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Accueil > Publications > Recherche par années > Années 1990 > 1999

1999

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A heteronuclear and homonuclear filtering strategy for studying the structure of membrane peptides in non-deuterated phospholipid vesicles

NMR study of membrane biomolecules comes up against a poor solubility in classical solvents. A strategy was elaborated to obtain structural information of peptides in non deuterated phospholipids vesicles. It is based on isotopic (HSQC-NOESY) and homonuclear selective filters, both using a fine water suppression. The method is illustrated with the substance P, a 11-residue membrane neuropeptide.

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A simplified force field for describing vibrational protein dynamics over the whole frequency range

The empirical force fields used for protein simulations contain short-ranged terms (chemical bond structure, steric effects, van der Waals interactions) and long-ranged electrostatic contributions. It is well known that both components are important for determining the structure of a protein. We show that the dynamics around a stable equilibrium state can be described by a much simpler midrange force field made up of the chemical bond structure terms plus unspecific harmonic terms with a distance-dependent force constant. A normal mode analysis of such a model can reproduce the experimental density of states as well as a conventional molecular dynamics simulation using a standard force field with long-range electrostatic terms. This finding is consistent with a recent observation that effective Coulomb interactions are short ranged for systems with a sufficiently homogeneous charge distribution. (C) 1999 American Institute of Physics. [S0021-9606(99)52348-9].

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A theoretical and experimental study of two thiazole orange derivatives with single- and double-stranded oligonucleotides, polydeoxyribonucleotides and DNA

The effect of interaction with DNA and oligonucleotides on the photophysical properties of two thiazole orange (TO) derivatives, with different side chains (-(CH2)(3)-N+ (CH3)(3) and -(CH2)(6)-I) linked to the nitrogen of the quinoline ring of the thiazole orange, is presented here. The first one called TO-PRO1 is a commercially available dye, whereas the second one called TO-MET has been specially synthesized for further covalent binding to oligonucleotides with the aim of being used for specific in situ detection of biomolecular interactions. Both photophysical measurements and molecular calculations have been done to assess their possible mode of interaction with DNA. When dissolved in buffered aqueous solutions both derivatives exhibit very low fluorescence quantum yields of 8 X 10(-5) and 2 X 10(-4), respectively.

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An integrated exobiology package for the search for life on Mars

A multi-user integrated suite of instruments designed to optimize the search for evidence of life on Mars is described. The package includes : * Surface inspection and surface environment analysis to identify the potential Mars landing sites, to inspect the surface geology and mineralogy, to search for visible surficial microbial macrofossils, to study the surface radiation budget and surface oxidation processes, to search for niches for extant life. * Analysis of surface and subsurface minerals and organics to characterize the surface mineralogy, to analyse the surface and subsurface oxidants, to analyze the mineralogy of subsurface aliquots, to analyze the organics present in the subsurface aliquots (elemental and molecular composition, isotopes, chirality). * Macroscopic and microscopic inspection of subsurface aliquots to search for life’s indicators (paleontological, biological, mineralogical) and to characterize the mineralogy of the subsurface aliquots. The study is led by ESA Manned Spaceflight and Microgravity Directorate. (C) 1999 COSPAR. Published by Elsevier Science Ltd.

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Analysis of domain motions in large proteins

We present a new approach for determining dynamical domains in large proteins, either based on a comparison of different experimental structures, or on a simplified normal mode calculation for a single conformation. In a first step, a deformation measure is evaluated for all residues in the protein ; a high deformation indicates highly flexible interdomain regions. The sufficiently rigid parts of the protein are then classified into rigid domains and low-deformation interdomain regions on the basis of their global motion. We demonstrate the techniques on three proteins : citrate synthase, which has been the subject of earlier domain analyses, HIV-1 reverse transcriptase, which has a rather complex domain structure, and aspartate transcarbamylase as an example of a very large protein. These examples show that the comparison of conformations and the normal mode analysis lead to essentially the same domain identification, except for cases where the experimental conformations differ by the presence of a large ligand, such as a DNA strand. Normal mode analysis has the advantage of requiring only one experimental structure and of providing a more detailed picture of domain movements, e.g. the splitting of domains into subdomains at higher frequencies. Proteins 1999 ;34:369-382, (C) 1999 Wiley-Liss, Inc.

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Androctonin, a novel antimicrobial peptide from scorpion Androctonus australis : Solution structure and molecular dynamics simulations in the presence of a lipid monolayer

Androctonin is a highly cationic antimicrobial peptide from scorpion exhibiting a broad spectrum of activities against bacteria and fungi. It contains 25 amino acids including four cysteine residues forming two disulfide bridges. We report here on the determination of its solution structure by conventional two-dimensional (2D) H-1-NMR spectroscopy and molecular modelling using distance geometry and molecular dynamics methods. The structure of androctonin involves a well-defined highly twisted anti-parallel beta-sheet with strands connected by a more variable positively charged turn. A comparison with the structure of tachyplesin I (horseshoe crab) reveals that the amphiphilic character of the protein surface of this homologous peptide is not observed in androctonin. We have undertaken a 200-ps molecular dynamics simulation study on a system including one androctonin molecule and a monolayer of DMPG (1,2-dimyristoylphosphatidylglycerol) lipids. On the basis of this simulation, the first steps of the membrane permeabilization process are discussed.

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AP site structural determinants for Fpg specific recognition

The binding of Escherichia coli and Lactococcus lactis Fapy-DNA glyosylase (Fpg) proteins to DNA containing either cyclic or non-cyclic abasic (AP) site analogs was investigated by electrophoretic mobility shift assay (EMSA) and by footprinting experiments. We showed that the reduced AP site is the best substrate analog for the E. coli and L. lactis enzymes (K-Dapp = 0.26 and 0.5 nM, respectively) as compared with the other analogs tested in this study (K-Dapp > 2.8 nM), The 1,3-propanediol (Pr) residue-containing DNA seems to be the minimal AP site structure allowing a Fpg specific DNA binding, since the ethyleneglycol residue is not specifically bound by these enzymes.

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Asymmetric recognition of psoralen interstrand crosslinks by the nucleotide excision repair and the error-prone repair pathways

Psoralen is an asymmetric photoreactive intercalator with a furane and a pyrone side. When intercalated at 5’-TpA-3’ sites and upon UVA irradiation, the psoralen can react with the thy-nine residues on both strands, introducing an interstrand crosslink. Using psoralen-coupled triple-helix-forming oligonucleotides, psoralen interstrand crosslinks can be site-specifically introduced in the coding sequence of URA3, a yeast auxotrophic marker carried on plasmid vectors. Ln addition, crosslinks introduced via a triple-helix-forming oligonuleotide are oriented with the furane side of the psoralen associated with a specific strand of the target sequence. Here, the transformation efficiency, the mutation frequency and the mutational spectra of site-specifically placed and oriented cross-links were examined in yeast cells.

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