Search results for "Biophysic"
showing 10 items of 3565 documents
Local dynamics of DNA probed with optical absorption spectroscopy of bound ethidium bromide
1997
We have studied the local dynamics of calf thymus double-helical DNA by means of an "optical labeling" technique. The study has been performed by measuring the visible absorption band of the cationic dye ethidium bromide, both free in solution and bound to DNA, in the temperature interval 360-30 K and in two different solvent conditions. The temperature dependence of the absorption line shape has been analyzed within the framework of the vibronic coupling theory, to extract information on the dynamic properties of the system; comparison of the thermal behavior of the absorption band of free and DNA-bound ethidium bromide gave information on the local dynamics of the double helix in the prox…
Influence of Dynamics on The Analysis of Solid-State NMR Data From Membrane-bound Peptides
2009
By isotope labeling of membrane-bound peptides, typically with 2H, 19F, or 15N, solid-state NMR experiments can yield data from which the orientation of peptides in a native membrane environment can be determined. Such an orientation is defined by a tilt angle and an azimuthal rotation angle.Here we show that to obtain correct values of the orientation angles, it is important to include dynamics in the analysis of the NMR data. Nevertheless the effects of dynamics are different depending on the type of isotope labeling and NMR experiment considered.To analyze the influence of dynamics in detail, we generated virtual NMR observables using a model peptide undergoing explicit Gaussian fluctuat…
Incoherent elastic and quasi-elastic neutron scattering investigation of hemoglobin dynamics.
2005
In this work we investigate the dynamic properties of hemoglobin in glycerolD(8)/D(2)O solution using incoherent elastic (ENS) and quasi-elastic (QENS) neutron scattering. Taking advantage of complementary energy resolutions of backscattering spectrometers at ILL (Grenoble), we explore motions in a large space-time window, up to 1 ns and 14 A; moreover, in order to cover the harmonic and anharmonic protein dynamics regimes, the elastic experiments have been performed over the wide temperature interval of 20-300 K. To study the dependence of the measured dynamics upon the protein quaternary structure, both deoxyhemoglobin (in T quaternary conformation) and carbonmonoxyhemoglobin (in R quater…
Solvent-induced free energy landscape and solute-solvent dynamic coupling in a multielement solute
1999
AbstractMolecular dynamics simulations using a simple multielement model solute with internal degrees of freedom and accounting for solvent-induced interactions to all orders in explicit water are reported. The potential energy landscape of the solute is flat in vacuo. However, the sole untruncated solvent-induced interactions between apolar (hydrophobic) and charged elements generate a rich landscape of potential of mean force exhibiting typical features of protein landscapes. Despite the simplicity of our solute, the depth of minima in this landscape is not far in size from free energies that stabilize protein conformations. Dynamical coupling between configurational switching of the syst…
Spectral hole burning study of protoporphyrin IX substituted myoglobin.
1992
Protoporphyrin IX substituted myoglobin reveals excellent hole burning properties. We investigated the frequency shift of persistent spectral holes under isotropic pressure conditions in a range from 0 to 2.4 MPa. In this range, the protein behaves like an elastic solid. The shift of the holes under pressure shows a remarkable frequency dependence from which the compressibility of the protein can be determined. The compressibility, in turn, allows for an estimation of the equilibrium volume fluctuations. Within the frame of the model used to interpret the pressure data, it is possible to determine the absorption frequency of the isolated chromophore and the associated solvent shift in the p…
Solution NMR structure of aD,L-alternating oligonorleucine as a model of ?-helix
2001
beta-Helix structures are of particular interest due to their capacity to form transmembrane channels with different transport properties. However, the relatively large number of beta-helices configurations does not allow a direct conformational analysis of beta-helical oligopeptides. A synthetic alternating D,L-oligopeptide with twelve norleucines (XIIMe) has been used as a model to get insight in the conformational features of beta-helix structures. The spatial configuration of XIIMe in solution has been determined by NMR. An extensive set of distances (nuclear Overhauser effect) and dihedral (J coupling constants) constraints have been included in molecular dynamics calculations. The NMR…
In silico molecular investigations of pyridine N-Oxide compounds as potential inhibitors of SARS-CoV-2: 3D QSAR, molecular docking modeling, and ADME…
2020
The new coronavirus SARS-CoV-2 virus is causing a severe pneumonia in human, provoking the serious outbreak epidemic CoV-2. Since its appearance in Wuhan, China on December 2019, CoV-2 becomes the biggest challenge the world is facing today, including the discovery of antiviral drug for SARS-CoV-2. In this study, the potential inhibitory of a class of human SARS inhibitors, namely pyridine N-oxide derivatives, against CoV-2 was addressed by quantitative structure-activity relationship 3 D-QSAR. The reliable CoMSIA developed model of 110 pyridine N-oxide based-antiviral compounds, showed Q
Uptake of silica covered Quantum Dots into living cells: Long term vitality and morphology study on hyaluronic acid biomaterials
2015
Quantum Dots (QDs) are promising very bright and stable fluorescent probes for optical studies in the biological field but water solubility and possible metal bio-contamination need to be addressed. In this work, a simple silica-QD hybrid system is prepared and the uptake in bovine chondrocytes living cells without any functionalization of the external protective silica shield is demonstrated. Moreover, long term treated cells vitality (up to 14 days) and the transfer of silica-QDs to the next cell generations are here reported. Confocal fluorescence microscopy was also used to determine the morphology of the so labelled cells and the relative silica-QDs distribution. Finally, we employ sil…
Quantum chemical structure-activity relationships on β-carbolines as natural monoamine oxidase inhibitors
1983
The electron density and the molecular electrostatic potential of the β-carbolines are studied using ab initioSTO-3G wave functions. The analysis was done from the point of view of a previous model built with monoamine oxidase substrates and irreversible inhibitors. The results confirm the usefulness of the model and make it possible to propose new precision to the molecular electrostatic potential patterns needed to have monoamine oxidase inhibitory activity.
Using neural networks for (13)c NMR chemical shift prediction-comparison with traditional methods.
2002
Abstract Interpretation of 13 C chemical shifts is essential for structure elucidation of organic molecules by NMR. In this article, we present an improved neural network approach and compare its performance to that of commonly used approaches. Specifically, our recently proposed neural network ( J. Chem. Inf. Comput. Sci. 2000, 40, 1169–1176) is improved by introducing an extended hybrid numerical description of the carbon atom environment, resulting in a standard deviation (std. dev.) of 2.4 ppm for an independent test data set of ∼42,500 carbons. Thus, this neural network allows fast and accurate 13 C NMR chemical shift prediction without the necessity of access to molecule or fragment d…