The Experts below are selected from a list of 303 Experts worldwide ranked by ideXlab platform
J. García De La Torre - One of the best experts on this subject based on the ideXlab platform.
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Hydrodynamic Properties of Wormlike Macromolecules: Monte Carlo Simulation and Global Analysis of Experimental Data
Macromolecules, 2011Co-Authors: D. Amorós, Álvaro Ortega, J. García De La TorreAbstract:A Monte Carlo simulation, coupled with Bead-Model hydrodynamic calculation, has been employed to predict hydrodynamic coefficients and other solution properties, of wormlike macromolecules, coverin...
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MULTIHYDRO and MONTEHYDRO: conformational search and Monte Carlo calculation of solution properties of rigid or flexible Bead Models.
Biophysical chemistry, 2005Co-Authors: J. García De La Torre, Álvaro Ortega, H. E. Perez Sanchez, J.g. Hernández CifreAbstract:Abstract A computer program, MULTIHYDRO, has been constructed for the calculation of hydrodynamic coefficients and other solution properties of multiple possible conformations of a Bead Model. With minimal additional programming to describe the Model under study, this program interfaces efficiently with HYDRO [J. Garcia de la Torre, S. Navarro, M. Lopez Martinez, F. Diaz, J. Cascales, HYDRO: a computer software for the prediction of hydrodynamic properties of macromolecules, Biophys. J. 67 (1994) 530–531] [3] for the calculation of solution properties, including hydrodynamic coefficients, radius of gyration, covolume, etc. A useful application is the conformation search of rigid macromolecules, because many possible conformations can be evaluated in a single run of the program. In this paper we also pay attention to the properties of flexible macromolecules, in the so-called Monte Carlo rigid-body approximation, which is virtually exact for the simpler solution properties. The theoretical aspects of the procedure are described, and we show how MULTIHYDRO can be employed for this calculation. However, for flexible molecules, a more general simulation scheme is importance-sampling Monte Carlo generation. We describe how this procedure is implemented in another computer program, MONTEHYDRO. Examples of the usage of these tools are provided.
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HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.
Journal of magnetic resonance (San Diego Calif. : 1997), 2000Co-Authors: J. García De La Torre, M.l. Huertas, B. CarrascoAbstract:The heteronuclear NMR relaxation of globular proteins depends on the anisotropic rotational diffusion tensor. Using our previous developments for prediction of hydrodynamic properties of arbitrarily shaped particles, by means of Bead Models, we have constructed a computational procedure to calculate the rotational diffusion tensor and other properties of proteins from their detailed, atomic-level structure. From the atomic coordinates file used to build the Bead Model, the orientation of the pertinent dipoles can be extracted and combined with the hydrodynamic information to predict, for each residue in the protein, the relaxation times. All of these developments have been implemented in a computer program, HYDRONMR, which will be of public domain.
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Calculation of NMR relaxation, covolume, and scattering-related properties of Bead Models using the SOLPRO computer program.
European biophysics journal : EBJ, 1999Co-Authors: J. García De La Torre, Stephen E. Harding, B. CarrascoAbstract:The hydrodynamic properties of macromolecules and bioparticles, represented by Bead Models, can be calculated using methods implemented in the computer routine HYDRO. Recently, a new computer routine, SOLPRO, has been presented for the calculation of various SOLution PROperties. These include (1) time-dependent electro-optic and spectroscopic properties related to rotational diffusion, (2) non-dynamic properties like scattering curves, and (3) dimensionless quantities that combine two or more solution properties in a form which depends on the shape of the macromolecule but not on its size. In the present work we describe the inclusion of more of those types of properties in a new version of SOLPRO. Particularly, we describe the calculation of relaxation rates in nuclear magnetic resonance (NMR). For dipolar coupling, given the direction of the dipole the program calculates values of the spectral density, from which the NMR relaxation times can be obtained. We also consider scattering-related properties, namely the distribution of distances for the Bead Model, which is directly related to the angular dependence of scattered intensity, and the particle's longest distance. We have devised and programmed a procedure to calculate the covolume of the Bead Model, related to the second virial coefficient and, in general, to the concentration dependence of solution properties. Various shape-dependent dimensionless quantities involving the covolume are calculated. In this paper we also discuss some aspects, namely Bead overlapping and hydration, that are not explicitely included in SOLPRO, but should be considered by the user.
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Intrinsic viscosity and rotational diffusion of Bead Models for rigid macromolecules and bioparticles
European Biophysics Journal, 1998Co-Authors: J. García De La Torre, B. CarrascoAbstract:The conventional Kirkwood-Riseman (K-R) treatment of the intrinsic viscosity of macromolecular Bead Models shows a deficiency when it is applied to Models with few Beads, whose sizes are not much smaller than of the Modelled particle. We present a complete derivation of the intrinsic viscosity up to first order in interBead distances (Oseen-type hydrodynamic interaction), finding that a term that belongs to the zeroth-order contribution is missing in the usual description. This term is simply proportional to the total volume of the Bead Model. The nature of this correction for viscosity is similar to a previously described correction for rotational coefficients. We discuss the performance of these corrections for various simple Models, including ellipsoids as well as oligomeric structures in rodlike, chainlike and polyhedral conformations.
B. Carrasco - One of the best experts on this subject based on the ideXlab platform.
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HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.
Journal of magnetic resonance (San Diego Calif. : 1997), 2000Co-Authors: J. García De La Torre, M.l. Huertas, B. CarrascoAbstract:The heteronuclear NMR relaxation of globular proteins depends on the anisotropic rotational diffusion tensor. Using our previous developments for prediction of hydrodynamic properties of arbitrarily shaped particles, by means of Bead Models, we have constructed a computational procedure to calculate the rotational diffusion tensor and other properties of proteins from their detailed, atomic-level structure. From the atomic coordinates file used to build the Bead Model, the orientation of the pertinent dipoles can be extracted and combined with the hydrodynamic information to predict, for each residue in the protein, the relaxation times. All of these developments have been implemented in a computer program, HYDRONMR, which will be of public domain.
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Calculation of NMR relaxation, covolume, and scattering-related properties of Bead Models using the SOLPRO computer program.
European biophysics journal : EBJ, 1999Co-Authors: J. García De La Torre, Stephen E. Harding, B. CarrascoAbstract:The hydrodynamic properties of macromolecules and bioparticles, represented by Bead Models, can be calculated using methods implemented in the computer routine HYDRO. Recently, a new computer routine, SOLPRO, has been presented for the calculation of various SOLution PROperties. These include (1) time-dependent electro-optic and spectroscopic properties related to rotational diffusion, (2) non-dynamic properties like scattering curves, and (3) dimensionless quantities that combine two or more solution properties in a form which depends on the shape of the macromolecule but not on its size. In the present work we describe the inclusion of more of those types of properties in a new version of SOLPRO. Particularly, we describe the calculation of relaxation rates in nuclear magnetic resonance (NMR). For dipolar coupling, given the direction of the dipole the program calculates values of the spectral density, from which the NMR relaxation times can be obtained. We also consider scattering-related properties, namely the distribution of distances for the Bead Model, which is directly related to the angular dependence of scattered intensity, and the particle's longest distance. We have devised and programmed a procedure to calculate the covolume of the Bead Model, related to the second virial coefficient and, in general, to the concentration dependence of solution properties. Various shape-dependent dimensionless quantities involving the covolume are calculated. In this paper we also discuss some aspects, namely Bead overlapping and hydration, that are not explicitely included in SOLPRO, but should be considered by the user.
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Intrinsic viscosity and rotational diffusion of Bead Models for rigid macromolecules and bioparticles
European Biophysics Journal, 1998Co-Authors: J. García De La Torre, B. CarrascoAbstract:The conventional Kirkwood-Riseman (K-R) treatment of the intrinsic viscosity of macromolecular Bead Models shows a deficiency when it is applied to Models with few Beads, whose sizes are not much smaller than of the Modelled particle. We present a complete derivation of the intrinsic viscosity up to first order in interBead distances (Oseen-type hydrodynamic interaction), finding that a term that belongs to the zeroth-order contribution is missing in the usual description. This term is simply proportional to the total volume of the Bead Model. The nature of this correction for viscosity is similar to a previously described correction for rotational coefficients. We discuss the performance of these corrections for various simple Models, including ellipsoids as well as oligomeric structures in rodlike, chainlike and polyhedral conformations.
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Bead Modeling using HYDRO and SOLPRO of the conformation of multisubunit proteins: sunflower and rape-seed 11S globulins.
Biophysical chemistry, 1998Co-Authors: B. Carrasco, Stephen E. Harding, José García De La TorreAbstract:Oil seed globulins from sunflower and rape seed are multi-subunit, oligomeric proteins whose native 11S form is a hexamer. In this work we try to determine the spatial structure in which the six subunits of 11S globulin are arranged. Experimental values of solution properties, including radius of gyration, sedimentation and diffusion coefficients and intrinsic viscosity, are compared with theoretical predictions for hexamers of various geometries. Bead Model calculations of solution properties are carried out using the HYDRO and SOLPRO computer programs. A most compact shape, the regular octahedron, is the hexameric structure that fits best the experimental values.
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Usefulness of the Bead Model Algorithm SOLPRO for Modeling the Conformation of Seed Globulins
Plant Proteins from European Crops, 1998Co-Authors: B. Carrasco, Stephen E. Harding, J. García De La TorreAbstract:SOLPRO is a new program for the calculation of SOLution PROperties of rigid macromolecules and bioparticles (Garcia de la Torre et al., 1997). These properties have traditionally been valuable sources of information on the size and shape of biological macromolecules, and their interest has been increasing over the years.
Cédric Boutillier - One of the best experts on this subject based on the ideXlab platform.
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The Bead Model and limit behaviors of dimer Models
The Annals of Probability, 2009Co-Authors: Cédric BoutillierAbstract:In this paper, we study the Bead Model: Beads are threaded on a set of wires on the plane represented by parallel straight lines. We add the constraint that between two consecutive Beads on a wire; there must be exactly one Bead on each neighboring wire. We construct a one-parameter family of Gibbs measures on the Bead configurations that are uniform in a certain sense. When endowed with one of these measures, this Model is shown to be a determinantal point process, whose marginal on each wire is the sine process (given by eigenvalues of large hermitian random matrices). We prove then that this process appears as a limit of any dimer Model on a planar bipartite graph when some weights degenerate.
Michael Kühl - One of the best experts on this subject based on the ideXlab platform.
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Tools for studying growth patterns and chemical dynamics of aggregated Pseudomonas aeruginosa exposed to different electron acceptors in an alginate Bead Model.
NPJ biofilms and microbiomes, 2018Co-Authors: Majken Sønderholm, Klaus Koren, Daniel Wangpraseurt, Peter Østrup Jensen, Mette Kolpen, Kasper Nørskov Kragh, Thomas Bjarnsholt, Michael KühlAbstract:In chronic infections, bacterial pathogens typically grow as small dense cell aggregates embedded in a matrix consisting of, e.g., wound bed sludge or lung mucus. Such biofilm growth mode exhibits extreme tolerance towards antibiotics and the immune defence system. The bacterial aggregates are exposed to physiological heterogeneity and O2 limitation due to steep chemical gradients through the matrix, which is are hypothesised to contribute to antibiotic tolerance. Using a novel combination of microsensor and bioimaging analysis, we investigated growth patterns and chemical dynamics of the pathogen Pseudomonas aeruginosa in an alginate Bead Model, which mimics growth in chronic infections better than traditional biofilm experiments in flow chambers. Growth patterns were strongly affected by electron acceptor availability and the presence of chemical gradients, where the combined presence of O2 and nitrate yielded highest bacterial growth by combined aerobic respiration and denitrification.
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Tools for studying growth patterns and chemical dynamics of aggregated Pseudomonas aeruginosa exposed to different electron acceptors in an alginate Bead Model
npj Biofilms and Microbiomes, 2018Co-Authors: Majken Sønderholm, Klaus Koren, Daniel Wangpraseurt, Peter Østrup Jensen, Mette Kolpen, Kasper Nørskov Kragh, Thomas Bjarnsholt, Michael KühlAbstract:Bacterial growth is strongly affected by levels and gradients of electron accepting chemicals such as nitrate ions and oxygen molecules. Thomas Bjarnsholt, Michael Kühl, and colleagues at the University of Copenhagen grew Pseudomonas aeruginosa bacteria in Beads composed of a natural carbohydrate called alginate. This method Models the growth patterns in chronic infections more effectively than conventional procedures. The Model reflects the fact that chronic infections typically involve dense aggregates of cells embedded in materials such as wound debris or mucus. This renders the bacteria resistant to antibiotics and immune defences. The researchers investigated the effect of varying concentration gradients and flow patterns of several electron acceptors. Bacterial growth was strongly influenced by the distribution of the electron acceptors. Adding electron acceptors to treatment regimes may enhance the activity of antibiotics against chronic infections. In chronic infections, bacterial pathogens typically grow as small dense cell aggregates embedded in a matrix consisting of, e.g., wound bed sludge or lung mucus. Such biofilm growth mode exhibits extreme tolerance towards antibiotics and the immune defence system. The bacterial aggregates are exposed to physiological heterogeneity and O_2 limitation due to steep chemical gradients through the matrix, which is are hypothesised to contribute to antibiotic tolerance. Using a novel combination of microsensor and bioimaging analysis, we investigated growth patterns and chemical dynamics of the pathogen Pseudomonas aeruginosa in an alginate Bead Model, which mimics growth in chronic infections better than traditional biofilm experiments in flow chambers. Growth patterns were strongly affected by electron acceptor availability and the presence of chemical gradients, where the combined presence of O_2 and nitrate yielded highest bacterial growth by combined aerobic respiration and denitrification.
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pseudomonas aeruginosa aggregate formation in an alginate Bead Model system exhibits in vivo like characteristics
Applied and Environmental Microbiology, 2017Co-Authors: Majken Sønderholm, Klaus Koren, Peter Østrup Jensen, Kasper Nørskov Kragh, Tim Holm Jakobsen, Sophie E Darch, Maria Alhede, Marvin Whiteley, Michael KühlAbstract:Alginate Beads represent a simple and highly reproducible in vitro Model system for diffusion-limited bacterial growth. In this study, alginate Beads were inoculated with Pseudomonas aeruginosa and followed for up to 72 h. Confocal microscopy revealed that P. aeruginosa formed dense clusters similar in size to in vivo aggregates observed ex vivo in cystic fibrosis lungs and chronic wounds. Bacterial aggregates primarily grew in the Bead periphery and decreased in size and abundance toward the center of the Bead. Microsensor measurements showed that the O2 concentration decreased rapidly and reached anoxia ∼100 μm below the alginate Bead surface. This gradient was relieved in Beads supplemented with NO3- as an alternative electron acceptor allowing for deeper growth into the Beads. A comparison of gene expression profiles between planktonic and alginate-encapsulated P. aeruginosa confirmed that the bacteria experienced hypoxic and anoxic growth conditions. Furthermore, alginate-encapsulated P. aeruginosa exhibited a lower respiration rate than the planktonic counterpart and showed a high tolerance toward antibiotics. The inoculation and growth of P. aeruginosa in alginate Beads represent a simple and flexible in vivo-like biofilm Model system, wherein bacterial growth exhibits central features of in vivo biofilms. This was observed by the formation of small cell aggregates in a secondary matrix with O2-limited growth, which was alleviated by the addition of NO3- as an alternative electron acceptor, and by reduced respiration rates, as well as an enhanced tolerance to antibiotic treatment.IMPORTANCEPseudomonas aeruginosa has been studied intensively for decades due to its involvement in chronic infections, such as cystic fibrosis and chronic wounds, where it forms biofilms. Much research has been dedicated to biofilm formation on surfaces; however, in chronic infections, most biofilms form small aggregates of cells not attached to a surface, but embedded in host material. In this study, bacteria were encapsulated in small alginate Beads and formed aggregates similar to what is observed in chronic bacterial infections. Our findings show that aggregates are exposed to steep oxygen gradients, with zones of oxygen depletion, and that nitrate may serve as an alternative to oxygen, enabling growth in oxygen-depleted zones. This is important, as slow growth under low-oxygen conditions may render the bacteria tolerant toward antibiotics. This Model provides an alternative to surface biofilm Models and adds to the comprehension that biofilms do not depend on a surface for formation.
Hiromi Yamakawa - One of the best experts on this subject based on the ideXlab platform.
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Transport coefficients of helical wormlike chains. 5. Translational diffusion coefficient of the touched-Bead Model and its application to oligo- and polystyrenes
Macromolecules, 1992Co-Authors: Takeshi Yamada, Takenao Yoshizaki, Hiromi YamakawaAbstract:The translational diffusion coefficient D of the helical wormlike (HW) touched-Bead Model is evaluated theoretically using the Kirkwood formula in the same spirit as in the evaluation of the intrinsic viscosity. The results are compared with those obtained previousvly on the basis of the HW cylinder Model. Experimental results for D determined from dynamic light scattering are also reported for atactic oligo- and polystyrenes in cyclohexane at 34.5°C (θ). The agreement between the experimental and theoretical values is shown fto be fairly good over the whole range of M w down to the trimer