacterial uptake through the surface protein internalin B. Binding of ligand to the MET receptor is proposed to lead to receptor dimerization. Read More

    Wavelet-based protocols for ion channel electrophysiology.
    BMC Biophys 2013 Mar 14;6. Epub 2013 Mar 14.
    Physics Department, Loyola University New Orleans, New Orleans, LA, 70118, USA.
    Background: Fluctuation-induced phenomena caused by both random and deterministic stimuli have been previously studied in a variety of contexts. They are based on the interplay between the spectro-temporal patterns of the signal and the kinetics of the system it is applied to. The aim of this study was to develop a method for designing fluctuating inputs into nonlinear system which would elicit the most desired system output and to implement the method to studies of ion channels. Read More

    A biophysical model for transcription factories.
    BMC Biophys 2013 Feb 9;6. Epub 2013 Feb 9.
    MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK.
    Summary: Transcription factories are nuclear domains where gene transcription takes place although the molecular basis for their formation and maintenance are unknown. In this study, we explored how the properties of chromatin as a polymer may contribute to the structure of transcription factories. We found that transcriptional active chromatin contains modifications like histone H4 acetylated at Lysine 16 (H4K16ac). Read More

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