MLDB: macromolecule ligand database

MLDB (macromolecule ligand database) is a knowledge base containing ligands co-crystallized with the three-dimensional structures available in the Protein Data Bank. The proposed knowledge base serves as an open resource for the analysis and visualization of all ligands and their interactions with macromolecular structures. MLDB can be used to search ligands, and their interactions can be visualized both in text and graphical formats. MLDB will be updated at regular intervals (weekly) with automated Perl scripts. The knowledge base is intended to serve the scientific community working in the areas of molecular and structural biology. It is available free to users around the clock and can be accessed at http://dicsoft2.physics.iisc.ernet.in/mldb/.

Facile preparation and some applications of an affinity matrix with a cleavable connector arm containing a disulfide bond

A versatile affinity matrix in which the ligand of interest is linked to the matrix through a connector arm containing a disulfide bond is described. It can be synthesized from any amino-substituted matrix by successive reaction with 2-imino-thio-lane, 5, 5'-dithiobis(2-nitrobenzoic acid), and a thiol derivative of the ligand of choice. The repertoire of ligands can be significantly increased by the appropriate use of avidin-biotin bridges. After adsorption of the material to be fractionated, elution can be effected by reducing the disulfide bond in the connector arm with dithiothreitol. Examples of the preparation and use of various affinity matrices based on amino-substituted Sepharose 6MB are given. One involves the immobilization of the Fab' fragment of a monoclonal antibody against Aspergillus oryzae β-galactosidase and the specific binding of that enzyme to the resulting immunoaffinity matrix. Another involves the immobilization of N-biotinyl-2-thioethylamine followed by complex formation with avidin. The resulting avidin-substituted matrix was used for the selective adsorption and subsequent recovery of mouse hybridoma cells producing anti-avidin antibodies. By further complexing the avidin-substituted matrix with appropriate biotinylated antigens, it should be possible to fractionate cells producing antibodies against a variety of antigens.

The RecA intein of Mycobacterium tuberculosis promotes cleavage of ectopic DNA sites. Implications for the dispersal of inteins in natural populations

The RecA intein of Mycobacterium tuberculosis, a novel double-stranded DNA endonuclease, requires both Mn(2+) and ATP for efficient cleavage of the inteinless recA allele. In this study, we show that Mg(2+) alone was sufficient to stimulate PI-MtuI to cleave double-stranded DNA at ectopic sites. In the absence of Mg(2+), PI-MtuI formed complexes with topologically different forms of DNA containing ectopic recognition sequences with equal affinity but failed to cleave DNA. We observed that PI-MtuI was able to inflict double-strand breaks robustly within the ectopic recognition sequence to generate either a blunt end or 1-2-nucleotide 3'-hydroxyl overhangs. Mutational analyses of the presumptive metal ion-binding ligands (Asp(122), Asp(222), and Glu(220)) together with immunoprecipitation assays provided compelling evidence to link both the Mg(2+)- and Mn(2+) and ATP-dependent endonuclease activities to PI-MtuI. The kinetic mechanism of PI-MtuI promoted cleavage of ectopic DNA sites proceeded through a sequential mechanism with transient accumulation of nicked circular duplex DNA as an intermediate. Together, these data suggest that PI-MtuI, like group II introns, might mediate ectopic DNA transposition and hence its lateral transfer in natural populations.

Adducts of bis(acetylacetonato)zinc(II) with 1,10-phenanthroline and 2,2'-bipyridine

In each of the zinc(II) complexes bis(acetylacetonato-kappa(2)O,O')(1,10-phenanthroline-kappa(2)N,N')zinc(II), [Zn(C(5)H(7)O(2))(2)(C(12)H(8)N(2))], (I), and bis(acetylacetonato-kappa(2)O,O')(2,2'-bipyridine-kappa(2)N,N')zinc(II), [Zn(C(5)H(7)O(2))(2)(C(10)H(8)N(2))], (II), the metal center has a distorted octahedral coordination geometry. Compound (I) has crystallographically imposed twofold symmetry, with Z' = 0.5. The presence of a rigid phenanthroline group precludes intramolecular hydrogen bonding, whereas the rather flexible bipyridyl ligand is twisted to form an intramolecular C-H...O interaction [the chelated bipyridyl ligand is nonplanar, with the pyridyl rings inclined at an angle of 13.4 (1) degrees]. The two metal complexes are linked by dissimilar C-H...O interactions into one-dimensional chains. The present study demonstrates the distinct effects of two commonly used ligands, viz. 1,10-phenanthroline and 2,2'-bipyridine, on the structures of metal complexes and their assembly.

Design, Synthesis, and DNA Binding Properties of Photoisomerizable Azobenzene−Distamycin Conjugates: An Experimental and Computational Study

Here, we present the synthesis, photochemical, and DNA binding properties of three photoisomerizable azobenzene−distamycin conjugates in which two distamycin units were linked via electron-rich alkoxy or electron-withdrawing carboxamido moieties with the azobenzene core. Like parent distamycin A, these molecules also demonstrated AT-specific DNA binding. Duplex DNA binding abilities of these conjugates were found to depend upon the nature and length of the spacer, the location of protonatable residues, and the isomeric state of the conjugate. The changes in the duplex DNA binding efficiency of the individual conjugates in the dark and with their respective photoirradiated forms were examined by circular dichroism, thermal denaturation of DNA, and Hoechst displacement assay with poly[d(A-T).d(T-A)] DNA in 150 mM NaCl buffer. Computational structural analyses of the uncomplexed ligands using ab initio HF and MP2 theory and molecular docking studies involving the conjugates with duplex d[(GC(AT)10CG)]2 DNA were performed to rationalize the nature of binding of these conjugates.

Synthesis and structural characterization of a new ruthenium hydride ethylene complex

A ruthenium(II) ethylene complex, trans-[Ru(H)(C2H4)- (dppm)(2)][BF4], hearing two 1,1-bis(diphenylphosphino) methane (dppm) ligands has been synthesized and structurally characterized using X-ray crystallography. In the molecular structure, the Ru-II center shows a distorted octahedral coordination geometry formed by four P atoms of the two chelating dppm ligands, a hydride, and an ethylene ligands. The four dppm P atoms are almost co-planar with the hydride and the ethylene ligands perpendicular to this plane. The C-C bond distance of the bound ethylene is 1.375(6) angstrom, which is elongated by 0.042 angstrom as compared to free ethylene (1.333(2) angstrom). The packing diagram of the complex shows two voids or channels, which are occupied by BF4- counterion and water molecules.

Functional interaction of diphenols with polyphenol oxidase - Molecular determinants of substrate/inhibitor specificity SO FEBS JOURNAL

Polyphenol oxidase (PPO) catalyzes the oxidation of o-diphenols to their respective quinones. The quinones autopolymerize to form dark pigments, an undesired effect. PPO is therefore the target for the development of antibrowning and antimelanization agents. A series of phenolic compounds experimentally evaluated for their binding affinity and inhibition constants were computationally docked to the active site of catechol oxidase. Docking studies suggested two distinct modes of binding, dividing the docked ligands into two groups. Remarkably, the first group corresponds to ligands determined to be substrates and the second group corresponds to reversible inhibitors. Analyses of the complexes provide structural explanations for correlating subtle changes in the position and nature of the substitutions on o-diphenols to their functional properties as substrates and inhibitors. Higher reaction rates and binding are reckoned by additional interactions of the substrates with key residues that line the hydrophobic cavity. The docking results suggest that inhibition of oxidation stems from an interaction between the aromatic carboxylic acid group and the apical His 109 of the four coordinates of the trigonal pyramidal coordination polyhedron of CuA. The spatial orientation of the hydroxyl in relation to the carboxylic group either allows a perfect fit in the substrate cavity, leading to inhibition, or because of a steric clash flips the molecule vertically, facilitating oxidation. This is the first study to explain, at the molecular level, the determinants Of substrate and inhibitor specificity of a catechol oxidase, thereby providing a platform for the design of selective inhibitors useful to both the food and pharmaceutical industries.

N,N′-Bis(aryl)pyridine-2,6-dicarboxamide complexes of ruthenium: Synthesis, structure and redox properties

Reaction of five N,N′-bis(aryl)pyridine-2,6-dicarboxamides (H2L-R, where H2 denotes the two acidic protons and R (R = OCH3, CH3, H, Cl and NO2) the para substituent in the aryl fragment) with [Ru(trpy)Cl3](trpy = 2,2′,2″-terpyridine) in refluxing ethanol in the presence of a base (NEt3) affords a group of complexes of the type [RuII(trpy)(L-R)], each of which contains an amide ligand coordinated to the metal center as a dianionic tridentate N,N,N-donor along with a terpyridine ligand. Structure of the [RuII(trpy)(L-Cl)] complex has been determined by X-ray crystallography. All the Ru(II) complexes are diamagnetic, and show characteristic 1H NMR signals and intense MLCT transitions in the visible region. Cyclic voltammetry on the [RuII(trpy)(L-R)] complexes shows a Ru(II)–Ru(III) oxidation within 0.16–0.33 V versus SCE. An oxidation of the coordinated amide ligand is also observed within 0.94–1.33 V versus SCE and a reduction of coordinated terpyridine ligand within −1.10 to −1.15 V versus SCE. Constant potential coulometric oxidation of the [RuII(trpy)(L-R)] complexes produces the corresponding [RuIII(trpy)(L-R)]+ complexes, which have been isolated as the perchlorate salts. Structure of the [RuIII(trpy)(L-CH3)]ClO4 complex has been determined by X-ray crystallography. All the Ru(III) complexes are one-electron paramagnetic, and show anisotropic ESR spectra at 77 K and intense LMCT transitions in the visible region. A weak ligand-field band has also been shown by all the [RuIII(trpy)(L-R)]ClO4 complexes near 1600 nm.

Supramolecular Organization in Tetra Aqua (mu-8-Hydroxyquinoline-5-sulfonate) Barium (II) and Ag center dot center dot center dot I Interactions in a Pseudopolymorphic Form of (7-Iodo-8-hydroxyquinoline-5-sulfonate) Silver (I) Monohydrate

The complexes, Ba (HQS) (H2O)(4) (HQS = 8-hydroxyquinoline-5-sulfonic acid) (1) and Ag (HIQS) (H2O) (Ferron = 7-iodo-8-hydroxyquinoline-5-sulfonic acid) (2) have been synthesized and characterized by X-ray diffraction analysis and spectroscopic studies. In compound 1, Ba2+ ion has a nine-coordinate monocapped antiprismatic geometry. In compound 2, Ag+ has distorted tetrahedral coordination and Ag center dot center dot center dot I interactions generate the supramolecular architectures. The complexes have been characterized by FT-IR and UV-Visible measurements. In both the structures, the inversion-related organic ligands are stacked over one another leading to three-dimensional networks.

Parallel implementation of AutoDock

Computational docking of ligands to protein structures is a key step in structure-based drug design. Currently, the time required for each docking run is high and thus limits the use of docking in a high-throughput manner, warranting parallelization of docking algorithms. AutoDock, a widely used tool, has been chosen for parallelization. Near-linear increases in speed were observed with 96 processors, reducing the time required for docking ligands to HIV-protease from 81 min, as an example, on a single IBM Power-5 processor ( 1.65 GHz), to about 1 min on an IBM cluster, with 96 such processors. This implementation would make it feasible to perform virtual ligand screening using AutoDock.

Rationalizing the effects of amino acid side chain, pyridine, and imidazole on the assembly and reversible disassembly of a octanuclear Cu(III) complex

This paper reports the observation of a reversible disassembly process for a previously reported octanuclear Cu(II) complex with imidazole. To identify the factors responsible for the process, five Cu(II) complexes of different nuclearity with different amino acid-derived tetradentate ligands were structurally characterized. The results show that the coordination geometry preference of Cu(II), the tendency of imidazole to act as in-plane ligand, and H-bonding played important role in the formation and disassembly of the octanuclear complex. A general scheme describing the effect of different amino acid side arms, solvents, and exogenous ligands on the nuclearity of the Cu(II) complexes has been presented. The crystals of the complexes also showed formation of multifaceted networks in the resulting complexes.

Preparation and Characterization of Glycolipid-Bearing Multilamellar and Unilamellar Liposomes

The carbohydrate residues of glycosphingolipids were implicated in many biologic processes such as cell-to-cell interactions; and as receptors for some viruses, bacterial and plant toxins, hormones, and so forth, and invariably for all the lectins (1). However, their receptor functions remained poorly defined for a long time as they form micelles even at very low concentrations in aqueous medium. In micelles, the oligosaccharide chains are not expected to have a well defined orientation suitable for recognition by macromolecular ligands. This problem was overcome by incorporating them in model membranes, namely, the liposomes. The demonstration of lectin-glycolipid interaction using liposomal model membranes was a crucial development that established glycolipids as biological receptors. Moreover, glycolipid-bearing liposomes provide a convenient system for investigating the role of glycolipid density, orientation, and exposure of their oligosaccharide chains at the membrane interface relevant to their receptor function (2–4).

Molten globule-like state of peanut lectin monomer retains its carbohydrate specificity - Implications in protein folding and legume lectin oligomerization

A central question in biological chemistry is the minimal structural requirement of a protein that would determine its specificity and activity, the underlying basis being the importance of the entire structural element of a protein with regards to its activity vis a vis the overall integrity and stability of the protein. Although there are many reports on the characterization of protein folding/ unfolding intermediates, with considerable secondary structural elements but substantial loss of tertiary structure, none of them have been reported to show any activity toward their respective ligands. This may be a result of the conditions under which such intermediates have been isolated or due to the importance of specific structural elements for the activity. In this paper we report such an intermediate in the unfolding of peanut agglutinin that seems to retain, to a considerable degree, its carbohydrate binding specificity and activity. This result has significant implications on the molten globule state during the folding pathway(s) of proteins in general and the quaternary association in legume lectins in particular, where precise subunit topology is required for their biologic activities.

Amino acid sequence of the winged bean (Psophocarpus tetragonolobus) basic lectin. Adenine binding and identification of the active-site tryptophan residue

The complete amino acid sequence of winged bean basic agglutinin (WBA I) was obtained by a combination of manual and gas-phase sequencing methods. Peptide fragments for sequence analyses were obtained by enzymatic cleavages using trypsin and Staphylococcus aureus V8 endoproteinase and by chemical cleavages using iodosobenzoic acid, hydroxylamine, and formic acid. COOH-terminal sequence analysis of WBA I and other peptides was performed using carboxypeptidase Y. The primary structure of WBA I was homologous to those of other legume lectins and more so to Erythrina corallodendron. Interestingly, the sequence shows remarkable identities in the regions involved in the association of the two monomers of E. corallodendron lectin. Other conserved regions are the double metal-binding site and residues contributing to the formation of the hydrophobic cavity and the carbohydrate-binding site. Chemical modification studies both in the presence and absence of N-acetylgalactosamine together with sequence analyses of tryptophan-containing tryptic peptides demonstrate that tryptophan 133 is involved in the binding of carbohydrate ligands by the lectin. The location of tryptophan 133 at the active center of WBA I for the first time subserves to explain a role for one of the most conserved residues in legume lectins.

Carbohydrate binding specificity of the B-cell maturation mitogen from Artocarpus integrifolia seeds

Artocarpin, a mannose-specific lectin, is a homotetrameric protein (M(r) 65,000) devoid of covalently attached carbohydrates and consists of four isolectins with pI in the range 5-6.5. Investigations of its carbohydrate binding specificity reveal that among monosaccharides, mannose is preferred over glucose. Among mannooligosaccharides, mannotriose (Man alpha 1-3[Man alpha 1-6]Man) and mannopentaose are the strongest ligands followed by Man alpha 1-3Man. Extension of these ligands by GlcNAc at the reducing ends of mannooligosaccharides tested remarkably improves their inhibitory potencies, while substitution of both the alpha 1-3 and alpha 1-6 mannosyl residues of mannotriose and the core pentasaccharide of N-linked glycans (Man alpha 1-3[Man alpha 1-6]Man beta 1-4GlcNAc beta 1-4GlcNAc) by GlcNAc or N-acetyllactosamine in beta 1-2 linkage diminishes their inhibitory potencies. Sialylated oligosaccharides are non-inhibitory. Moreover, the substitution of either alpha 1-3 or alpha 1-6 linked mannosyl residues of M5Gn or both by mannose in alpha 1-2 linkage leads to a considerable reduction of their inhibitory power. Addition of a xylose residue in beta 1-2 linkage to the core pentasaccharide improves the inhibitory activity. Considering the fact that artocarpin has the strongest affinity for the xylose containing hepasaccharide from horseradish peroxidase, which differs significantly from all the mannose/glucose-specific lectins, it should prove a useful tool for the isolation and characterization of glycoproteins displaying such structure.