Lysis dynamics and membrane oligomerization pathways for Cytolysin A (ClyA) pore-forming toxin

Pore-forming toxins are known for their ability to efficiently form transmembrane pores which eventually leads to cell lysis. The dynamics of lysis and underlying self-assembly or oligomerization pathways leading to pore formation are incompletely understood. In this manuscript the pore-forming kinetics and lysis dynamics of Cytolysin-A (ClyA) toxins on red blood cells (RBCs) are quantified and compared with experimental lysis data. Lysis experiments are carried out on a fixed mass of RBCs, under isotonic conditions in phosphate-buffered saline, for different initial toxin concentrations ranging from 2.94-14.7 nM. Kinetic models which account for monomer binding, conformation and oligomerization to form the dodecameric ClyA pore complex are developed and lysis is assumed to occur when the number of pores per RBC (n(p)) exceeds a critical number, n(pc). By analysing the model in a sublytic regime (n(p) < n(pc)) the number of pores per RBC to initiate lysis is found to lie between 392 and 768 for the sequential oligomerization mechanism and between 5300 and 6300 for the non-sequential mechanism. Rupture rates which are first order in the number of RBCs are seen to provide the best agreement with the lysis experiments. The time constants for pore formation are estimated to lie between 1 and 20 s and monomer conformation time scales were found to be 2-4 times greater than the oligomerization times. Cell rupture takes places in 100s of seconds, and occurs predominantly with a steady number of pores ranging from 515 to 11 000 on the RBC surface for the sequential mechanism. Both the sequential irreversible and non-sequential kinetics provide similar predictions of the hemoglobin release dynamics, however the hemoglobin released as a function of the toxin concentration was accurately captured only with the sequential model. Each mechanism develops a distinct distribution of mers on the surface, providing a unique experimentally observable fingerprint to identify the underlying oligomerization pathways. Our study offers a method to quantify the extent and dynamics of lysis which is an important aspect of developing novel drug and gene delivery strategies based on pore-forming toxins.

Photocurrent spectroscopic studies of diketopyrrolopyrrole-based statistical copolymers

Diketopyrrolopyrrole (DPP) containing copolymers have gained a lot of interest in organic optoelectronics with great potential in organic photovoltaics. In this work, DPP based statistical copolymers, with slightly different bandgap energies and a varying fraction of donor-acceptor ratio are investigated using monochromatic photocurrent spectroscopy and Fourier-transform photocurrent spectroscopy (FTPS). The statistical copolymer with a lower DPP fraction, when blended with a fullerene derivative, shows the signature of an inter charge transfer complex state in photocurrent spectroscopy. Furthermore, the absorption spectrum of the blended sample with a lower DPP fraction is seen to change as a function of an external bias, qualitatively similar to the quantum confined Stark effect, from where we estimate the exciton binding energy. The statistical copolymer with a higher DPP fraction shows no signal of the inter charge transfer states and yields a higher external quantum efficiency in a photovoltaic structure. In order to gain insight into the origin of the observed charge transfer transitions, we present theoretical studies using density-functional theory and time-dependent density-functional theory for the two pristine DPP based statistical monomers.

Photocurrent spectroscopic studies of diketopyrrolopyrrole-based statistical copolymers

Diketopyrrolopyrrole (DPP) containing copolymers have gained a lot of interest in organic optoelectronics with great potential in organic photovoltaics. In this work, DPP based statistical copolymers, with slightly different bandgap energies and a varying fraction of donor-acceptor ratio are investigated using monochromatic photocurrent spectroscopy and Fourier-transform photocurrent spectroscopy (FTPS). The statistical copolymer with a lower DPP fraction, when blended with a fullerene derivative, shows the signature of an inter charge transfer complex state in photocurrent spectroscopy. Furthermore, the absorption spectrum of the blended sample with a lower DPP fraction is seen to change as a function of an external bias, qualitatively similar to the quantum confined Stark effect, from where we estimate the exciton binding energy. The statistical copolymer with a higher DPP fraction shows no signal of the inter charge transfer states and yields a higher external quantum efficiency in a photovoltaic structure. In order to gain insight into the origin of the observed charge transfer transitions, we present theoretical studies using density-functional theory and time-dependent density-functional theory for the two pristine DPP based statistical monomers.

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Role of different factors affecting interdiffusion in Cu(Ga) and Cu(Si) solid solutions

A detailed diffusion study was carried out on Cu(Ga) and Cu(Si) solid solutions in order to assess the role of different factors in the behaviour of the diffusing components. The faster diffusing species in the two systems, interdiffusion, intrinsic and impurity diffusion coefficients, are determined to facilitate the discussion. It was found that Cu was more mobile in the Cu-Si system, whereas Ga was the faster diffusing species in the Cu-Ga system. In both systems, the interdiffusion coefficients increased with increasing amount of solute (e.g. Si or Ga) in the matrix (Cu). Impurity diffusion coefficients for Si and Ga in Cu, found out by extrapolating interdiffusion coefficient data to zero composition of the solute, were both higher than the Cu tracer diffusion coefficient. These observed trends in diffusion behaviour could be rationalized by considering: (i) formation energies and concentration of vacancies, (ii) elastic moduli (indicating bond strengths) of the elements and (iii) the interaction parameters and the related thermodynamic factors. In summary, we have shown here that all the factors introduced in this paper should be considered simultaneously to understand interdiffusion in solid solutions. Otherwise, some of the aspects may look unusual or even impossible to explain.

Residue specific contributions to stability and activity inferred from saturation mutagenesis and deep sequencing

Multiple methods currently exist for rapid construction and screening of single-site saturation mutagenesis (SSM) libraries in which every codon or nucleotide in a DNA fragment is individually randomized. Nucleotide sequences of each library member before and after screening or selection can be obtained through deep sequencing. The relative enrichment of each mutant at each position provides information on its contribution to protein activity or ligand-binding under the conditions of the screen. Such saturation scans have been applied to diverse proteins to delineate hot-spot residues, stability determinants, and for comprehensive fitness estimates. The data have been used to design proteins with enhanced stability, activity and altered specificity relative to wild-type, to test computational predictions of binding affinity, and for protein model discrimination. Future improvements in deep sequencing read lengths and accuracy should allow comprehensive studies of epistatic effects, of combinational variation at multiple sites, and identification of spatially proximate residues.

A Probe for the Selective and Parts-per-Billion-Level Detection of Copper(II) and Mercury(II) using a Micellar Medium and Its Utility in Cell Imaging

A novel colorimetric probe 1 based on the picolyl moiety has been designed and synthesized. Probe 1 is composed of a pyrene and a bispicolyl amine (BPA) unit, in which the BPA moiety acts as a binding unit and the binding phenomenon is sensed from the changes in the signaling subunit. The probe detects Cu2+ specifically in water and both Cu2+ and Hg2+ efficiently in neutral Brij-58 micellar media. The probe shows a color change visible to the naked eye upon addition of metal ions. Notably, in a micellar medium, probe 1 can detect both the Cu2+ and Hg2+ ions even at parts-per-billion levels. Furthermore, the probe shows ratiometric detection of both the metal ions making the sensing quantitative. The two metal ions could be discriminated both visibly under a UV lamp and with the use of fluorescence spectroscopy. The probe could be also used in biological cell lines for the detection of both Hg2+ and Cu2+ ions.

Dielectric and Raman investigations of structural phase transitions in (C2H5NH3)(2)CdCl4

Temperature-dependent Raman and dielectric measurements have been carried out on (C2H5NH3)(2)CdCl4 single crystals. Raman studies reveal the presence of two structural phase transitions below room temperature at 216 K and 114 K. The phase transitions are marked by anomalies in temperature dependence of wave-number and full width half maximum (FWHM) of several vibrational modes. The transitions are also accompanied by anomalies in dielectric measurements. Raman and dielectric data indicate that the transition at 216 K is order-disorder in nature and is driven by re-orientation of organic ions, while the transition at 114 K is due to coupling between the CdCl6 octahedron and the organic chain. Further high temperature dielectric measurements reveal the presence of one more structural phase transition around 473 K across which dispersion in dielectric parameters is observed. The activation energies and relaxation time obtained for high temperature dielectric phases are characteristic of combined reorientation motions of alkyl ammonium cations.

Autoinhibitory mechanism and activity-related structural changes in a mycobacterial adenylyl cyclase

An adenylyl cyclase from Mycobacterium avium, Mal 120, is a functional orthologue of a pseudogene Rv1120c from Mycobacterium tuberculosis. We report the crystal structure of Mal 120 in a monomeric form and its truncated construct as a dimer. Mal 120 exists as a monomer in solution and crystallized as a monomer in the absence of substrate or inhibitor. An additional alpha-helix present at the N-terminus of the monomeric structure blocks the active site by interacting with the substrate binding residues and occupying the dimer interface region. However, the enzyme has been found to be active in solution, indicating the movement of the helix away from the interface to facilitate the formation of active dimers in conditions favourable for catalysis. Thus, the N-terminal helix of Ma1120 keeps the enzyme in an autoinhibited state when it is not active. Deletion of this helix enabled us to crystallize the molecule as an active homodimer in the presence of a P-site inhibitor 2',5'-dideoxy-3'-ATP, or pyrophosphate along with metal ions. The substrate specifying lysine residue plays a dual role of interacting with the substrate and stabilizing the dimer. The dimerization loop region harbouring the second substrate specifying residue, an aspartate, shows significant differences in conformation and position between the monomeric and dimeric structures. Thus, this study has not only revealed that significant structural transitions are required for the interconversion of the inactive and the active forms of the enzyme, but also provided precise nature of these transitions. (C) 2015 Elsevier Inc. All rights reserved.

Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications

17 independent crystal structures of family I uracil-DNA glycosylase from Mycobacterium tuberculosis (MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 50 position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.

Growth of TiO2 Films by RF Magnetron Sputtering for MOS Gate Dielectrics: Influence of Substrate Temperature

Titanium dioxide thin films were deposited by RF reactive magnetron sputtering technique on p-type silicon(100) substrates held at temperatures in the range 303-673 K. The influence of substrate temperature on the core level binding energies, chemical bonding configuration, crystallographic structure and dielectric properties was investigated. X-ray photoelectron spectroscopy studies and Fourier transform infrared transmittance data confirmed the formation of stoichiometric films with anatase phase at a substrate temperature of 673 K. The films formed at 303 K were nanocrystalline with amorphous matrix while those deposited at 673 K were transformed in to crystalline phase and growth of grains in pyramidal like structure as confirmed by X-ray diffraction and atomic force microscopy respectively. Metal-oxide-semiconductor capacitors were fabricated with the configuration of Al/TiO2/Si structures. The current voltage, capacitance voltage and conductance voltage characteristics were studied to understand the electrical conduction and dielectric properties of the MOS devices. The leakage current density (at gate voltage of 2 V) decreased from 2.2 x 10(-6) to 1.7 x 10(-7) A/cm(2), the interface trap density decreased from 1.2 x 10(13) to 2.1 x 10(12) cm(-2) eV(-1) and the dielectric constant increased from 14 to 36 with increase of substrate temperature from 303 to 673 K.

Solid-state optical absorption from optimally tuned time-dependent range-separated hybrid density functional theory

We present a framework for obtaining reliable solid-state charge and optical excitations and spectra from optimally tuned range-separated hybrid density functional theory. The approach, which is fully couched within the formal framework of generalized Kohn-Sham theory, allows for the accurate prediction of exciton binding energies. We demonstrate our approach through first principles calculations of one- and two-particle excitations in pentacene, a molecular semiconducting crystal, where our work is in excellent agreement with experiments and prior computations. We further show that with one adjustable parameter, set to produce the known band gap, this method accurately predicts band structures and optical spectra of silicon and lithium fluoride, prototypical covalent and ionic solids. Our findings indicate that for a broad range of extended bulk systems, this method may provide a computationally inexpensive alternative to many-body perturbation theory, opening the door to studies of materials of increasing size and complexity.

Multivariate PLS Modeling of Apicomplexan FabD-Ligand Interaction Space for Mapping Target-Specific Chemical Space and Pharmacophore Fingerprints

Biomolecular recognition underlying drug-target interactions is determined by both binding affinity and specificity. Whilst, quantification of binding efficacy is possible, determining specificity remains a challenge, as it requires affinity data for multiple targets with the same ligand dataset. Thus, understanding the interaction space by mapping the target space to model its complementary chemical space through computational techniques are desirable. In this study, active site architecture of FabD drug target in two apicomplexan parasites viz. Plasmodium falciparum (PfFabD) and Toxoplasma gondii (TgFabD) is explored, followed by consensus docking calculations and identification of fifteen best hit compounds, most of which are found to be derivatives of natural products. Subsequently, machine learning techniques were applied on molecular descriptors of six FabD homologs and sixty ligands to induce distinct multivariate partial-least square models. The biological space of FabD mapped by the various chemical entities explain their interaction space in general. It also highlights the selective variations in FabD of apicomplexan parasites with that of the host. Furthermore, chemometric models revealed the principal chemical scaffolds in PfFabD and TgFabD as pyrrolidines and imidazoles, respectively, which render target specificity and improve binding affinity in combination with other functional descriptors conducive for the design and optimization of the leads.

The SPL7013 dendrimer destabilizes the HIV-1 gp120-CD4 complex

The poly (l-lysine)-based SPL7013 dendrimer with naphthalene disulphonate surface groups blocks the entry of HIV-1 into target cells and is in clinical trials for development as a topical microbicide. Its mechanism of action against R5 HIV-1, the HIV-1 variant implicated in transmission across individuals, remains poorly understood. Using docking and fully atomistic MD simulations, we find that SPL7013 binds tightly to R5 gp120 in the gp120-CD4 complex but weakly to gp120 alone. Further, the binding, although to multiple regions of gp120, does not occlude the CD4 binding site on gp120, suggesting that SPL7013 does not prevent the binding of R5 gp120 to CD4. Using MD simulations to compute binding energies of several docked structures, we find that SPL7013 binding to gp120 significantly weakens the gp120-CD4 complex. Finally, we use steered molecular dynamics (SMD) to study the kinetics of the dissociation of the gp120-CD4 complex in the absence of the dendrimer and with the dendrimer bound in each of the several stable configurations to gp120. We find that SPL7013 significantly lowers the force required to rupture the gp120-CD4 complex and accelerates its dissociation. Taken together, our findings suggest that SPL7013 compromises the stability of the R5 gp120-CD4 complex, potentially preventing the accrual of the requisite number of gp120-CD4 complexes across the virus-cell interface, thereby blocking virus entry.

Sulfurization of sputtered Ag-In precursors for AgInS2 solar cell absorber layers

Silver indium sulfide (AgInS2) thin films are deposited by sequential sputtering of metallic precursor Ag/In] followed by sulfurization. Effect of substrate temperature (Tsub) during sulfurization process on the film growth is studied by varying the substrate temperature from 350 to 500 degrees C. Films prepared above 350 degrees C showed a mixture of orthorhombic and tetragonal phases of AgInS2 with tetragonal phase being dominant. Better crystalline, nearly stoichiometric and p-type films are obtained at a substrate temperature of 500 degrees C. The characteristic A(1) mode of AgInS2 chalcopyrite structure is observed in the Raman spectra at 274 cm(-1) for the films prepared above 350 degrees C. The grain size of the film increases from 489 to 895 nm with the increase in substrate temperature. The binding energies of the constituent elements are determined using XPS. The band gap of AgInS2 films is in the range of 1.64-1.92 eV and the absorption coefficient is found to be >10(4) cm(-1). Preliminary studies on the AgInS2/ZnS solar cell showed an efficiency of 0.3%. (C) 2015 Elsevier B.V. All rights reserved.