DNA Binding and Oxidative Cleavage Activity of Ternary (alpha-Lipoic Acid) Copper(II) Complex of Heterocyclic Base

Ternary copper(II) complex Cu(a-lipo)(phen)(Cl)](NO3) where a-lipo = a-lipoic acid, phen is N, N-donor heterocyclic base, 1,10-phenanthroline was synthesized, characterized, and its DNA binding and cleavage activity were studied. Binding interactions of the complex with calf thymus (CT) DNA has been investigated by emission, viscosity, and DNA melting studies. The complex shows efficient oxidative cleavage of SC-DNA in the presence of 3-mercaptopropionic acid involving hydroxyl radical species, and results of control experiments exhibit the inhibition of DNA cleavage in the presence of hydroxyl radical scavengers, viz. DMSO and KI.

Force and ATP hydrolysis dependent regulation of RecA nucleoprotein filament by single-stranded DNA binding protein

In Escherichia coli, the filament of RecA formed on single-stranded DNA (ssDNA) is essential for recombinational DNA repair. Although ssDNA-binding protein (SSB) plays a complicated role in RecA reactions in vivo, much of our understanding of the mechanism is based on RecA binding directly to ssDNA. Here we investigate the role of SSB in the regulation of RecA polymerization on ssDNA, based on the differential force responses of a single 576-nucleotide-long ssDNA associated with RecA and SSB. We find that SSB outcompetes higher concentrations of RecA, resulting in inhibition of RecA nucleation. In addition, we find that pre-formed RecA filaments de-polymerize at low force in an ATP hydrolysis- and SSB-dependent manner. At higher forces, re-polymerization takes place, which displaces SSB from ssDNA. These findings provide a physical picture of the competition between RecA and SSB under tension on the scale of the entire nucleoprotein SSB array, which have broad biological implications particularly with regard to competitive molecular binding.

A constant factor approximation algorithm for boxicity of circular arc graphs

Boxicity of a graph G(V, E) is the minimum integer k such that G can be represented as the intersection graph of k-dimensional axis parallel boxes in Rk. Equivalently, it is the minimum number of interval graphs on the vertex set V such that the intersection of their edge sets is E. It is known that boxicity cannot be approximated even for graph classes like bipartite, co-bipartite and split graphs below O(n0.5-ε)-factor, for any ε > 0 in polynomial time unless NP = ZPP. Till date, there is no well known graph class of unbounded boxicity for which even an nε-factor approximation algorithm for computing boxicity is known, for any ε < 1. In this paper, we study the boxicity problem on Circular Arc graphs - intersection graphs of arcs of a circle. We give a (2+ 1/k)-factor polynomial time approximation algorithm for computing the boxicity of any circular arc graph along with a corresponding box representation, where k ≥ 1 is its boxicity. For Normal Circular Arc(NCA) graphs, with an NCA model given, this can be improved to an additive 2-factor approximation algorithm. The time complexity of the algorithms to approximately compute the boxicity is O(mn+n2) in both these cases and in O(mn+kn2) which is at most O(n3) time we also get their corresponding box representations, where n is the number of vertices of the graph and m is its number of edges. The additive 2-factor algorithm directly works for any Proper Circular Arc graph, since computing an NCA model for it can be done in polynomial time.

Site-specific N-Linked Glycosylation of Receptor Guanylyl Cyclase C Regulates Ligand Binding, Ligand-mediated Activation and Interaction with Vesicular Integral Membrane Protein 36, VIP36

Guanylyl cyclase C (GC-C) is a multidomain, membrane-associated receptor guanylyl cyclase. GC-C is primarily expressed in the gastrointestinal tract, where it mediates fluid-ion homeostasis, intestinal inflammation, and cell proliferation in a cGMP-dependent manner, following activation by its ligands guanylin, uroguanylin, or the heat-stable enterotoxin peptide (ST). GC-C is also expressed in neurons, where it plays a role in satiation and attention deficiency/hyperactive behavior. GC-C is glycosylated in the extracellular domain, and differentially glycosylated forms that are resident in the endoplasmic reticulum (130 kDa) and the plasma membrane (145 kDa) bind the ST peptide with equal affinity. When glycosylation of human GC-C was prevented, either by pharmacological intervention or by mutation of all of the 10 predicted glycosylation sites, ST binding and surface localization was abolished. Systematic mutagenesis of each of the 10 sites of glycosylation in GC-C, either singly or in combination, identified two sites that were critical for ligand binding and two that regulated ST-mediated activation. We also show that GC-C is the first identified receptor client of the lectin chaperone vesicular integral membrane protein, VIP36. Interaction with VIP36 is dependent on glycosylation at the same sites that allow GC-C to fold and bind ligand. Because glycosylation of proteins is altered in many diseases and in a tissue-dependent manner, the activity and/or glycan-mediated interactions of GC-C may have a crucial role to play in its functions in different cell types.

Synthesis, crystal structure, DNA binding and cleavage activities of oximato bridged cationic dinuclear copper(II) complex having labile ligands

Oximato bridged dinuclear copper(II) complex Cu(L)(CH3OH)](2)(ClO4)(2) with an oxime-Schiff base ligand, viz. 3-2-(dimethylamino)ethyl]imino]-2-butanoneoxime (HL), has been synthesized and structurally characterized. The dinuclear copper(II) complex crystallizes in monoclinic space group P2(1)/n with the unit cell parameters, a = 13.3564(9) angstrom, b = 12.0821(8) angstrom, c = 17.5045(11) angstrom, beta = 90.097, V = 2824.8(3) angstrom(3), Z = 4, R = 0.0769. The complex shows quasi-reversible cyclic voltammetric response at 0.844V (Delta E-p = 276 mV) at 100 mVs(-1). The binding studies of the complex with calf thymus DNA has been investigated using absorption spectrophotometry. Cleavage activity of the complex has been carried out on double stranded pBR 322 plasmid DNA by using gel electrophoresis experiments in the absence and in the presence of the oxidant, viz., H2O2.

Design and analysis of novel compression fracture specimen with constant form factor: Edge cracked semicircular disk (ECSD)

Inspired by the Brazilian disk geometry we examine the utility of an edge cracked semicircular disk (ECSD) specimen for rapid assessment of fracture toughness of brittle materials using compressive loading. It is desirable to optimize the geometry towards a constant form factor F for evaluating K-I. In this investigation photoelastic and finite element results for K-I evaluation highlight the effect of loading modeled using a Hertzian. A Hertzian loading subtending 4 degrees at the center leads to a surprisingly constant form factor of 1.36. This special case is further analyzed by applying uniform pressure over a chord for facilitating testing.

Crystal structures and binding studies of atovaquone and its derivatives with cytochrome bc(1): a molecular basis for drug design

Crystal structure of trans-atovaquone (antimalarial drug), its polymorph and its stereoisomer (cis) along with five other derivatives with different functional groups have been analyzed. Based on the conformational features of these compounds and the characteristics of the nature of intermolecular interactions, valuable insights into the atomistic details of protein-inhibitor interactions have been derived by docking studies. Atovaquone and its derivatives pack in the crystal lattice using intermolecular O-H center dot center dot center dot O hydrogen bond dimer motifs supported by surrogate weak interactions including C-H center dot center dot center dot O and C-H center dot center dot center dot Cl hydrogen bonds. The docking results of these molecules with cytochrome bc(1) show preferences to form N-H center dot center dot center dot O, O-H center dot center dot center dot O and O-H center dot center dot center dot Cl hydrogen bonds. The involvement of halogen atoms in the binding pocket appears to be significant and is contrary to the theoretically predicted mechanism of protein-ligand docking reported earlier based on mimicking experimental binding results of stigmatellin with cytochrome bc(1). The significance of subtle energy factors controlled by weak intermolecular interactions appears to play a major role in drug binding.

Regulation of protumorigenic pathways by Insulin like growth factor binding protein2 and its association along with beta-catenin in breast cancer lymph node metastasis

Background: Insulin like growth factor binding proteins modulate the mitogenic and pro survival effects of IGF. Elevated expression of IGFBP2 is associated with progression of tumors that include prostate, ovarian, glioma among others. Though implicated in the progression of breast cancer, the molecular mechanisms involved in IGFBP2 actions are not well defined. This study investigates the molecular targets and biological pathways targeted by IGFBP2 in breast cancer. Methods: Transcriptome analysis of breast tumor cells (BT474) with stable knockdown of IGFBP2 and breast tumors having differential expression of IGFBP2 by immunohistochemistry was performed using microarray. Differential gene expression was established using R-Bioconductor package. For validation, gene expression was determined by qPCR. Inhibitors of IGF1R and integrin pathway were utilized to study the mechanism of regulation of beta-catenin. Immunohistochemical and immunocytochemical staining was performed on breast tumors and experimental cells, respectively for beta-catenin and IGFBP2 expression. Results: Knockdown of IGFBP2 resulted in differential expression of 2067 up regulated and 2002 down regulated genes in breast cancer cells. Down regulated genes principally belong to cell cycle, DNA replication, repair, p53 signaling, oxidative phosphorylation, Wnt signaling. Whole genome expression analysis of breast tumors with or without IGFBP2 expression indicated changes in genes belonging to Focal adhesion, Map kinase and Wnt signaling pathways. Interestingly, IGFBP2 knockdown clones showed reduced expression of beta-catenin compared to control cells which was restored upon IGFBP2 re-expression. The regulation of beta-catenin by IGFBP2 was found to be IGF1R and integrin pathway dependent. Furthermore, IGFBP2 and beta-catenin are co-ordinately overexpressed in breast tumors and correlate with lymph node metastasis. Conclusion: This study highlights regulation of beta-catenin by IGFBP2 in breast cancer cells and most importantly, combined expression of IGFBP2 and beta-catenin is associated with lymph node metastasis of breast tumors.

Postliquefaction Undrained Shear Behavior of Sand-Silt Mixtures at Constant Void Ratio

A detailed study on the postliquefaction undrained shear behavior of sand-silt mixtures at constant void ratios is presented in this article. The influence of different parameters such as density, amplitude of cyclic shear stress, and drainage conditions on the postliquefaction undrained response of sand-silt mixtures has been investigated, in addition to the effect of fines content. The results showed that the limiting silt content plays a vital role in the strength of the soil under both cyclic and monotonic shear loading. Both the liquefaction resistance and postliquefaction shear strength of the soils are found to decrease with an increase in the fines content until the limiting silt content is reached. However, further increase in the silt content beyond the limiting silt content increases the liquefaction resistance as well as the postliquefaction shear strength of the soils. It is also observed that these variations on the liquefaction and postliquefaction resistance of soils are closely related to the variations in relative density. (C) 2013 American Society of Civil Engineers.

Elasticity of DNA and the effect of dendrimer binding

Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic properties of short double-stranded DNA (dsDNA) and the effect of dendrimer binding using fully atomistic molecular dynamics and numerical simulations. In equilibrium at room temperature, the contour length distribution P(L) and the end-to-end distance distribution P(R) are nearly Gaussian, the former gives an estimate of the stretch modulus gamma(1) of dsDNA in quantitative agreement with the literature value. The bend angle distribution P(.) of the dsDNA also has a Gaussian form and allows to extract a persistence length, L-p of 43 nm. When the dsDNA is compacted by positively charged dendrimer, the stretch modulus stays invariant but the effective bending rigidity estimated from the end-to-end distance distribution decreases dramatically due to backbone charge neutralization of dsDNA by dendrimer. We support our observations with numerical solutions of the worm-like-chain (WLC) model as well as using non-equilibrium dsDNA stretching simulations. These results are helpful in understanding the dsDNA elasticity at short length scales as well as how the elasticity is modulated when dsDNA binds to a charged object such as a dendrimer or protein.

Solution nuclear magnetic resonance structure of the GATase subunit and structural Basis of the interaction between GATase and ATPPase subunits in a two-subunit-type GMPS from methanocaldococcus jannaschii

The solution structure of the monomeric glutamine amidotransferase (GATase) subunit of the Methanocaldococcus janaschii (Mj) guanosine monophosphate synthetase (GMPS) has been determined using high-resolution nuclear magnetic resonance methods. Gel filtration chromatography and N-15 backbone relaxation studies have shown that the Mj GATase subunit is present in solution as a 21 kDa (188-residue) monomer. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35 +/- 0.06 angstrom for backbone atoms and 0.8 +/- 0.06 angstrom for all heavy atoms. Furthermore, 99.4% of the backbone dihedral angles are present in the allowed region of the Ramachandran map, indicating the stereochemical quality of the structure. The core of the tertiary structure of the GATase is composed of a seven-stranded mixed beta-sheet that is fenced by five alpha-helices. The Mj GATase is similar in structure to the Pyrococcus horikoshi (Ph) GATase subunit. Nuclear magnetic resonance (NMR) chemical shift perturbations and changes in line width were monitored to identify residues on GATase that were responsible for interaction with magnesium and the ATPPase subunit, respectively. These interaction studies showed that a common surface exists for the metal ion binding as well as for the protein-protein interaction. The dissociation constant for the GATase-Mg2+ interaction has been found to be similar to 1 mM, which implies that interaction is very weak and falls in the fast chemical exchange regime. The GATase-ATPPase interaction, on the other hand, falls in the intermediate chemical exchange regime on the NMR time scale. The implication of this interaction in terms of the regulation of the GATase activity of holo GMPS is discussed.

CXI-benzo-84 reversibly binds to tubulin at colchicine site and induces apoptosis in cancer cells

Here, we have discovered CXI-benzo-84 as a potential anticancer agent from a library of benzimidazole derivatives using cell based screening strategy. CXI-benzo-84 inhibited cell cycle progression in metaphase stage of mitosis and accumulated spindle assembly checkpoint proteins Mad2 and BubR1 on kinetochores, which subsequently activated apoptotic cell death in cancer cells. CXI-benzo-84 depolymerized both interphase and mitotic microtubules, perturbed EB1 binding to microtubules and inhibited the assembly and GTPase activity of tubulin in vitro. CXI-benzo-84 bound to tubulin at a single binding site with a dissociation constant of 1.2 +/- 0.2 mu M. Competition experiments and molecular docking suggested that CXI-benzo-84 binds to tubulin at the colchicine-site. Further, computational analysis provided a significant insight on the binding site of CXI-benzo-84 on tubulin. In addition to its potential use in cancer chemotherapy, CXI-benzo-84 may also be useful to screen colchicine-site agents and to understand the colchicine binding site on tubulin. (C) 2013 Elsevier Inc. All rights reserved.

Fast and accurate quantification using Genetic Algorithm optimized H-1-C-13 refocused constant-time INEPT

Using Genetic Algorithm, a global optimization method inspired by nature's evolutionary process, we have improved the quantitative refocused constant-time INEPT experiment (Q-INEPT-CT) of Makela et al. (JMR 204 (2010) 124-130) with various optimization constraints. The improved `average polarization transfer' and `min-max difference' of new delay sets effectively reduces the experimental time by a factor of two (compared with Q-INEPT-CT, Makela et al.) without compromising on accuracy. We also discuss a quantitative spectral editing technique based on average polarization transfer. (C) 2013 Elsevier Inc. All rights reserved.

Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pK(a) of ionizable residues in proteins

Residue depth accurately measures burial and parameterizes local protein environment. Depth is the distance of any atom/residue to the closest bulk water. We consider the non-bulk waters to occupy cavities, whose volumes are determined using a Voronoi procedure. Our estimation of cavity sizes is statistically superior to estimates made by CASTp and VOIDOO, and on par with McVol over a data set of 40 cavities. Our calculated cavity volumes correlated best with the experimentally determined destabilization of 34 mutants from five proteins. Some of the cavities identified are capable of binding small molecule ligands. In this study, we have enhanced our depth-based predictions of binding sites by including evolutionary information. We have demonstrated that on a database (LigASite) of similar to 200 proteins, we perform on par with ConCavity and better than MetaPocket 2.0. Our predictions, while less sensitive, are more specific and precise. Finally, we use depth (and other features) to predict pK(a)s of GLU, ASP, LYS and HIS residues. Our results produce an average error of just <1 pH unit over 60 predictions. Our simple empirical method is statistically on par with two and superior to three other methods while inferior to only one. The DEPTH server (http://mspc.bii.a-star.edu.sg/depth/) is an ideal tool for rapid yet accurate structural analyses of protein structures.