Iron(III) Schiff base complexes of arginine and lysine as netropsin mimics showing AT-selective DNA binding and photonuclease activity

Iron(III) complexes [Fe(L)(2)]Cl (1-3), where L is monoanionic N-salicylidene-arginine (sal-argH for 1), hydroxynaphthylidene-arginine (nap-argH for 2) and N-salicylidene-lysine (sal-lysH for 3), were prepared and their DNA binding and photo-induced DNA cleavage activity studied. Complex 3 as its hexafluorophosphate salt [Fe(sal-lysH)(2)](PF6)center dot 6H(2)O (3a) was structurally characterized by single crystal Xray crystallography. The crystals belonged to the triclinic space group P-1. The complex has two tridentate ligands in FeN2O4 coordination geometry with two pendant cationic amine moieties. Complexes 1 and 2 with two pendant cationic guanidinium moieties are the structural models for the antitumor antibiotics netropsin. The complexes are stable and soluble in water. They showed quasi-reversible Fe(III)/Fe(II) redox couple near 0.6 V in H2O-0.1 M KCl. The high-spin 3d(5)-iron(III) complexes with mu(eff) value of similar to 5.9 mu(B) displayed ligand-to-metal charge transfer electronic band near 500 mm in Tris-HCl buffer. The complexes show binding to Calf Thymus (CT) DNA. Complex 2 showed better binding propensity to the synthetic oligomer poly(dA)center dot poly(dT) than to CT-DNA or poly(dG)center dot poly(dC). All the complexes displayed chemical nuclease activity in the presence of 3-mercaptopropionic acid as a reducing agent and cleaved supercoiled pUC19 DNA to its nicked circular form. They exhibited photo-induced DNA cleavage activity in UV-A light and visible light via a mechanistic pathway that involves the formation of reactive hydroxyl radical species. (C) 2010 Elsevier Inc. All rights reserved.

An ab-initio study of the proton affinity of conjugated schiff-base and related nitrogen compounds: an analysis of the triggering site of bacteriorhodopsin

The chemical groups which take part in the proton transfer reaction in bacteriorhodopsin have been studied by ab initio quantum chemical methods. The various factors such as conjugation with a linear system, electron delocalization of the guanidine type, cis-trans isomerism, geometry distortion and hydrogen bonding with charged groups can influence the properties of a given chemical group. Several systems are studied at 4-31G and STO-3G levels. Some of the Schiff-base analogues and guanidine type molecules are characterized by their molecular orbital diagrams, energy levels and the nature of charge distribution. Also, the effects of the above-mentioned factors on proton affinity are studied. It is hoped that the values thus obtained can be helpful in evaluating various structural models for proton transfer.

ESR and optical studies of Mo5+ and W5+ ions in phosphomolybdate and phosphotungstate glasses

ESR and optical studies of phosphomolybdate and phosphotungstate glasses are discussed. Both the ESR and optical results indicate that molybdenum or tungsten ions are present in distorted octahedral environments in these glasses. In addition, ESR spectra of Mo5+ and W5+ ions show that the d electrons are localized on molybdenum and tungsten sites respectively. The variation of gperpendicular and gshort parallel values has been examined using appropriate structural models of these glasses.

Transport properties of phosphomolybdate and phosphotungstate glasses

The d.c. conductivity of phosphomolybdate and phosphotungstate glasses is discussed. The conductivity of these glasses is due to the hopping of electrons between two valence states (Mo5+ to Mo6+ or W5+ W6+). In some of the glasses, the activation energy itself is found to be a function of temperature. This appears to be due to thermally activated and variable-range hopping mechanisms operating in different temperature regimes. The relation between conductivity and the [M5+]/[Mtotal](M ≡ Mo, W) ratio does not show any systematic variation. This anomaly can be understood using the structural models of these glasses. In contrast, Mott's theory and the Triberis and Friedman model have been used to obtain conductivity parameters such as the percolation distance Rij and 2agrRij (agr is the tunnelling probability). The conductivity parameter 2agrRij is quite useful to resolve the controversy regarding the tunnelling term exp(2agrRij) existing in the literature. For low values of 2agrRij, it is shown that the exp (2agrRij) term is very significant.

Modulation of Catalytic Activity in Multi-Domain Protein Tyrosine Phosphatases

Signaling mechanisms involving protein tyrosine phosphatases govern several cellular and developmental processes. These enzymes are regulated by several mechanisms which include variation in the catalytic turnover rate based on redox stimuli, subcellular localization or protein-protein interactions. In the case of Receptor Protein Tyrosine Phosphatases (RPTPs) containing two PTP domains, phosphatase activity is localized in their membrane-proximal (D1) domains, while the membrane-distal (D2) domain is believed to play a modulatory role. Here we report our analysis of the influence of the D2 domain on the catalytic activity and substrate specificity of the D1 domain using two Drosophila melanogaster RPTPs as a model system. Biochemical studies reveal contrasting roles for the D2 domain of Drosophila Leukocyte antigen Related (DLAR) and Protein Tyrosine Phosphatase on Drosophila chromosome band 99A (PTP99A). While D2 lowers the catalytic activity of the D1 domain in DLAR, the D2 domain of PTP99A leads to an increase in the catalytic activity of its D1 domain. Substrate specificity, on the other hand, is cumulative, whereby the individual specificities of the D1 and D2 domains contribute to the substrate specificity of these two-domain enzymes. Molecular dynamics simulations on structural models of DLAR and PTP99A reveal a conformational rationale for the experimental observations. These studies reveal that concerted structural changes mediate inter-domain communication resulting in either inhibitory or activating effects of the membrane distal PTP domain on the catalytic activity of the membrane proximal PTP domain.

Rationalization and prediction of drug resistant mutations in targets for clinical anti-tubercular drugs

Resistance to therapy limits the effectiveness of drug treatment in many diseases. Drug resistance can be considered as a successful outcome of the bacterial struggle to survive in the hostile environment of a drug-exposed cell. An important mechanism by which bacteria acquire drug resistance is through mutations in the drug target. Drug resistant strains (multi-drug resistant and extensively drug resistant) of Mycobacterium tuberculosis are being identified at alarming rates, increasing the global burden of tuberculosis. An understanding of the nature of mutations in different drug targets and how they achieve resistance is therefore important. An objective of this study is to first decipher sequence as well as structural bases for the observed resistance in known drug resistant mutants and then to predict positions in each target that are more prone to acquiring drug resistant mutations. A curated database containing hundreds of mutations in the 38 drug targets of nine major clinical drugs, associated with resistance is studied here. Mutations have been classified into those that occur in the binding site itself, those that occur in residues interacting with the binding site and those that occur in outer zones. Structural models of the wild type and mutant forms of the target proteins have been analysed to seek explanations for reduction in drug binding. Stability analysis of an entire array of 19 mutations at each of the residues for each target has been computed using structural models. Conservation indices of individual residues, binding sites and whole proteins are computed based on sequence conservation analysis of the target proteins. The analyses lead to insights about which positions in the polypeptide chain have a higher propensity to acquire drug resistant mutations. Thus critical insights can be obtained about the effect of mutations on drug binding, in terms of which amino acid positions and therefore which interactions should not be heavily relied upon, which in turn can be translated into guidelines for modifying the existing drugs as well as for designing new drugs. The methodology can serve as a general framework to study drug resistant mutants in other micro-organisms as well.

Experimental Studies on the Mechanics of Cohesive Frictional Granular Media

The mechanical behaviour of cohesive-frictional granular materials is a combination of the strength pervading as intergranular friction (represented as an angle of internal friction - Phi), and the cohesion (C) between these particles. Most behavioral or constitutive models of this class of granular materials comprise of a cohesion and frictional component with no regard to the length scale i.e. from the micro structural models through the continuum models. An experimental study has been made on a model granular material, viz. angular sand with different weights of binding agents (varying degrees of cohesion) at multiple length scales to physically map this phenomenon. Cylindrical specimen of various diameters - 10, 20, 38, 100, 150 mm (and with an aspect ratio of 2) are reconstituted with 2, 4 and 8% by weight of a binding agent. The magnitude of this cohesion is analyzed using uniaxial compression tests and it is assumed to correspond to the peak in the normalized stress-strain plot. Increase in the cohesive strength of the material is seen with increasing size of the specimen. A possibility of ``entanglement'' occurring in larger specimens is proposed as a possible reason for deviation from a continuum framework.

First-principles study of the influence of different interfaces and core types on the properties of CdSe/CdS core-shell nanocrystals

With the expanding field of nanoengineering and the production of nanocrystals (NCs) with higher quality and tunable size, having reliable theoretical calculations to complement the experimental results is very important. Here we present such a study of CdSe/CdS core-shell NCs using density functional theory, where we focus on dependence of the properties of these NCs on core types and interfaces between the core and the shell, as well as on the core/shell ratio. We show that the density of states and the absorption indices depend rather weakly on the type of interface and core type. We demonstrate that the HOMO wavefunction is mainly localised in the core of the nanocrystal, depending primarily on the core/shell ratio. On the other hand the LUMO wavefunction spreads more into the shell of the nanocrystal, where its confinement in the core is almost the same in each of the studied structural models. Furthermore, we show that the radiative lifetimes decrease with increasing core sizes due to changes in the dipolar overlap integral of the HOMO and LUMO wavefunctions. In addition, the electron-hole Coulomb interaction energies follow a similar pattern as the localisation of the wavefunctions, with the smaller NCs having higher Coulomb interaction energies.

Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping

T-cell responses in humans are initiated by the binding of a peptide antigen to a human leukocyte antigen (HLA) molecule. The peptide-HLA complex then recruits an appropriate T cell, leading to cell-mediated immunity. More than 2000 HLA class-I alleles are known in humans, and they vary only in their peptide-binding grooves. The polymorphism they exhibit enables them to bind a wide range of peptide antigens from diverse sources. HLA molecules and peptides present a complex molecular recognition pattern, as many peptides bind to a given allele and a given peptide can be recognized by many alleles. A powerful grouping scheme that not only provides an insightful classification, but is also capable of dissecting the physicochemical basis of recognition specificity is necessary to address this complexity. We present a hierarchical classification of 2010 class-I alleles by using a systematic divisive clustering method. All-pair distances of alleles were obtained by comparing binding pockets in the structural models. By varying the similarity thresholds, a multilevel classification was obtained, with 7 supergroups, each further subclassifying to yield 72 groups. An independent clustering performed based only on similarities in their epitope pools correlated highly with pocket-based clustering. Physicochemical feature combinations that best explain the basis of clustering are identified. Mutual information calculated for the set of peptide ligands enables identification of binding site residues contributing to peptide specificity. The grouping of HLA molecules achieved here will be useful for rational vaccine design, understanding disease susceptibilities and predicting risk of organ transplants.

Adlayer Structures of DL-Homocysteine and L-Homocysteine Thiolactone on Au(111) Surface: an in situ STM Study

The adsorption Of DL-homocysteine (Hcy) and L-homocysteine thiolactone (HTL) on Au(1 1 1) electrode was investigated in 0.1 M HClO4 by cyclic voltammetry and in situ scanning tunneling microscopy (STM). Hcy and HTL molecules formed highly ordered adlayers on Au(1 1 1) surface. High-resolution STM images revealed the orientation and packing arrangement in the ordered adlayers. Hcy molecules formed (2root3 x 3root3)R30degrees adlayer structure and H-bonds between carboxyl groups were assumed to be responsible for the origin of tail-to-tail or head-to-head molecular arrangement, while HTL molecules formed (4 x 6) adlayer structure, and two different orientations and appearances in the ordered adlayer were found. Structural models were proposed for the two adlayers.

Design, synthesis and characterization of sequence-specific DNA-cleaving metalloproteins

This thesis describes research pursued in two areas, both involving the design and synthesis of sequence specific DNA-cleaving proteins. The first involves the use of sequence-specific DNA-cleaving metalloproteins to probe the structure of a protein-DNA complex, and the second seeks to develop cleaving moieties capable of DNA cleavage through the generation of a non-diffusible oxidant under physiological conditions.

Chapter One provides a brief review of the literature concerning sequence-specific DNA-binding proteins. Chapter Two summarizes the results of affinity cleaving experiments using leucine zipper-basic region (bZip) DNA-binding proteins. Specifically, the NH_2-terminal locations of a dimer containing the DNA binding domain of the yeast transcriptional activator GCN4 were mapped on the binding sites 5'-CTGACTAAT-3' and 5'ATGACTCTT- 3' using affinity cleaving. Analysis of the DNA cleavage patterns from Fe•EDTA-GCN4(222-281) and (226-281) dimers reveals that the NH_2-termini are in the major groove nine to ten base pairs apart and symmetrically displaced four to five base pairs from the central C of the recognition site. These data are consistent with structural models put forward for this class of DNA binding proteins. The results of these experiments are evaluated in light of the recently published crystal structure for the GCN4-DNA complex. Preliminary investigations of affinity cleaving proteins based on the DNA-binding domains of the bZip proteins Jun and Fos are also described.

Chapter Three describes experiments demonstrating the simultaneous binding of GCN4(226-281) and 1-Methylimidazole-2-carboxamide-netropsin (2-ImN), a designed synthetic peptide which binds in the minor groove of DNA at 5'-TGACT-3' sites as an antiparallel, side-by-side dimer. Through the use of Fe•EDTA-GCN4(226-281) as a sequence-specific footprinting agent, it is shown that the dimeric protein GCN4(226-281) and the dimeric peptide 2- ImN can simultaneously occupy their common binding site in the major and minor grooves of DNA, respectively. The association constants for 2-ImN in the presence and in the absence of Fe•EDTA-GCN4(226-281) are found to be similar, suggesting that the binding of the two dimers is not cooperative.

Chapter Four describes the synthesis and characterization of PBA-β-OH-His- Hin(139-190), a hybrid protein containing the DNA-binding domain of Hin recombinase and the putative iron-binding and oxygen-activating domain of the antitumor antibiotic bleomycin. This 54-residue protein, comprising residues 139-190 of Hin recombinase with the dipeptide pyrimidoblamic acid-β-hydroxy-L-histidine (PBA-β-OH-His) at the NH2 terminus, was synthesized by solid phase methods. PBA-β-OH-His-Hin(139- 190) binds specifically to DNA at four distinct Hin binding sites with affinities comparable to those of the unmodified Hin(139-190). In the presence of dithiothreitol (DTT), Fe•PB-β-OH-His-Hin(139-190) cleaves DNA with specificity remarkably similar to that of Fe•EDTA-Hin(139-190), although with lower efficiency. Analysis of the cleavage pattern suggests that DNA cleavage is mediated through a diffusible species, in contrast with cleavage by bleomycin, which occurs through a non-diffusible oxidant.

Análisis del riesgo de contraparte a través del modelo estructural de Merton en el marco de Solvencia II

[ES] La entrada en vigor del proyecto de Solvencia II transformará por completo el sistema de determinación de las necesidades de capital del sector asegurador europeo. Recientemente se ha presentado el último estudio de impacto cuantitativo (QIS5), donde se establece la forma de cálculo del modelo estándar para la determinación de los requerimientos de capital. Este trabajo trata de analizar la adecuación de la calibración del riesgo de crédito de la contraparte mediante los modelos que se proponen en los últimos informes de impacto cuantitativo (cuarto y quinto). Para ello comparamos las necesidades de capital que se obtienen por ambas alternativas, frente a las que resultarían de aplicar un modelo de simulación basado en el enfoque estructural. Los resultados obtenidos muestran que el uso de probabilidades basadas en la metodología de Merton frente a aquellas basadas en ratings, dan lugar a requerimientos de capital sustancialmente mayores. Además, el modelo propuesto en QIS4 basado en la distribución de Vasicek no es adecuado cuando el número de contrapartes es reducido, situación habitual en el sector asegurador europeo. Por otra parte, la nueva propuesta (QIS5 o modelo de Ter Berg) es más versátil y adecuada que su antecesora pero requiere analizar con más detenimiento las hipótesis de calibración para de este modo aproximar mejor las estimaciones al riesgo realmente asumido.

Estimating relative abundance from catch and effort data, using neural networks

We develop and test a method to estimate relative abundance from catch and effort data using neural networks. Most stock assessment models use time series of relative abundance as their major source of information on abundance levels. These time series of relative abundance are frequently derived from catch-per-unit-of-effort (CPUE) data, using general linearized models (GLMs). GLMs are used to attempt to remove variation in CPUE that is not related to the abundance of the population. However, GLMs are restricted in the types of relationships between the CPUE and the explanatory variables. An alternative approach is to use structural models based on scientific understanding to develop complex non-linear relationships between CPUE and the explanatory variables. Unfortunately, the scientific understanding required to develop these models may not be available. In contrast to structural models, neural networks uses the data to estimate the structure of the non-linear relationship between CPUE and the explanatory variables. Therefore neural networks may provide a better alternative when the structure of the relationship is uncertain. We use simulated data based on a habitat based-method to test the neural network approach and to compare it to the GLM approach. Cross validation and simulation tests show that the neural network performed better than nominal effort and the GLM approach. However, the improvement over GLMs is not substantial. We applied the neural network model to CPUE data for bigeye tuna (Thunnus obesus) in the Pacific Ocean.