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1999

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Molecular dynamics simulations of the ErbB-2 transmembrane domain within an explicit membrane environment : comparison with vacuum simulations

Two 500-ps molecular dynamics simulations performed on the single transmembrane domain of the ErbB-2 tyrosine kinase receptor immersed in a fully solvated dilauroylphosphatidyl-ethanolamine bilayer (DLPE) are compared to vacuum simulations. One membrane simulation shows that the initial alpha helix undergoes a local pi helix conversion in the peptide part embedded in the membrane core similar to that found in simulation vacuum. Lipid/water/peptide interaction analysis shows that in the helix core, the intramolecular peptide interactions are largely dominant compared to the interactions with water and lipids whereas the helix extremities are much more sensitive to these interactions at the membrane interfaces. Our results suggest that simulations in a lipid environment are required to understand the dynamics of transmembrane helices, but can be reasonably supplemented by in vacuo simulations to explore rapidly its conformational space and to describe the internal deformation of the hydrophobic core. (C) 1999 Elsevier Science B.V. All rights reserved.

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NMR solution structure of a DNA dodecamer containing a transplatin interstrand GN7-CN3 cross-link

The DNA duplex d(CTCTCG*AGTCTC)d(GAGACTC*GAGAG) containing a single trans-diammine-dichloroplatinum(ll) interstrand cross-link (where G* and C* represent the platinated bases) has been studied by two-dimensional NMR, All the exchangeable and non-exchangeable proton resonance lines were assigned (except H5’/H5 ") and the NOE intensities were transformed into distances via the RELAZ program. By combining the NOESY and COSY data (330 constraints) and NMR-constrained molecular mechanics using JUMNA, a solution structure of the cross-linked duplex has been determined.

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Nuclear and electronic relaxation of Eu-(aq)(2+) : An extremely labile aqua ion

Variable-temperature (at 4.7 and 9.4 T) and variable-pressure (9.4 T) O-17 nuclear relaxation rates were measured for the Eu(TI) aqua ion. Variable-temperature H-1 nuclear magnetic relaxation dispersion(NMRD) profiles were recorded. In addition, EPR spectra of the Eu(II) aqua ion are reported as a function of temperature at 0.34, 2.7, 5.4, and 8.1 T. The simultaneous fit of the nuclear and electronic relaxation rate data results in k(ex)(298) = 4.4 x 10(9) s(-1) for the water exchange rate with activation parameters Delta H-double dagger = 15.7 kJ mol(-1) and Delta S-double dagger = -7.0 J K-1 mol(-1), Delta V-double dagger = -11.3 cm(3) mol(-1) for the volume of activation for exchange, and tau(R)(298) = 16.3 ps for the rotational correlation time. Water exchange at Eu-(aq)(2+) occurs via an associative mechanism and has the highest rate ever measured at an aqua ion by magnetic resonance.:The high-field EPR spectra, reported here for the first time for divalent Eu, show hyperfine coupling to Eu-151 and Eu-153 and the coupling constants are determined (37.3 and 16.4 G for Eu-151 and Eu-153, respectively). The electronic relaxation times, T-1e and T-2e, are longer than for the isoelectronic Gd(III) aqua ion. The implications of these results for ligand exchange at Ca(II) and for magnetic resonance imaging contrast agents are discussed.

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Nucleomimetic strategy for the inhibition of HIV-1 nucleocapsid protein NCp7 activities

We report the synthesis and biological properties of three modified dinucleotides T*G, G*T and T*T in winch the natural phosphodiester linkage has been replaced by a methylene carboxamide unit. They have been designed to act as nucleomimetics of a sequence recognized by the HIV-1 nucleocapsid protein NCp7 and to inhibit this interaction. (C) 1999 Elsevier Science Ltd. All rights reserved.

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Optimized conditions to couple two water-soluble biomolecules through alkylamine thiolation and thioetherification

A simple method far introducing, in buffered saline, a reactive sulfhydryl group on water-soluble molecules bearing an alkyl-amino group is described. This method is based on the use of two water-soluble reagents : 2-iminothiolane and 6,6’-dithiodinicotinic acid. The first one is open upon reaction with an amino group, and the generated thiol group is immediately protected by action of the second reagent. The optimal conditions were determined by taking into account the stability and the reactivity of both reagents with regards to pH and temperature. This method was validated through two applications, the substitution of bovine serum albumin with a bromoacetyl peptide and the substitution of an amino link at the 5’ end of an oligonucleotide by reaction with either a fluorescent tag, iodoacetamidofluorescein, or a bromoacetyl peptide, upon reduction of the protected disulfide bridge with a third water-soluble reagent, namely tris(2-carboxyethyl)phosphine.

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Phylogenetic analysis of Mos1-like transposable elements in the Drosophilidae

We have performed a phylogenetic analysis of 59,mariner elements in 14 Drosophilidae species that are related to the active Drosophila mauritiana Mos1 element. This includes 38 previously described sequences and 21 new sequences amplified by PCR from 10 species. Most of the elements detected are nonfunctional due to several frameshifts and deletions. They have been subdivided into four groups according to specific signatures in the nucleotidic and amino acid sequences. The mean nucleotide diversity is 4.8 0.1% and reflects mainly the divergence of inactive elements over different periods. Although this probably gives rise to occasional homoplasies between distantly related taxa, the elements of each species remain grouped together. Horizontal transfer, reported previously between D. mauritiana and Zaprionus tuberculatus, can be extended to Z. verruca, while the Mos1-like element of Z. indianus belongs to another group. Interpretation of the phylogeny leads to a comparison of the influence of common ancestral sequences and putative horizontal transfers.

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R-Selected benthic foraminifera with associated bacterial colonies in Upper Pleistocene sediments of the Ross Sea (Antarctica) : implications for calcium carbonate preservation

Investigations on foraminifera from Upper Pleistocene-Holocene sediments cored in the continental slope of the western Ross Sea (2383 m water depth) revealed that the record of calcareous assemblages was restricted to a limited time interval (approximately 6 kyr) and characterized by a dominance of phytodetritus-exploiting taxa, such as Alabaminella weddellensis and Epistominella exigua. Rod-shaped calcified, fossil bacteria infest the partially dissolved calcareous foraminiferal surfaces, either as clusters or as isolated cells, suggesting that significant changes (from under-to oversaturated conditions with respect to calcium carbonate) in the chemistry of the seawater developed before the final burial of the foraminiferal tests. We postulate that bacterial activity on a microenvironmental scale (interface and pore water) in the sea floor could influence pore water conditions in such a way as to preserve carbonate in deep marine regions where environmental conditions usually prevent the establishment of carbonate secreting communities. (C) 1999 Elsevier Science B.V. All rights reserved.

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