Publications (19) View all
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Article: Understanding the relative affinity and specificity of the pleckstrin homology domain of protein kinase B for inositol phosphates.
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ABSTRACT: Protein kinase B (PKB) is a serine/threonine kinase that plays a key role in the phosphoinositide 3-kinase (PI3K) pathway-one of the most frequently activated proliferation pathways in cancer. In this pathway, PKB is recruited to the plasma membrane by direct interaction of its pleckstrin homology (PH) domain with the inositol phosphate head-group of phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P(3)] or phosphatidylinositol 3,4-bisphosphate [PtdIns(3,4)P(2)]. This recruitment is a critical stage in the activation of PKB, whose downstream effectors play important roles in cell survival, proliferation and growth. It is therefore of great interest to understand PKB's mode of binding, as well as its specificity and affinity for different phosphoinositides. We have used a total of 3 μs of molecular dynamics (MD) simulations to better understand the interactions of the PKB PH domain with the inositol phosphate head-groups of phosphoinositides involved in the PI3K pathway. Our computational models successfully mirror PKB's in vivo selectivity for 3-phosphorylated phosphoinositides. Furthermore, the models also help to rationalize unexpected in vitro data in which inositol 1,4,5-trisphosphate [Ins(1,4,5)P(3)] binds with a relatively high affinity to the PKB PH domain, despite its parent lipid phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P(2)] being known not to bind in vivo. With the support of computational simulations, we propose that when not bonded to a phosphatidate tail Ins(1,4,5)P(3) binds in an orientation in which its inositol ring is flipped with respect to the 3-phosphorylated inositol phosphate ligands and its parent lipid.Physical Chemistry Chemical Physics 11/2011; 14(2):929-36. · 3.57 Impact Factor -
Article: Complexation of Cs+, K+ and Na+ by norbadione A triggered by the release of a strong hydrogen bond: nature and stability of the complexes.
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ABSTRACT: Norbadione A (NBA) is a pigment present in edible mushrooms which is presumed to selectively complex Cs(+) cations. Due to a very uncommon complexation mechanism, we used a combination of several experimental techniques, including (1)H-NMR, (133)Cs-NMR, isothermal calorimetric, potentiometric titrations and molecular dynamics MD simulations to determine the nature of the complexed species, as well as their stability constants for the NBA-M(+) systems (M(+) = Cs(+), K(+), Na(+)) in methanol:water 80:20 solutions at 25.0 degrees C. We show that almost no complexation occurs below pH 7.5, as long as a proton, involved in a strong hydrogen bond, bridges both carboxylic and enolic groups of each pulvinic moiety of NBA. Thus, neutralization of that proton is necessary to both set free potential coordination sites and to trigger a conformational change, two conditions needed to bind successively a first, then a second metallic cation. The stability constants determined in this study are in good agreement with each other, leading to the stability order Cs(+) > K(+) > Na(+) for both mono- and bimetallic complexes, which is the reversed order to the one generally observed for low molecular weight carboxylic ligands in water. According to MD simulations in solution, complexation involves a mixture of Z/E isomers and conformers of NBA with a broad diversity of binding modes. Some pH and environment dependent aggregation phenomena are considered to also contribute to the binding process, and to possibly explain the accumulation of radionuclides in mushrooms.Physical Chemistry Chemical Physics 11/2009; 11(44):10299-310. · 3.57 Impact Factor -
Article: Design and synthesis of 4″,6″-unsaturated cyclic ADP-carbocyclic-ribose, a Ca2+-mobilizing agent selectively active in T cells
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ABSTRACT: We previously developed cyclic ADP-carbocyclic-ribose (cADPcR, 3a) as a stable mimic of cyclic ADP-ribose (cADPR, 1), a Ca2+-mobilizing second messenger. The unsaturated carbocyclic-ribose analogs of cADPR, i.e., 4″,6″-didehydro-cADPcR (8a) and its inosine congener 4″,6″-didehydro-cIDPcR (8b) were newly designed and successfully synthesized using the key intramolecular condensation reaction with S-phenyl phosphorothioate-type substrates. The Ca2+-mobilizing potency of the compounds was examined in sea urchin egg homogenates, NG108-15 neuronal cells, and permeabilized Jurkat T-lymphocytes, which may indicate that 4″,6″-didehydro-cADPcR is the first cADPR analog selectively active in T cells. Acid–base behavior and conformation of 8a were also investigated and compared with those of cADPcR.Graphical abstractTetrahedron. 01/2008; 64(41):9754-9765. -
Article: Influence of metal cations on the intramolecular hydrogen-bonding network and pKa in phosphorylated compounds.
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ABSTRACT: The binding of the most common metal cations of cytoplasm (Li+, Na+, K+, Mg2+ and Ca2+) to a model molecule having an intramolecular hydrogen-bonding network, myo-inositol-2-monophosphate, was studied using first principles. A strong correlation between the conformation of metal inositol phosphate complexes with the type of metal cation, degree of deprotonation state, and the surrounding environment has been observed. On the basis of the hydrogen-bonding network analysis of the cation-phosphate complexes (Mn+-Ins(2)P1), the alkali cations show little effect on the conformational preference while the conformational preference for the binding of the alkaline earth cations is pH-dependent and solvent-dependent. For example, these calculations predict that Mg2+-Ins(2)P1(0) and Mg2+-Ins(2)P1(2-) favor the 1a/5e form while Mg2+-Ins(2)P1(1-) favors the 5a/1e conformation. The Ca2+-Ins(2)P1(2-) complex prefers the 1a/5e conformation in the gas phase and in a nonpolar protein environment, but inverts to the 5a/1e conformation upon entering the polar aqueous phase. The binding affinities of the cations and the pK(a) values for the cation-phosphate complexes are derived from thermodynamical analysis.The Journal of Physical Chemistry A 06/2007; 111(18):3602-12. · 2.95 Impact Factor -
Article: Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: thermodynamics and effect on the kissing-loop to duplex conversion.
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ABSTRACT: Owing to a striking, and most likely fortuitous, structural and sequence similarity with the bacterial 16 S ribosomal A site, the RNA kissing-loop complex formed by the HIV-1 genomic RNA dimerization initiation site (DIS) specifically binds 4,5-disubstituted 2-deoxystreptamine (2-DOS) aminoglycoside antibiotics. We used chemical probing, molecular modeling, isothermal titration calorimetry (ITC) and UV melting to investigate aminoglycoside binding to the DIS loop-loop complex. We showed that apramycin, an aminoglycoside containing a bicyclic moiety, also binds the DIS, but in a different way than 4,5-disubstituted 2-DOS aminoglycosides. The determination of thermodynamic parameters for various aminoglycosides revealed the role of the different rings in the drug-RNA interaction. Surprisingly, we found that the affinity of lividomycin and neomycin for the DIS (K(d) approximately 30 nM) is significantly higher than that obtained in the same experimental conditions for their natural target, the bacterial A site (K(d) approximately 1.6 microM). In good agreement with their respective affinity, aminoglycoside increase the melting temperature of the loop-loop interaction and also block the conversion from kissing-loop complex to extended duplex. Taken together, our data might be useful for selecting new molecules with improved specificity and affinity toward the HIV-1 DIS RNA.Nucleic Acids Research 02/2007; 35(21):7128-39. · 8.03 Impact Factor
