Chemistry

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Catalytic signal amplification was used for the colorimetric detection of CN− in aqueous media by using the enzyme catalase in tandem with mesoporous silica nanoparticle based synthetic HRP enzyme mimic Fe-MSNs. Signal amplification up to a maximum of eight fold was observed for the reporter “oxidized TMB” with respect to the added CN− ion. © 2013 The Royal Society of Chemistry.

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Chemical Communications

Catalytic signal amplification using [FeIII(biuret-amide)]-mesoporous silica nanoparticles: Visual cyanide detection

Change in pH plays a crucial role in the stability and function of the dengue envelope (DENV) protein during conformational transition from dimeric (pre-fusion state) to trimeric form (post-fusion state). In the present study we have performed various molecular dynamics (MD) simulations of the trimeric DENV protein at different pH and ionic concentrations. We have used total binding energy to justify the stability of the complex using the MMPBSA method. We found a remarkable increase in the stability of the complex at neutral pH (pH ∼ 7) due to the increment of sodium ions. However, at very low pH (pH ∼ 4), the total energy of the complex becomes high enough to destabilize the complex. At a specific pH, almost at a range of 6, the stability of the complex is significantly better than the stability of the trimer at neutral pH, which connotes that the trimer is most stable at this pH (pH ∼ 6). © 2012 Elsevier B.V. All rights reserved.

Biochimica et Biophysica Acta - Proteins and Proteomics

Stability of trimeric DENV envelope protein at low and neutral pH: An insight from MD study

Temperature dependent steady state and time resolved fluorescence measurements have been performed to explore the interaction and dynamics in polymer-electrolyte composite of the following general formula: 0.85 PEG 0.15{f KNO3 (1-f) LiNO3}, with f denoting fraction of potassium ion in the 0.15 mol electrolyte present in the medium. Poly(ethylene glycol) with number-averaged molecular weight of 300 (PEG300) has been employed as polymer and C153 as the fluorescent probe. Substantial excitation wavelength dependence of probe fluorescence emission in presence of electrolyte suggests presence of spatial heterogeneity which vanishes either upon raising temperature or removing the electrolyte. This has been interpreted as arising from the cation-induced arrest of polymer segmental motion. Temporal heterogeneity in these composites is manifested via fractional viscosity dependence of average solvation and rotation rates of the dissolved probe. Viscosity decoupling of these rates in composites is found to depend on cation identity and is also reflected via the corresponding activation energies. The degree of decoupling differs between solvation and rotation, inducing an analogy to the observations made in deeply supercooled liquids. In addition, conformity to hydrodynamic predictions is recovered by measuring f dependent solute rotation at higher temperatures. Several complimentary but different experiments are suggested to re-examine the mechanism proposed here, based on the fluorescence results, for the emergence of spatio-temporal heterogeneity in these composites and its disappearance either in the absence of any electrolyte or at higher temperatures. © 2013 American Institute of Physics.

Journal of Chemical Physics

Ionic arrest of segmental motion and emergence of spatio-temporal heterogeneity: A fluorescence investigation of (polyethylene glycol electrolyte) composites

Computational techniques are one of the most emerging topics in structural and molecular biology. Molecular dynamics (MD) simulations are used not only to explore the conformational aspects of biological systems but also to have significant scope in protein-ligand interactions. Then the binding free energy calculations are readily applied to the simulated systems in order to predict the binding affinities. The thermodynamic properties are directly related to protein-ligand interactions which are dependent upon a few specific parameters. In the present review, we highlight some facts related to protein-ligand complexes, by starting with a survey of MD simulations and binding free energy calculations and ending with some successful implementations of these computational techniques. © 2013 Bentham Science Publishers.

Current Computer-Aided Drug Design

Recent advances in protein-ligand interactions: Molecular dynamics simulations and binding free energy

Background: Members of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of PBP ligand binding specificity was recently altered when the structure of the Thermotoga maritima cellobiose-binding protein (tmCBP) was solved. The tmCBP binding site is bipartite, comprising a canonical solvent-excluded region (subsite one), adjacent to a solvent-filled cavity (subsite two) where specific and semi-specific ligand recognition occur, respectively. Results: A molecular level understanding of binding pocket adaptation mechanisms that simultaneously allow both ligand specificity at subsite one and promiscuity at subsite two has potentially important implications in ligand binding and drug design studies. We sought to investigate the determinants of ligand binding selectivity in tmCBP through biophysical characterization of tmCBP in the presence of varying β-glucan oligosaccharides. Crystal structures show that whilst the amino acids that comprise both the tmCBP subsite one and subsite two binding sites remain fixed in conformation regardless of which ligands are present, the rich hydrogen bonding potential of water molecules may facilitate the ordering and the plasticity of this unique PBP binding site. Conclusions: The identification of the roles these water molecules play in ligand recognition suggests potential mechanisms that can be utilized to adapt a single ligand binding site to recognize multiple distinct ligands. © 2013 Munshi et al.; licensee BioMed Central Ltd.

BMC Structural Biology

Molecular details of ligand selectivity determinants in a promiscuous β-glucan periplasmic binding protein

Here a combined dynamic fluorescence and all-atom molecular dynamics simulation study of aqueous pool-size dependent solvation energy and rotational relaxations of a neutral dipolar solute, C153, trapped in AOT (charged) and IGPAL (neutral) reverse micelles (RMs) at 298 K, is described. RMs in simulations have been represented by a reduced model where SPC/E water molecules interact with a trapped C153 that possesses realistic charge distributions for both ground and excited states. In large aqueous pools, measured average solvation and rotation rates are smaller for the neutral RMs than those in charged ones. Interestingly, while the measured average solvation and rotation rates increase with pool size for the charged RMs, the average rotation rates for the neutral RMs exhibit a reverse dependence. Simulations have qualitatively reproduced this experimental trend and suggested interfacial location for the solute for all cases. The origin for the subnanosecond Stokes shift dynamics has been investigated and solute-interface interaction contribution quantified. Simulated layer-wise translational and rotational diffusions of water molecules re-examine the validity of the core-shell model and provide a resolution to a debate regarding the origin of the subnanosecond solvation component in dynamic Stokes shift measurements with aqueous RMs but not detected in ultrafast IR measurements. © 2013 American Chemical Society.

Journal of Physical Chemistry B

Solute and solvent dynamics in confined equal-sized aqueous environments of charged and neutral reverse micelles: A combined dynamic fluorescence and all-atom molecular dynamics simulation study

This article describes synthesis, characterization and properties of blends of benzoxazine (Bz) monomers, i.e., m-alkylphenyl-3,4-dihydro-2H-benzoxazine (Bz-C), 6,6′-(propane-2,2-diyl)bis(3-phenyl-3,4-dihydro-2H-benzoxazine (Bz-A) and 3-phenyl-3,4-dihydro-2H-benzoxazine-p-carboxylic acid (Bz-pA). Binary blends of Bz-C with Bz-pA, and Bz-A with Bz-pA were prepared by first synthesizing Bz-C or Bz-A followed by the addition of all the ingredients of Bz-pA. In a similar manner, ternary blends of Bz-C, Bz-A and Bz-pA were prepared by first synthesizing Bz-C and subsequent addition of all the ingredients of Bz-A and Bz-pA in one pot. The Bz monomer blends were characterized by 1H-NMR, FTIR spectroscopy, and differential scanning calorimetry. The temperature of onset of curing (T o), due to ring-opening polymerization of Bz was found to decrease significantly by incorporation of carboxyl groups (Bz-pA) showing thereby the catalytic effect of acid functionality. Bz polymers showed good thermal stability and incorporation of Bz-pA in blends resulted in a highly cross-linked network. The interlaminar shear strength of glass fabric reinforced composites and the lap shear strength of metal-metal joints using these resin blends was also investigated. © 2012 Akadémiai Kiadó, Budapest, Hungary.

Journal of Thermal Analysis and Calorimetry

Blends of benzoxazine monomers: Effect of structure and composition on polymer properties

In the area of catalysis, nanoparticles and enzymes are two of the most important systems. By amalgamating the two, we present here proof of the concept that it is possible to prepare a multifunctional catalyst that can carry out a "relay" reaction. The catalyst consists of a surface bound enzyme on a metalcore-silicashell nanoparticle architecture. Here the enzyme catalyzes the 1st reaction and the metal nanoparticles act as a catalyst for the 2nd reaction of the product from the 1st reaction. In particular, we have studied the catalytic activity of glucosidase grafted Au@mSiO2 on 4-nitrophenyl-β-glucopyranoside, where glucosidase will catalyse the 1st step to generate 4-nitrophenol, which acts as a substrate for the next reduction step which is catalysed by the Au nanoparticles present inside the mesoporous silica shell. © 2013 The Royal Society of Chemistry.

RSC Advances

Development of a multifunctional catalyst for a "relay" reaction

Copper(II) complexes [Cu(Fc-aa)(cur)] (1-3) of curcumin (Hcur) and N-ferrocenylmethyl-l-amino acids (Fc-aa), viz., ferrocenylmethyl-l-tyrosine (Fc-TyrH), ferrocenylmethyl-l-tryptophan (Fc-TrpH) and ferrocenylmethyl-l- methionine (Fc-MetH), were prepared and characterized. The DNA photocleavage activity, photocytotoxicity and cellular localization in HeLa and MCF-7 cancer cells of these complexes were studied. Acetylacetonate (acac) complexes [Cu(Fc-aa)(acac)] (4-6) were prepared and used as controls. The chemical nuclease inactive complexes showed efficient pUC19 DNA cleavage activity in visible light. Complexes 1-3 showed high photocytotoxicity with low dark toxicity thus giving remarkable photodynamic effect. FACScan analysis showed apoptosis of the cancer cells. Fluorescence microscopic studies revealed primarily cytosolic localization of the complexes. {\textcopyright} 2013 Elsevier Masson SAS. All rights reserved.

European Journal of Medicinal Chemistry

Photocytotoxicity of copper(II) complexes of curcumin and N-ferrocenylmethyl-l-amino acids

The intramolecular Dötz benzannulation with alkyne-tethered aryloxy Fischer carbenes has been applied to synthesize a nine membered diaryl ether linked macrocyclic library. Insilico tools, that is, shape space analysis was used to assess the diversity of the library, and polar surface area (PSA) of the compounds were deduced to understand the range of their surface electrostatic potential. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.