Http Dx Doi Org 10 1080 07391102 1989 10508510, May 21, 2012
The structure of the complex formed between ditercalinium, 2,2'-[4,4'-bipiperidin... more The structure of the complex formed between ditercalinium, 2,2'-[4,4'-bipiperidine-1,1'-bis-(ethane-1,2-diyl)]bis(10-me thoxy-7H- pyrido[4,3-c]carbazolium) tetramethane sulfonate (NSC 366241), and the self-complementary tetranucleotide duplex d(CpGpCpG)2 has been investigated by means of a novel theoretical approach for modelling the conformational flexibility of nucleic acids. The methodology used is the JUMNA procedure, a molecular mechanics systematics capable of evaluating the internal energy and the interaction energy of a complex formed from a large number of fragments. In the best energy-minimized structures, the piperidinium chains of ditercalinium are located in the major groove of the right-handed oligonucleotide. Calculations show a distortion of the base-paired d(CpGpCpG)2 minihelix consisting of lateral dislocation of one base pair with respect to another along an axis parallel to the long axis; strong propeller twist and tilt of the end base pairs; a collective motion of all base pairs with respect to the helical axis towards the drug; and an overwinding at the exclusion site. The proposed structure of the complex is in good agreement with reported proton NMR data, supporting the feasibility of such model.
A new class of toxin acting on potassium channels and cross-linked by four disulfide bridges inst... more A new class of toxin acting on potassium channels and cross-linked by four disulfide bridges instead of three has been recently described. Two peptides, Pi1 and Pi7, purified from the venom of the scorpion Pandinus imperator belong to this new class. Structural features of one of these new toxins, Pi1, have been investigated by proton nuclear magnetic resonance using a new technology that allows to work with very small amount of compound, in the nanomole range. It is shown that it is possible to collect high quality data set in terms of resolution, lineshape and sensitivity with nanomolar amount of compound using this technology. Preliminary results on Pi7 are also presented. The approach described here is quite attractive for the study of natural compounds such as toxins often available at low amounts.
1H and 31P NMR spectroscopy have been used together with molecular modelling to determine the fin... more 1H and 31P NMR spectroscopy have been used together with molecular modelling to determine the fine structure of a non-palindromic 16 bp DNA containing the NF-κB binding site. Much emphasis has been placed upon NMR optimization of both two-dimensional 31P NMR techniques to extract structural information defining the phosphodiester backbone conformation and selective homonuclear 2D COSY experiments to determine sugar conformations. NMR data show evidence for a dynamic behaviour of steps flanking the ten base-pairs of the NF-κB binding site. A BI-BII equilibrium at these steps is demonstrated and two models for each extreme conformation are proposed in agreement with NMR data. In the refined BII structures, the NF-κB binding site exhibits an intrinsic curvature towards the major groove that is magnified by the four flanking steps in the BII conformation. Furthermore, the base-pairs are translated into the major groove. Thus, we present a novel mode of dynamic intrinsic curvature compatible with the DNA curvature observed in the X-ray structure of the p50-DNA complex.
We have determined the solution structure of Cn2, a β-toxin extracted from the venom of the New W... more We have determined the solution structure of Cn2, a β-toxin extracted from the venom of the New World scorpion Centruroides noxius Hoffmann. Cn2 belongs to the family of scorpion toxins that affect the sodium channel activity, and is very toxic to mammals (LD50 = 0.4 μg/20 g mouse mass). The three-dimensional structure was determined using 1H-1H two-dimensional NMR spectroscopy, torsion angle dynamics, and restrained energy minimization. The final set of 15 structures was calculated from 876 experimental distance constraints and 58 angle constraints. The structures have a global r.m.s.d. of 1.38 Å for backbone atoms and 2.21 Å for all heavy atoms. The overall fold is similar to that found in the other scorpion toxins acting on sodium channels. It is made of a triple-stranded antiparallel β-sheet and an α-helix, and is stabilized by four disulfide bridges. A cis-proline residue at position 59 induces a kink of the polypeptide chain in the C-terminal region. The hydrophobic core of the protein is made up of residues L5, V6, L51, A55, and by the eight cysteine residues. A hydrophobic patch is defined by the aromatic residues Y4, Y40, Y42, W47 and by V57 on the side of the β-sheet facing the solvent. A positively charged patch is formed by K8 and K63 on one edge of the molecule in the C-terminal region. Another positively charged spot is represented by the highly exposed K35. The structure of Cn2 is compared with those of other scorpion toxins acting on sodium channels, in particular Aah II and CsE-v3. This is the first structural report of an anti-mammal β-scorpion toxin and it provides the necessary information for the design of recombinant mutants that can be used to probe structure-function relationships in scorpion toxins affecting sodium channel activity.
Resonances of H alpha, H beta, and HN (amide) protons have been assigned in the NMR spectrum for ... more Resonances of H alpha, H beta, and HN (amide) protons have been assigned in the NMR spectrum for ten residues in a region of beta-sheet structure of lysozyme. The assignments were achieved primarily by interpretation of nuclear Overhauser effects in conjunction with spin decoupling. The HN hydrogens involved in main-chain hydrogen bonding were found to exchange slowly with D2O solvent, although one of the most slowly exchanging HN hydrogens is not classified as being involved in a hydrogen bond in the crystal structure. Spin-spin coupling constants between H alpha protons and HN and H beta protons correlated well with values predicted from the crystal structure by means of the Karplus relationship. For no residues are the coupling constant discrepancies greater than 2.5 HZ. This indicates that for the residues studied here the torsion angles phi and chi 1 defined in the crystal structure describe accurately, generally well within 20 degrees, those for the average solution state.
Http Dx Doi Org 10 1080 07391102 1989 10508510, May 21, 2012
The structure of the complex formed between ditercalinium, 2,2'-[4,4'-bipiperidin... more The structure of the complex formed between ditercalinium, 2,2'-[4,4'-bipiperidine-1,1'-bis-(ethane-1,2-diyl)]bis(10-me thoxy-7H- pyrido[4,3-c]carbazolium) tetramethane sulfonate (NSC 366241), and the self-complementary tetranucleotide duplex d(CpGpCpG)2 has been investigated by means of a novel theoretical approach for modelling the conformational flexibility of nucleic acids. The methodology used is the JUMNA procedure, a molecular mechanics systematics capable of evaluating the internal energy and the interaction energy of a complex formed from a large number of fragments. In the best energy-minimized structures, the piperidinium chains of ditercalinium are located in the major groove of the right-handed oligonucleotide. Calculations show a distortion of the base-paired d(CpGpCpG)2 minihelix consisting of lateral dislocation of one base pair with respect to another along an axis parallel to the long axis; strong propeller twist and tilt of the end base pairs; a collective motion of all base pairs with respect to the helical axis towards the drug; and an overwinding at the exclusion site. The proposed structure of the complex is in good agreement with reported proton NMR data, supporting the feasibility of such model.
A new class of toxin acting on potassium channels and cross-linked by four disulfide bridges inst... more A new class of toxin acting on potassium channels and cross-linked by four disulfide bridges instead of three has been recently described. Two peptides, Pi1 and Pi7, purified from the venom of the scorpion Pandinus imperator belong to this new class. Structural features of one of these new toxins, Pi1, have been investigated by proton nuclear magnetic resonance using a new technology that allows to work with very small amount of compound, in the nanomole range. It is shown that it is possible to collect high quality data set in terms of resolution, lineshape and sensitivity with nanomolar amount of compound using this technology. Preliminary results on Pi7 are also presented. The approach described here is quite attractive for the study of natural compounds such as toxins often available at low amounts.
1H and 31P NMR spectroscopy have been used together with molecular modelling to determine the fin... more 1H and 31P NMR spectroscopy have been used together with molecular modelling to determine the fine structure of a non-palindromic 16 bp DNA containing the NF-κB binding site. Much emphasis has been placed upon NMR optimization of both two-dimensional 31P NMR techniques to extract structural information defining the phosphodiester backbone conformation and selective homonuclear 2D COSY experiments to determine sugar conformations. NMR data show evidence for a dynamic behaviour of steps flanking the ten base-pairs of the NF-κB binding site. A BI-BII equilibrium at these steps is demonstrated and two models for each extreme conformation are proposed in agreement with NMR data. In the refined BII structures, the NF-κB binding site exhibits an intrinsic curvature towards the major groove that is magnified by the four flanking steps in the BII conformation. Furthermore, the base-pairs are translated into the major groove. Thus, we present a novel mode of dynamic intrinsic curvature compatible with the DNA curvature observed in the X-ray structure of the p50-DNA complex.
We have determined the solution structure of Cn2, a β-toxin extracted from the venom of the New W... more We have determined the solution structure of Cn2, a β-toxin extracted from the venom of the New World scorpion Centruroides noxius Hoffmann. Cn2 belongs to the family of scorpion toxins that affect the sodium channel activity, and is very toxic to mammals (LD50 = 0.4 μg/20 g mouse mass). The three-dimensional structure was determined using 1H-1H two-dimensional NMR spectroscopy, torsion angle dynamics, and restrained energy minimization. The final set of 15 structures was calculated from 876 experimental distance constraints and 58 angle constraints. The structures have a global r.m.s.d. of 1.38 Å for backbone atoms and 2.21 Å for all heavy atoms. The overall fold is similar to that found in the other scorpion toxins acting on sodium channels. It is made of a triple-stranded antiparallel β-sheet and an α-helix, and is stabilized by four disulfide bridges. A cis-proline residue at position 59 induces a kink of the polypeptide chain in the C-terminal region. The hydrophobic core of the protein is made up of residues L5, V6, L51, A55, and by the eight cysteine residues. A hydrophobic patch is defined by the aromatic residues Y4, Y40, Y42, W47 and by V57 on the side of the β-sheet facing the solvent. A positively charged patch is formed by K8 and K63 on one edge of the molecule in the C-terminal region. Another positively charged spot is represented by the highly exposed K35. The structure of Cn2 is compared with those of other scorpion toxins acting on sodium channels, in particular Aah II and CsE-v3. This is the first structural report of an anti-mammal β-scorpion toxin and it provides the necessary information for the design of recombinant mutants that can be used to probe structure-function relationships in scorpion toxins affecting sodium channel activity.
Resonances of H alpha, H beta, and HN (amide) protons have been assigned in the NMR spectrum for ... more Resonances of H alpha, H beta, and HN (amide) protons have been assigned in the NMR spectrum for ten residues in a region of beta-sheet structure of lysozyme. The assignments were achieved primarily by interpretation of nuclear Overhauser effects in conjunction with spin decoupling. The HN hydrogens involved in main-chain hydrogen bonding were found to exchange slowly with D2O solvent, although one of the most slowly exchanging HN hydrogens is not classified as being involved in a hydrogen bond in the crystal structure. Spin-spin coupling constants between H alpha protons and HN and H beta protons correlated well with values predicted from the crystal structure by means of the Karplus relationship. For no residues are the coupling constant discrepancies greater than 2.5 HZ. This indicates that for the residues studied here the torsion angles phi and chi 1 defined in the crystal structure describe accurately, generally well within 20 degrees, those for the average solution state.
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Papers by Muriel Delepierre