Effect of spatial dispersion of the dielectric on the binding energy of D- ion in Si and Ge

Using a multivalley effective mass theory, we obtain the binding energy of a D- ion in Si and Ge taking into account the spatial variation of the host dielectric function. We find that on comparison with experimental results the effect of spatial dispersion is important in the estimation of binding energy for the D- formed by As in Si and Ge. The effect is less significant for the case of D- formed by P and Sb donors.

Identification of amino groups in the carbohydrate binding activity of winged bean acidic agglutinin

Chemical modification studies reveal that the modification of amino groups in WBA II leads to a complete loss in the hemagglutinating and saccharide binding activities. Since WBA II is a dimeric molecule and contains two binding sites, one amino group in each of the binding sites is inferred to be essential for its activity. The presence of amino group which has a potential to form hydrogen bonded interactions with the ligand, substantiates our observation regarding the forces involved in WBA II-receptor and WBA II-simple sugar interactions.

Immunochemical approach to the mapping of an assembled epitope of human chorionic gonadotropin: Proximity of CTP-alpha to the receptor binding region of the beta-subunit

A single-step solid-phase RIA (SS-SPRIA) developed in our laboratory using hybridoma culture supernatants has been utilised for the quantitation of epitope-paratope interactions. Using SS-SPRIA as a quantitative tool for the assessment of epitope stability, it was found that several assembled epitopes of human chorionic gonadotropin (hCG) are differentially stable to proteolysis and chemical modification. Based on these observations an approach has been developed for identifying the amino acid residues constituting an epitopic region. This approach has now been used to map an assembled epitope at/near the receptor binding region of the hormone. The mapped site forms a part of the seat belt region and the cystine knot region (C34-C38-C88-C90-H106). The carboxy terminal region of the alpha-subunit forms a part of the epitope indicating its proximity to the receptor binding region. These results are in agreement with the reported receptor binding region identified through other approaches and the X-ray crystal structure of hCG.

Synthesis, crystal structures, DNA binding and cleavage activity of L-glutamine copper(II) complexes of heterocyclic bases

Ternary L-glutamine (L-gln) copper(II) complexes [Cu(L-gln)(B)(H2O)](X) (B = 2,2'-bipyridine (bpy), X = 0.5SO(4)(2-), 1; B = 1,10-phenanthroline (phen), X = ClO4-, 2) and [Cu(L-gln)(dpq)(ClO4)] (3) (dpq, dipyridoquinoxaline) are prepared and characterized by physicochemical methods. The DNA binding and cleavage activity of the complexes have been studied. Complexes 1-3 are structurally characterized by X-ray crystallography. The complexes show distorted square pyramidal (4+1) CuN3O2 coordination geometry in which the N,O-donor amino acid and the N, N-donor heterocyclic base bind at the basal plane with a H2O or perchlorate as the axial ligand. The crystal structures of the complexes exhibit chemically significant hydrogen bonding interactions besides showing coordination polymer formation. The complexes display a d-d electronic band in the range of 610-630 nm in aqueous-dimethylformamide (DMF) solution (9:1 v/v). The quasireversible cyclic voltammetric response observed near -0.1 V versus SCE in DMF-TBAP is assignable to the Cu(II)/Cu(I) couple. The binding affinity of the complexes to calf thymus (CT) DNA follows the order: 3 (dpq) > 2 (phen) >> 1 (bpy). Complexes 2 and 3 show DNA cleavage activity in dark in the presence of 3-mercaptopropionic acid (MPA) as a reducing agent via a mechanistic pathway forming hydroxyl radical as the reactive species. The dpq complex 3 shows efficient photoinduced DNA cleavage activity on irradiation with a monochromatic UV light of 365 nm in absence of any external reagent. The cleavage efficiency of the DNA minor groove binding complexes follows the order:3 > 2 >> 1. The dpq complex exhibits photocleavage of DNA on irradiation with visible light of 647.1 nm. Mechanistic data on the photo-induced DNA cleavage reactions reveal the involvement of singlet oxygen (O-1(2)) as the reactive species in a type-II pathway. (C) 2008 Elsevier B.V. All rights reserved.

Axial binding of 2-methylimidazole to the tetraarylcarboxylatodiruthenium (II, III) core: X-ray crystal structure of [Ru-2(O2CC6H4-p-OMe)(4)(2-mimH)(2)](ClO4). 1.75CH(2)Cl(2).H2O

Diruthenium (II. III) complexes of the type [Ru-2(O2CAr)(4) (2-mimH)(2)](ClO4) (Ar = C6H4-p-X : X=OMe,1, X=Me, 2, 2-mimH=2-methylimidazole) have been isolated from the reaction of Ru2Cl(O2CAr)(4) with 2-mimH in CH2Cl2 followed by the addition of NaClO4. The crystal structure of 1.1.75CH(2)Cl(2).H2O has been determined. The crystal belongs to the monoclinic space group p2(1)/c with the following unit cell dimensions for the C40H40N4O16ClRu2.1.75CH(2)Cl(2).H2O (M = 1237.0) : a = 12.347(3)Angstrom, b = 17.615(5)Angstrom, c = 26.148(2)Angstrom,beta = 92.88(1)degrees. v = 5679(2)Angstrom(3). Z=4, D-c = 1.45 g cm(-3). lambda(Mo-K-alpha) = 0.7107 Angstrom, mu(Mo-K-alpha) = 8.1 cm(-1), T = 293 K, R = 0.0815 (wR(2) = 0.2118) for 5834 reflections with 1 > 2 sigma(I). The complex has a tetracarboxylatodiruthenium (II, III) core and two axially bound 2-methylimidazole ligands. The Ru-Ru bond length is 2.290(1)Angstrom. The Ru-Ru bond order is 2.5 and the complex is three-electron paramagnetic. The complex shows an irreversible Ru-2(II,III)-->Ru-2(Il,II) reduction near -0.2 V vs SCE in CH2Cl2-0. 1 MTBAP. The complexes exemplify the first adduct of the tetracarboxylatodiruthenium (II,III) core having N-donor ligands

PocketMatch: A new algorithm to compare binding sites in protein structures

Recognizing similarities and deriving relationships among protein molecules is a fundamental requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison. Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. A comparison with other site matching algorithms is also presented. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless combined with chemical nature of amino acids. Conclusion: A new algorithm has been developed to compare binding sites in accurate, efficient and high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250(th) second for one comparison on a single processor. A parallel version on BlueGene has also been implemented.

High Oxygen Storage Capacity and High Rates of CO Oxidation and NO Reduction Catalytic Properties of Ce1-xSnxO2 and Ce0.78Sn0.2Pd0.02O2-delta

Ce1-xSnxO2 (x = 0.1-0.5) solid solution and its Pd substituted analogue have been prepared by a single step solution combustion method using tin oxalate precursor. The compounds were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), and H-2/temperature programmed redution (TPR) studies. The cubic fluorite structure remained intact up to 50% of Sri substitution in CeO2, and the compounds were stable up to 700 C. Oxygen storage capacity of Ce1-xSnxO2 was found to be much higher than that of Ce1-xZrxO2 due to accessible Ce4+/Ce3+ and Sn4+/Sn2+ redox couples at temperatures between 200 and 400 C. Pd 21 ions in Ce0.78Sn0.2Pd0.02O2-delta are highly ionic, and the lattice oxygen of this catalyst is highly labile, leading to low temperature CO to CO2 conversion. The rate of CO oxidation was 2 mu mol g(-1) s(-1) at 50 degrees C. NO reduction by CO with 70% N-2 selectivity was observed at similar to 200 degrees C and 100% N-2 selectivity below 260 degrees C with 1000-5000 ppm NO. Thus, Pd2+ ion substituted Ce1-xSnxO2 is a superior catalyst compared to Pd2+ ions in CeO2, Ce1-xZrxO2, and Ce1-xTixO2 for low temperature exhaust applications due to the involvement of the Sn2+/Sn4+ redox couple along with Pd2+/Pd-0 and Ce4+/Ce3+ couples.

Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: the role of Asn(341), Tyr(60) and Phe(351) in tetrahydrofolate binding

SHMT (serine hydoxymethyltransferase), a type I pyridoxal 5'-phosphate-dependent enzyme, catalyses the conversion of L-serine and THF (tetrahydrofolate) into glycine and 5,10-methylene THE SHMT also catalyses several THF-independent side reactions such as cleavage of P-hydroxy amino acids, trans-amination, racemization and decarboxylation. In the present study, the residues Asn(341), Tyr(60) and Phe(351), which are likely to influence THF binding, were mutated to alanine, alanine and glycine respectively, to elucidate the role of these residues in THF-dependent and -independent reactions catalysed by SHMT. The N341A and Y60A bsSHMT (Bacillus stearothermophilus SHMT) mutants were inactive for the THF-dependent activity, while the mutations had no effect on THF-independent activity. However, mutation of Phe(351) to glycine did not have any effect oil either of the activities. The crystal structures of the glycine binary complexes of the mutants showed that N341A bsSHMT forms an external aldimine as in bsSHMT, whereas Y60A and F351G bsSHMTs exist as a Mixture of internal/external aldimine and gem-diamine forms. Crystal structures of all of the three Mutants obtained in the presence of L-allo-threonine were similar to the respective glycine binary complexes. The structure of the ternary complex of F351G bsSHMT with glycine and FTHF (5-formyl THF) showed that the monoglutamate side chain of FTHF is ordered in both the subunits of the asymmetric unit, unlike in the wild-type bsSHMT. The present studies demonstrate that the residues Asn(341) and Tyr(60) are pivotal for the binding of THF/FTHF, whereas Phe(351) is responsible for the asymmetric binding of FTHF in the two subunits of the dimer.

Orchestration of Haemophilus influenzae RecJ Exonuclease by Interaction with Single-Stranded DNA-Binding Protein

RecJ exonuclease plays crucial roles in several DNA repair and recombination pathways, and its ubiquity in bacterial species points to its ancient origin and vital cellular function. RecJ exonuclease from Haemophilus influenzae is a 575-amino-acid protein that harbors the characteristic motifs conserved among RecJ homologs. The purified protein exhibits a process 5'-3' single-stranded-DNA-specific exonuclease activity. The exonuclease activity of H. influenzae RecJ (HiRecJ) was supported by Mg2+ or Mn2+ and inhibited by Cd2+ suggesting a different mode of metal binding in HiRecJ as compared to Escherichia coli RecJ (EcoRecJ). Site-directed mutagenesis of highly conserved residues in HiRecJ abolished enzymatic activity. Interestingly, substitution of alanine for aspartate 77 resulted in a catalytically inactive enzyme that bound to DNA with a significantly higher affinity as compared to the wild-type enzyme. Noticeably, steady-state kinetic studies showed that H. influenzae single-stranded DNA-binding protein (HiSSB) increased the affinity of HiRecJ for single-stranded DNA and stimulated its exonuclease activity. HiSSB, whose C-terminal tail had been deleted, failed to enhance RecJ exonuclease activity. More importantly, HiRecJ was found to directly associate with its cognate single-stranded DNA-binding protein (SSB), as demonstrated by various in vitro assays, Interaction studies carried out with the truncated variants of HiRecJ and HiSSB revealed that the two proteins interact via the C-terminus of SSB protein and the core-catalytic domain of RecJ. Taken together, these results emphasize direct interactio between RecJ and SSB, which confers functional cooperativity to these two proteins. In addition, these results implicate SSB as being involved in the recruitment of RecJ to DNA and provide insights into the interplay between these proteins in repair and recombination pathways.

Bearing capacity of circular footing on geocell-sand mattress overlying clay bed with void

The potential benefits of providing geocell reinforced sand mattress over clay subgrade with void have been investigated through a series of laboratory scale model tests. The parameters varied in the test programme include, thickness of unreinforced sand layer above clay bed, width and height of geocell mattress, relative density of the sand fill in the geocells, and influence of an additional layer of planar geogrid placed at the base of the geocell mattress. The test results indicate that substantial improvement in performance can be obtained with the provision of geocell mattress, of adequate size, over the clay subgrade with void. In order to have beneficial effect, the geocell mattress must spread beyond the void at least a distance equal to the diameter of the void. The influence of the void over the performance of the footing reduces for height of geocell mattress greater than 1.8 times the diameter of the footing. Better improvement in performance is obtained for geocells filled with dense soil. (C) 2008 Elsevier Ltd. All rights reserved.

Remarkable Capacity Retention of Nanostructured Manganese Oxide upon Cycling as an Electrode Material for Supercapacitor

Electrochemical capacity retention of nearly X-ray amorphous nanostructured manganese oxide (nanoMnO2) synthesized by mixing directly KMnO4 with ethylene glycol under ambient conditions for supercapacitor studies is enhanced significantly. Although X-ray diffraction (XRD) pattern of nanoMnO2 shows poor crystallinity, it is found that by Mn K-edge X-ray absorption near edge structure (XANES) measurement that the nanoMnO2 obtained is locally arranged in a δ-MnO2-type layered structure composed of edge-shared network of MnO6 octahedra. Field emission scanning electron microscopy and XANES measurements show that nanoMnO2 contains nearly spherical shaped morphology with δ-MnO2 structure, and 1D nanorods of α-MnO2 type structure (powder XRD) in the annealed (600 °C) sample. Volumetric nitrogen adsorption−desorption isotherms, inductively coupled plasma analysis, and thermal analysis are carried out to obtain physicochemical properties such as surface area (230 m2 g−1), porosity of nanoMnO2 (secondary mesopores of diameter 14.5 nm), water content, composition, etc., which lead to the promising electrochemical properties as an electrode for supercapacitor. The nanoMnO2 shows a very high stability even after 1200 cycles with capacity retention of about 250 F g−1.

Prediction of Ultimate Capacity of Laterally Loaded Piles in Clay: A Relevance Vector Machine Approach

This study investigates the potential of Relevance Vector Machine (RVM)-based approach to predict the ultimate capacity of laterally loaded pile in clay. RVM is a sparse approximate Bayesian kernel method. It can be seen as a probabilistic version of support vector machine. It provides much sparser regressors without compromising performance, and kernel bases give a small but worthwhile improvement in performance. RVM model outperforms the two other models based on root-mean-square-error (RMSE) and mean-absolute-error (MAE) performance criteria. It also stimates the prediction variance. The results presented in this paper clearly highlight that the RVM is a robust tool for prediction Of ultimate capacity of laterally loaded piles in clay.

Theoretical-Studies on the Modes of Binding of Some of the Beta-Glycosidically Linked Glucobioses to Concanavalin-A

The probable modes of binding for methyl-α-d-sophoroside, methyl-β-d-sophoroside, laminariboise and cellobiose to concanavalin A have been determined using theoretical methods. Methyl-d-sophorosides can bind to concanavalin A in two modes, i.e. by placing their reducing as well as non-reducing sugar units in the carbohydrate specific binding site, whereas laminaribiose and cellobiose can reach the binding site only with their non-reducing glucose units. However, the probability for methyl-α-d-sophoroside to bind to concanavalin A with its reducing sugar residue as the occupant of the binding site is much higher than it is with its non-reducing sugar residue as the occupant of the sugar binding site. A few of the probable conformers of methyl-β-d-sophoroside can bind to concanavalin A with either the reducing or non-reducing glucose unit. Higher energy conformers of cellobiose or laminaribiose can reach the binding site with their non-reducing residues alone. The relative differences in the binding affinities of these disaccharides are mainly due to the differences in the availability of proper conformers which can reach the binding site and to non-covalent interactions between the sugar and the protein. This study also suggests that though the sugar binding site of concanavalin A accommodates a single sugar residue, the residue outwards from the binding site also interacts with concanavalin A, indicating the existence of extended concanavalin A carbohydrate interactions.

Cholinergic Muscarinic Receptors in Human Fetal Brain: Ontogeny of [3H]Quinuclidinyl Benzilate Binding Sites in Corpus Striatum, Brainstem, and Cerebellum

The ontogeny of muscarinic receptors was studied in human fetal striatum, brainstem, and cerebellum to investigate general principles of synaptogenesis as well as the physiological balance between various chemical synapses during development in a given region of the brain. [3H]Quinuclidinyl benzilate ([-'H]QNB) binding was assayed in total particulate fraction (TPF) from various parts of brain. In the corpus striatum, QNB binding sites are present at 16 weeks of gestation (average concentration 180 fmol/mg protein of TPF), slowly increase up to 24 weeks (average concentration 217 fmol/mg protein), and rapidly increase during the third trimester to 480 fmol/mg protein of TPF. In contrast, dopaminergic receptors exist as two subpopulations. one with low affinity and the other with high affinity up to the 24th week of gestation; all of them acquire the highaffinity characteristic during the third trimester. In brainstem, the muscarinic receptors show maximum concentration by 16 weeks of age (360 fmolimg protein of TPF). Subsequently the muscarinic receptor concentration shows a gradual decline in the brainstem. In cerebellum, except for a slight increase at 24 weeks (average concentration 90 fmol/mg protein of TPF), the receptor concentration remained nearly constant at about 60-70 fmolimg protein of TPF throughout fetal life. This study demonstrates that the ontogeny of muscarinic receptors varies among the different regions, and the patterns observed suggest that receptor formation occurs principally in the third trimester. Also noteworthy is the finding that the QNB binding sites decreased in all regions of the human brain during adult life. Key Words: Cholinergic muscarinic receptors-Quinuclidinyl benzilate-Corpus striaturn-Brainstem-Cerebellum. Ravikumar B. V. and Sastry P. S. Cholinergic muscarinic receptors in human fetal brain: Ontogeny of [3H]quinuclidinyl benzilate binding sites in corpus striatum, brainstem, and cerebellum. J. Neurochem. 45, 1948- 1950 (1985).