Thiol/disulphide exchange reaction: A key regulatory process in biological systems

Cysteine residues in proteins serve many important functions such as stabilizing and maintaining the three-dimensional conformation of many proteins(1), in enzyme catalysis, as a residue undergoing post-translational 2 and in the formation of DNA-binding modification domain of a class of transcriptional activators(3), It is also involved in biological redox coupling(4) and xenobiotic metabolism(5). Disulphide bonds formed by xenobiotic metabolism oxidation of cysteine residues have been used as a probe to study the structure/function relationships of proteins, Introducing novel disulphide bonds in proteins to increase their thermal stability and, therefore, the shelf life is an important goal of protein engineering(6,7), In addition, the thiol group of cysteine residue participates in a reaction termed as thiol/disulphide exchange reaction, the biological significance of this reaction being the theme of this review.

Synthesis of Co(II), Ni(II) and Cu(II) Complexes from Schiff base Ligand and Reactivity Studies with Thermosetting Epoxy Resin

A hybrid thermosetting maleimido epoxy compound 4-(N-maleimidophenyl) glycidylether (N-MPGE) containing Co(II), Ni(II) and Cu(II) ions was prepared by curing N-MPGE and tetradentate Schiff base Co(II), Ni(II) and Cu(II) complexes. The curing polymerization reaction of N-MPGE with metal complexes as curing agents was studied. The cured samples were studied for thermal stability, chemical (acid/alkali/solvent) and water absorption resistance and homogeneity of the cured systems. The tetradentate Schiff base, 3-(Z)-2-piperazin-1-yl-ethylimino]-1,3-dihydro indol-2-one was synthesized by the condensation of Isatin (Indole-2, 3-dione) with 1-(2-aminoethyl)piperazine (AEP). Its complexes with Co(II), Ni(II) and Cu(II) have been synthesized and characterized by microanalysis, conductivity, Uv-Visible, FT-IR, TGA and magnetic susceptibility measurements. The spectral data revealed that the ligand acts as a neutral tetradentate Schiff base and coordinating through the azomethine nitrogen, two piperazine nitrogen atoms and carbonyl oxygen.

Magnetism in MnPSe3: a layered 3d(5) antiferromagnet with unusually large XY anisotropy

The anisotropic magnetic susceptibilities of single crystals of the isostructural layered antiferromagnets, MnPS3 (T-N = 78 K) and MnPSe3 (T-N = 74 K), have been measured as functions of temperature. In both compounds, divalent manganese is present in the high-spin S = 5/2 state. The anisotropies in the susceptibilities of the two are, however, very different; while the susceptibility of MnPS3 is isotropic, that of MnPSe3 shows a large XY anisotropy, unusual for a manganese compound. The anisotropic susceptibilities are described by the zero-field spin Hamiltonian: H = DSiz2 - Sigma J(ij).(S) over right arrow (S) over right arrow(j) with the quadratic single-ion anisotropy term introducing anisotropy in an otherwise isotropic situation. The exchange J and the single-ion zero-field-splitting (ZFS) parameter D were evaluated using the correlated effective-field theory of Lines. For MnPSe3, J/k = -5.29 K and D/k = 26.6 K, while for isotropic MnPS3, J/k = -8.1 K. It is suggested that the large value of the ZFS parameter for MnPSe3 as compared to MnPS3 could be due to the large ligand spin-orbit contribution of the heavier selenium.

Crystal structure of nonadentate tricompartmental ligand derived from pyridine-2,6-dicarboxylic acid: Spectroscopic, electrochemical and thermal investigations of its transition metal(II) complexes

The coordinating behavior of a new dihydrazone ligand, 2,6-bis(3-methoxysalicylidene) hydrazinocarbonyl]pyridine towards manganese(II), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) has been described. The metal complexes were characterized by magnetic moments, conductivity measurements, spectral (IR, NMR, UV-Vis, FAB-Mass and EPR) and thermal studies. The ligand crystallizes in triclinic system, space group P-1, with alpha=98.491(10)degrees, beta=110.820(10)degrees and gamma=92.228(10)degrees. The cell dimensions are a=10.196(7)angstrom, b=10.814(7)angstrom, c=10.017(7)angstrom, Z=2 and V=1117.4(12). IR spectral studies reveal the nonadentate behavior of the ligand. All the complexes are neutral in nature and possess six-coordinate geometry around each metal center. The X-band EPR spectra of copper(II) complex at both room temperature and liquid nitrogen temperature showed unresolved broad signals with g(iso) = 2.106. Cyclic voltametric studies of copper(II) complex at different scan rates reveal that all the reaction occurring are irreversible. (C) 2011 Elsevier B.V. All rights reserved.

Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions

In this article, we present a novel application of a quantum clustering (QC) technique to objectively cluster the conformations, sampled by molecular dynamics simulations performed on different ligand bound structures of the protein. We further portray each conformational population in terms of dynamically stable network parameters which beautifully capture the ligand induced variations in the ensemble in atomistic detail. The conformational populations thus identified by the QC method and verified by network parameters are evaluated for different ligand bound states of the protein pyrrolysyl-tRNA synthetase (DhPylRS) from D. hafniense. The ligand/environment induced re-distribution of protein conformational ensembles forms the basis for understanding several important biological phenomena such as allostery and enzyme catalysis. The atomistic level characterization of each population in the conformational ensemble in terms of the re-orchestrated networks of amino acids is a challenging problem, especially when the changes are minimal at the backbone level. Here we demonstrate that the QC method is sensitive to such subtle changes and is able to cluster MD snapshots which are similar at the side-chain interaction level. Although we have applied these methods on simulation trajectories of a modest time scale (20 ns each), we emphasize that our methodology provides a general approach towards an objective clustering of large-scale MD simulation data and may be applied to probe multistate equilibria at higher time scales, and to problems related to protein folding for any protein or protein-protein/RNA/DNA complex of interest with a known structure.

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

The design and synthesis of redox core-alpha amino acid composites based on thiol-disulfide exchange mechanism and a comparative study of their zinc abstraction potential from [CCXX] boxes in proteins

The design and synthesis of agents that can abstract zinc from their [CCXX] (C=cysteine; X=cysteine/histidine) boxes by thioldisulfide exchange-having as control, the redox parities of the core sulfur ligands of the reagent and the enzyme, has been illustrated, and their efficiency demonstrated by monitoring the inhibition of the transcription of calf thymus DNA by E. coli RNA polymerase, which harbors two zinc atoms in their [CCXX] boxes of which one is exchangeable. Maximum inhibition possible with removal of the exchangeable zinc was seen with redox-sulfanilamide-glutamate composite. In sharp contrast, normal chelating agents (EDTA, phenanthroline) even in a thousand fold excess showed only marginal inhibition, thus supporting an exchange mechanism for the metal removal. (C) 2002 Elsevier Science Ltd. All rights reserved.

Critical properties of the double-exchange ferromagnet Nd(0.6)Pb(0.4)MnO(3)

Results of a study of dc magnetization M(T,H), performed on a Nd(0.6)Pb(0.4)MnO(3) single crystal in the temperature range around T(C) (Curie temperature) which embraces the supposed critical region \epsilon\=\T-T(C)\/T(C)less than or equal to0.05 are reported. The magnetic data analyzed in the critical region using the Kouvel-Fisher method give the values for the T(C)=156.47+/-0.06 K and the critical exponents beta=0.374+/-0.006 (from the temperature dependence of magnetization) and gamma=1.329+/-0.003 (from the temperature dependence of initial susceptibility). The critical isotherm M(T(C),H) gives delta=4.54+/-0.10. Thus the scaling law gamma+beta=deltabeta is fulfilled. The critical exponents obey the single scaling equation of state M(H,epsilon)=epsilon(beta)f(+/-)(H/epsilon(beta+gamma)), where f(+) for T>T(C) and f(-) for T

Probing the mobility of lithium in LISICON: Li+/H+ exchange studies in Li2ZnGeO4 and Li2+2xZn1-xGeO4

We investigated Li+/H+ exchange in the lithium ion conductors (LISICONS) [ Li2+2xZn1-xGeO4; x = 0.5 ( I) and x = 0.75 (II)] and their parent, gamma-Li2ZnGeO4. Facile exchange of approximately 2x lithium ions per formula unit occurs with both the LISICONS in dilute acetic acid, while the parent material does not exhibit an obvious Li+/H+ exchange under the same conditions. The results can be understood in terms of lithium ion distribution in the crystal structures: the parent Li2ZnGeO4, where all the lithium ions form part of the tetrahedral framework structure, does not exhibit a ready Li+/H+ exchange; LISICONS, where lithium ions are distributed between framework ( tetrahedral) and nonframework sites, undergo a facile Li+/H+ exchange of the nonframework site lithium ions. Accordingly, Li+/H+ exchange in dilute aqueous acetic acid provides a convenient probe to distinguish between the mobile and the immobile lithium ions in lithium ion conductors.

Ligand-modulated Parallel Mechanical Unfolding Pathways of Maltose-binding Proteins

Protein folding and unfolding are complex phenomena, and it is accepted that multidomain proteins generally follow multiple pathways. Maltose-binding protein (MBP) is a large (a two-domain, 370-amino acid residue) bacterial periplasmic protein involved in maltose uptake. Despite the large size, it has been shown to exhibit an apparent two-state equilibrium unfolding in bulk experiments. Single-molecule studies can uncover rare events that are masked by averaging in bulk studies. Here, we use single-molecule force spectroscopy to study the mechanical unfolding pathways of MBP and its precursor protein (preMBP) in the presence and absence of ligands. Our results show that MBP exhibits kinetic partitioning on mechanical stretching and unfolds via two parallel pathways: one of them involves a mechanically stable intermediate (path I) whereas the other is devoid of it (path II). The apoMBP unfolds via path I in 62% of the mechanical unfolding events, and the remaining 38% follow path II. In the case of maltose-bound MBP, the protein unfolds via the intermediate in 79% of the cases, the remaining 21% via path II. Similarly, on binding to maltotriose, a ligand whose binding strength with the polyprotein is similar to that of maltose, the occurrence of the intermediate is comparable (82% via path I) with that of maltose. The precursor protein preMBP also shows a similar behavior upon mechanical unfolding. The percentages of molecules unfolding via path I are 53% in the apo form and 68% and 72% upon binding to maltose and maltotriose, respectively, for preMBP. These observations demonstrate that ligand binding can modulate the mechanical unfolding pathways of proteins by a kinetic partitioning mechanism. This could be a general mechanism in the unfolding of other large two-domain ligand-binding proteins of the bacterial periplasmic space.

Synthesis and DNA binding studies of Ni(II), Co(II), Cu(II) and Zn(II) metal complexes of N(1),N(5)-bis[pyridine-2-methylene]-thiocarbohydrazone Schiff-base ligand

The thiocarbohydrazone Schiff-base ligand with a nitrogen and sulphur donor was synthesized through condensation of pyridine-2-carbaldehyde and thiocarbohydrazide. Schiff-base ligands have the ability to conjugate with metal salts. A series of metal complexes with a general formula [MCl(2)(H(2)L)]center dot nH(2)O (M=Ni, Co, Cu and Zn) were synthesized by forming complexes of the N(1),N5-bis[pyridine-2-methylene]thiocarbohydrazone (H2L) Schiff-base ligand. These metal complexes and ligand were characterized by using ultraviolet-visible (UV-Vis), Fourier Transform Infrared (FT-IR), (1)H and (13)C NMR spectroscopy and mass spectroscopy, physicochemical characterization, CHNS and conductivity. The biological activity of the synthesized ligand was investigated by using Escherichia coli DNA as target. The DNA interaction of the synthesized ligand and complexes on E. coli plasmid DNA was investigated in the aqueous medium by UV-Vis spectroscopy and the binding constant (K(b)) was calculated. The DNA binding studies showed that the metal complexes had an improved interaction due to trans-geometrical isomers of the complexes than ligand isomers in cis-positions. (C) 2011 Elsevier B.V. All rights reserved.

Synergy between the N-terminal and C-terminal domains of Mycobacterium tuberculosis HupB is essential for high-affinity binding, DNA supercoiling and inhibition of RecA-promoted strand exchange

The occurrence of DNA architectural proteins containing two functional domains derived from two different architectural proteins is an interesting emerging research theme in the field of nucleoid structure and function. Mycobacterium tuberculosis HupB, unlike Escherichia coli HU, is a two-domain protein that, in the N-terminal region, shows broad sequence homology with bacterial HU. The long C-terminal extension, on the other hand, contains seven PAKK/KAAK motifs, which are characteristic of the histone H1/H5 family of proteins. In this article, we describe several aspects of HupB function, in comparison with its truncated derivatives lacking either the C-terminus or N-terminus. We found that HupB binds a variety of DNA repair and replication intermediates with K(d) values in the nanomolar range. By contrast, the N-terminal fragment of M. tuberculosis HupB (HupB(MtbN)) showed diminished DNA-binding activity, with K(d) values in the micromolar range, and the C-terminal domain was completely devoid of DNA-binding activity. Unlike HupB(MtbN), HupB was able to constrain DNA in negative supercoils and introduce negative superhelical turns into relaxed DNA. Similarly, HupB exerted a robust inhibitory effect on DNA strand exchange promoted by cognate and noncognate RecA proteins, whereas HupB(MtbN), even at a 50-fold molar excess, had no inhibitory effect. Considered together, these results suggest that synergy between the N-terminal and C-terminal domains of HupB is essential for its DNA-binding ability, and to modulate the topological features of DNA, which has implications for processes such as DNA compaction, gene regulation, homologous recombination, and DNA repair.

A homobimetallic complex of chromium(0) with a sigma-borane component

The synthesis, characterization, and reactivity of a chromium(0) complex bearing an amine-borane moiety (eta(6)-C(6)H(5)CH(2)NMe(2)center dot BH(3))Cr(CO)(3) (2) is reported. Photolysis of complex 2 results in the elimination of a CO ligand followed by the formation of an intramolecular sigma-borane complex (eta(1)-(eta(6)- C(6)H(5)CH(2)NMe(2)center dot BH(2)-H))Cr(CO)(2) (3). This species was characterized in solution by NMR spectroscopy. Reaction of complex 2 with photochemically generated (OC)(5)Cr(THF) affords a novel homobimetallic sigma-borane complex (OC)(3)Cr(eta(6)-C(6)H(5)CH(2)NMe(2)center dot BH(2)-H-Cr(CO)(5)) (4), wherein one of the BH moieties is bound to the chromium center in an eta(1)-fashion. The sigma-borane complex 4 was isolated in moderate to good yield (72%). The BH(3) fragment in the complexes 3 and 4 are highly dynamic involving exchange of the BH hydrogen bound to the metal with the terminal BH hydrogen atoms. The dynamics has been studied using variable-temperature NMR spectroscopy. Complexes 2 and 4 have been characterized by X-ray crystallography.

Ion exchange equilibria between (Mn,Co)O solid solution and (Mn,Co)Cr2O4 and (Mn,Co)Al2O4 spinel solid solutions at 1100oC

The compositions of the (Mn,Co)O solid solution with rock salt structure in equilibrium with (Mn,Co)Cr2O4 and (Mn,Co)Al2O4 spinel solid solutions have been determined by X-ray diffraction measurements at 1100° C and an oxygen partial pressure of 10–10 atm. The ion exchange equilibria are quantitatively analysed, using values for activities in the (Mn,Co)O solid solution available in the literature, in order to obtain activities in the spinel solid solutions. The MnAl2O4-CoAl2O4 solid solution exhibits negative deviations from Raoult's law, consistent with the estimated cation disorder in the solid solution, while the MnCr2O4-CoCr2O4 solid solution shows slightly positive deviations. The difference in the Gibbs free energy of formation of the two pure chromites and aluminates derived from the results of this study are in good agreement with recent results obtained from solid oxide galvanic cells and gas-equilibrium techniques.

Inter and intra crystalline ion exchange equilibria in the system Fe Cr Al O

The tie lines delineating ion-exchange equilibria between FeCr2O4FeAl2O4 spinel solid solution and Cr2O3Al2O3 solid solution with corundum structure have been determined at 1373 K by electron microprobe and EDAX point count analysis of oxide phases equilibrated with metallic iron. Activities in the spinel solid solution are derived from the tie lines and the thermodynamic data on Cr2O3Al2O3 solid solution available in the literature. The oxygen potentials corresponding to the tie-line composition of oxide phases in equilibrium with metallic iron were measured using solid oxide galvanic cells with CaOZrO2 and Y2O3ThO2 electrolytes. These electrochemical measurements also yield activities in the spinel solid solution, in good agreement with those obtained from tie lines. The activity-composition relationship in the spinel solid solution is analysed in terms of the intra-crystalline ion exchange between the tetrahedral and octahedral sites of the spinel structures. The ion exchange is governed by site-preference energies of the cations and the entropy of cations mixing on each site.