Employing denaturation for rapid electrochemical detection of myoglobin using TiO2 nanotubes

An alternative antibody-free strategy for the rapid electrochemical detection of cardiac myoglobin has been demonstrated here using hydrothermally synthesized TiO2 nanotubes (Ti-NT). The denaturant induced unfolding of myoglobin led to easy access of the deeply buried electroactive heme center and thus the efficient reversible electron transfer from protein to electrode surface. The sensing performance of the Ti-NT modified electrodes were compared vis a vis commercially available titania and GCEs. The tubular morphology of the Ti-NT led to facile transfer of electrons to the electrode surface, which eventually provided a linear current response (obtained from cyclic voltammetry) over a wide range of Mb concentration. The sensitivity of the Ti-NT based sensor was remarkable and was equal to 18 mu A mg(-1) ml (detection limit = 50 nM). This coupled with the rapid analysis time of a few tens of minutes (compared to a few days for ELISA) demonstrates its potential usefulness for the early detection of acute myocardial infarction (AMI).

Analysis of designed beta-hairpin peptides: molecular conformation and packing in crystals

The crystal structures of several designed peptide hairpins have been determined in order to establish features of molecular conformations and modes of aggregation in the crystals. Hairpin formation has been induced using a centrally positioned (D)Pro-Xxx segment (Xxx = (L)Pro, Aib, Ac(6)c, Ala; Aib = alpha-aminoisobutyric acid; Ac(6)c = 1-aminocyclohexane-1-carboxylic acid). Structures of the peptides Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (1), Boc-Leu-Tyr-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (2, polymorphic forms labeled as 2a and 2b), Boc-Leu-Val-Val-(D)Pro-(L)Pro-Leu-Val-Val-OMe (3), Boc-Leu-Phe-Val-(D)Pro-Aib-Leu-Phe-Val-OMe (4, polymorphic forms labeled as 4a and 4b), Boc-Leu-Phe-Val-(D)Pro-Ac(6)c-Leu-Phe-Val-OMe (5) and Boc-Leu-Phe-Val-(D)Pro-Ala-Leu-Phe-Val-OMe (6) are described. All the octapeptides adopt type II' beta-turn nucleated hairpins, stabilized by three or four cross-strand intramolecular hydrogen bonds. The angle of twist between the two antiparallel strands lies in the range of -9.8 degrees to -26.7 degrees. A detailed analysis of packing motifs in peptide hairpin crystals is presented, revealing three broad modes of association: parallel packing, antiparallel packing and orthogonal packing. An attempt to correlate aggregation modes in solution with observed packing motifs in crystals has been made by indexing of crystal faces in the case of three of the peptide hairpins. The observed modes of hairpin aggregation may be of relevance in modeling multiple modes of association, which may provide insights into the structure of insoluble polypeptide aggregates.

Does aluminium bind to histidine? an NMR investigation of Amyloid beta 12 and Amyloid beta 16 fragments

Aluminium and zinc are known to be the major triggering agents for aggregation of amyloid peptides leading to plaque formation in Alzheimer's disease. While zinc binding to histidine in A (amyloid ) fragments has been implicated as responsible for aggregation, not much information is available on the interaction of aluminium with histidine. In the NMR study of the N-terminal A fragments, DAEFRHDSGYEV (A12) and DAEFRHDSGYEVHHQK (A16) presented here, the interactions of the fragments with aluminium have been investigated. Significant chemical shifts were observed for few residues near the C-terminus when aluminium chloride was titrated with A12 and A16 peptides. Surprisingly, it is nonhistidine residues which seem to be involved in aluminium binding. Based on NMR constrained structure obtained by molecular modelling, aluminium-binding pockets in A12 were around charged residues such as Asp, Glu. The results are discussed in terms of native structure propagation, and the relevance of histidine residues in the sequences for metal-binding interactions. We expect that the study of such short amyloid peptide fragments will not only provide clues for plaque formation in aggregated conditions but also facilitate design of potential drugs for these targets.

Scalable Preference Aggregation in Social Networks

In social choice theory, preference aggregation refers to computing an aggregate preference over a set of alternatives given individual preferences of all the agents. In real-world scenarios, it may not be feasible to gather preferences from all the agents. Moreover, determining the aggregate preference is computationally intensive. In this paper, we show that the aggregate preference of the agents in a social network can be computed efficiently and with sufficient accuracy using preferences elicited from a small subset of critical nodes in the network. Our methodology uses a model developed based on real-world data obtained using a survey on human subjects, and exploits network structure and homophily of relationships. Our approach guarantees good performance for aggregation rules that satisfy a property which we call expected weak insensitivity. We demonstrate empirically that many practically relevant aggregation rules satisfy this property. We also show that two natural objective functions in this context satisfy certain properties, which makes our methodology attractive for scalable preference aggregation over large scale social networks. We conclude that our approach is superior to random polling while aggregating preferences related to individualistic metrics, whereas random polling is acceptable in the case of social metrics.

Confinement induced stochastic sensing of charged coronene and perylene aggregates in alpha-hemolysin nanochannels

Biological nanopores provide optimum dimensions and an optimal environment to study early aggregation kinetics of charged polyaromatic molecules in the nano-confined regime. It is expected that probing early stages of nucleation will enable us to design a strategy for supramolecular assembly and biocrystallization processes. Specifically, we have studied translocation dynamics of coronene and perylene based salts, through the alpha-hemolysin (alpha-HL) protein nanopore. The characteristic blocking events in the time-series signal are a function of concentration and bias voltage. We argue that different blocking events arise due to different aggregation processes as captured by all atomistic molecular dynamics (MD) simulations. These confinement induced aggregations of polyaromatic chromophores during the different stages of translocation are correlated with the spatial symmetry and charge distribution of the molecules.

Stability of fluctuating and transient aggregates of amphiphilic solutes in aqueous binary mixtures: Studies of dimethylsulfoxide, ethanol, and tert-butyl alcohol

In aqueous binary mixtures, amphiphilic solutes such as dimethylsulfoxide (DMSO), ethanol, tertbutyl alcohol (TBA), etc., are known to form aggregates (or large clusters) at small to intermediate solute concentrations. These aggregates are transient in nature. Although the system remains homogeneous on macroscopic length and time scales, the microheterogeneous aggregation may profoundly affect the properties of the mixture in several distinct ways, particularly if the survival times of the aggregates are longer than density relaxation times of the binary liquid. Here we propose a theoretical scheme to quantify the lifetime and thus the stability of these microheterogeneous clusters, and apply the scheme to calculate the same for water-ethanol, water-DMSO, and water-TBA mixtures. We show that the lifetime of these clusters can range from less than a picosecond (ps) for ethanol clusters to few tens of ps for DMSO and TBA clusters. This helps explaining the absence of a strong composition dependent anomaly in water-ethanol mixtures but the presence of the same in water-DMSO and water-TBA mixtures. (C) 2013 AIP Publishing LLC.

Functional specificity among yeast mitochondrial Hsp70s paralogs and orthologs

The evolutionary diversity of the HSP70 gene family at the genetic level has generated complex structural variations leading to altered functional specificity and mode of regulation in different cellular compartments. By utilizing Saccharomyces cerevisiae as a model system for better understanding the global functional cooperativity between Hsp70 paralogs, we have dissected the differences in functional properties at the biochemical level between mitochondrial heat shock protein 70 (mtHsp70) Ssc1 and an uncharacterized Ssc3 paralog. Based on the evolutionary origin of Ssc3 and a high degree of sequence homology with Ssc1, it has been proposed that both have a close functional overlap in the mitochondrial matrix. Surprisingly, our results demonstrate that there is no functional cross-talk between Ssc1 and Ssc3 paralogs. The lack of in vivo functional overlap is due to altered conformation and significant lower stability associated with Ssc3. The substrate-binding domain of Ssc3 showed poor affinity toward mitochondrial client proteins and Tim44 due to the open conformation in ADP-bound state. In addition to that, the nucleotide-binding domain of Ssc3 showed an altered regulation by the Mge1 co-chaperone due to a high degree of conformational plasticity, which strongly promotes aggregation. Besides, Ssc3 possesses a dysfunctional inter-domain interface thus rendering it unable to perform functions similar to generic Hsp70s. Moreover, we have identified the critical amino acid sequence of Ssc1 and Ssc3 that can “make or break” mtHsp70 chaperone function. Together, our analysis provides the first evidence to show that the nucleotide-binding domain of mtHsp70s plays a critical role in determining the functional specificity among paralogs and orthologs across kingdoms.

Remarkable Regioisomer Control in the Hydrogel Formation from a Two-Component Mixture of Pyridine-End Oligo(p-phenylenevinylene)s and N-Decanoyl-L-alanine

N-Decanoyl-L-alanine (DA) was mixed with either colorless 4,4-bipyridine (BP) or various derivatives such as chromogenic oligo(p-phenylenevinylene) (OPV) functionalized with isomeric pyridine termini in specific molar ratios. This mixtures form salt-type gels in a water/ethanol (2:1, v/v) mixture. The gelation properties of these two-component mixtures could be modulated by variation of the position of the N atom of the end pyridyl groups in OPVs. The presence of acid-base interactions in the self-assembly of these two-component systems leading to gelation was probed in detail by using stoichiometry-dependent UV/Vis and FTIR spectroscopy. Furthermore, temperature-dependent UV/Vis and fluorescence spectroscopy clearly demonstrated a J-type aggregation mode of these gelator molecules during the sol-to-gel transition process. Morphological features and the arrangement of the molecules in the gels were examined by using scanning electron microscopy (SEM), atomic force microscopy (AFM), and X-ray diffraction (XRD) techniques. Calculation of the length of each molecular system by energy minimization in its extended conformation and comparison with the XRD patterns revealed that this class of gelator molecules adopts lamellar organizations. Rheological properties of these two-component systems provided clear evidence that the flow behavior could be modulated by varying the acid/amine ratio. Polarized optical microscopy (POM), differential scanning calorimetry (DSC), and XRD results revealed that the solid-phase behavior of such two-component mixtures (acid/base=2:1) varied significantly upon changing the proton-acceptor part from BP to OPV. Interestingly, the XRD pattern of these acid/base mixtures after annealing at their associated isotropic temperature was significantly different from that of their xerogels.

In vitro Evidence that an Aqueous Extract of Centella asiatica Modulates alpha-Synuclein Aggregation Dynamics

alpha-Synuclein aggregation is one of the major etiological factors implicated in Parkinson's disease (PD). The prevention of aggregation of alpha-synuclein is a potential therapeutic intervention for preventing PD. The discovery of natural products as alternative drugs to treat PD and related disorders is a current trend. The aqueous extract of Centella asiatica (CA) is traditionally used as a brain tonic and CA is known to improve cognition and memory. There are limited data on the role of CA in modulating amyloid-beta (A beta) levels in the brain and in A beta aggregation. Our study focuses on CA as a modulator of the alpha-synuclein aggregation pattern in vitro. Our investigation is focused on: (i) whether the CA leaf aqueous extract prevents the formation of aggregates from monomers (Phase I: alpha-synuclein + extract co-incubation); (ii) whether the CA aqueous extract prevents the formation of fibrils from oligomers (Phase II: extract added after oligomers formation); and (iii) whether the CA aqueous extract disintegrates the pre-formed fibrils (Phase III: extract added to mature fibrils and incubated for 9 days). The aggregation kinetics are studied using a thioflavin-T assay, circular dichroism, and transmission electron microscopy. The results showed that the CA aqueous extract completely inhibited the alpha-synuclein aggregation from monomers. Further, CA extract significantly inhibited the formation of oligomer to aggregates and favored the disintegration of the preformed fibrils. The study provides an insight in finding new natural products for future PD therapeutics.

Green ionothermal synthesis of hierarchical nanostructures of SnS2 and their Li-ion storage properties

Flower-like hierarchical architectures of layered SnS2 have been synthesized ionothermally for the first time, using a water soluble EMIM]BF4 ionic liquid (IL) as the solvent medium. At lower reaction temperatures, the hierarchical structures are formed of few-layered polycrystalline 2D nanosheet-petals composed of randomly oriented nanoparticles of SnS2. The supramolecular networks of the IL serve as templates on which the nanoparticles of SnS2 are glued together by combined effects of hydrogen bonding, electrostatic, hydrophobic and imidazolium stacking interactions of the IL, giving rise to polycrystalline 2D nanosheet-petals. At higher reaction temperatures, single crystalline plate-like nanosheets with well-defined crystallographic facets are obtained due to rapid inter-particle diffusion across the IL. Efficient surface charge screening by the IL favors the aggregation of individual nanosheets to form hierarchical flower-like architectures of SnS2. The mechanistic aspects of the ionothermal bottom-up hierarchical assembly of SnS2 nanosheets are discussed in detail. Li-ion storage properties of the pristine SnS2 samples are examined and the electrochemical performance of the sample synthesized at higher temperatures is found to be comparable to that reported for pristine SnS2 samples in the literature.

Pristine and graphitized-MWCNTs as durable cathode-catalyst supports for PEFCs

Long-term deterioration in the performance of PEFCs is attributed largely to reduction in active area of the platinum catalyst at cathode, usually caused by carbon-support corrosion. Multi-walled carbon-nanotubes (MWCNTs) as cathode-catalyst support are found to enhance long-term stability of platinum catalyst (Pt) in relation to non-graphitic carbon. In addition, highly graphitic MWCNTs (G-MWCNTs) are found to be electrochemically more stable than pristine MWCNTs. This is because graphitic-carbon-supported-Pt (Pt/MWCNTs) cathodes exhibit higher resistance to carbon corrosion in-relation to non-graphitic-carbon-supported-Pt (Pt/C) cathodes in PEFCs during accelerated stress-test (AST) as evidenced by chronoamperometry and carbon dioxide studies. The corresponding change in electrochemical surface area (ESA), cell performance, and charge-transfer resistance are monitored through cyclic voltammetry, cell polarization, and impedance measurements, respectively. The extent of crystallinity, namely amorphous or graphitic nature of the three supports, is examined by Raman spectroscopy. X-ray diffraction and transmission electron microscopy studies both prior and after AST suggest lesser deformation in catalyst layer and catalyst particles for Pt/G-MWCNTs and Pt/MWCNTs cathodes in relation to Pt/C cathodes, reflecting that graphitic carbon-support resists carbon corrosion and helps mitigating aggregation of Pt particles. It is also found that with increasing degree of graphitization, the electrochemical stability for MWCNTs increases due to the lesser surface defects.

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with x(TBA) approximate to 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at x(TBA) approximate to 0.05. We note that ``islands'' of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, x(TBA) approximate to 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level. (C) 2014 AIP Publishing LLC.

Insights into the AIEE of 1,8-Naphthalimides (NPIs): Inverse Effects of Intermolecular Interactions in Solution and Aggregates

Systematic structural perturbation has been used to fine-tune and understand the luminescence properties of three new 1,8-naphthalimides (NPIs) in solution and aggregates. The NPIs show blue emission in the solution state and their fluorescence quantum yields are dependent upon their molecular rigidity. In concentrated solutions of the NPIs, intermolecular interactions were found to quench the fluorescence due to the formation of excimers. In contrast, upon aggregation (in THF/H2O mixtures), the NPIs show aggregation-induced emission enhancement (AIEE). The NPIs also show moderately high solid-state emission quantum yields (ca. 10-12.7 %). The AIEE behaviour of the NPIs depends on their molecular rigidity and the nature of their intermolecular interactions. The NPIs 1-3 show different extents of intermolecular (pi-pi and C-H center dot center dot center dot O) interactions in their solid-state crystal structures depending on their substituents. Detailed photophysical, computational and structural investigations suggest that an optimal balance of structural flexibility and intermolecular communication is necessary for achieving AIEE characteristics in these NPIs.

Hydrophobic hydration driven self-assembly of curcumin in water: Similarities to nucleation and growth under large metastability, and an analysis of water dynamics at heterogeneous surfaces

As the beneficial effects of curcumin have often been reported to be limited to its small concentrations, we have undertaken a study to find the aggregation properties of curcumin in water by varying the number of monomers. Our molecular dynamics simulation results show that the equilibrated structure is always an aggregated state with remarkable structural rearrangements as we vary the number of curcumin monomers from 4 to 16 monomers. We find that the curcumin monomers form clusters in a very definite pattern where they tend to aggregate both in parallel and anti-parallel orientation of the phenyl rings, often seen in the formation of beta-sheet in proteins. A considerable enhancement in the population of parallel alignments is observed with increasing the system size from 12 to 16 curcumin monomers. Due to the prevalence of such parallel alignment for large system size, a more closely packed cluster is formed with maximum number of hydrophobic contacts. We also follow the pathway of cluster growth, in particular the transition from the initial segregated to the final aggregated state. We find the existence of a metastable structural intermediate involving a number of intermediate-sized clusters dispersed in the solution. We have constructed a free energy landscape of aggregation where the metatsable state has been identified. The course of aggregation bears similarity to nucleation and growth in highly metastable state. The final aggregated form remains stable with the total exclusion of water from its sequestered hydrophobic core. We also investigate water structure near the cluster surface along with their orientation. We find that water molecules form a distorted tetrahedral geometry in the 1st solvation layer of the cluster, interacting rather strongly with the hydrophilic groups at the surface of the curcumin. The dynamics of such quasi-bound water molecules near the surface of curcumin cluster is considerably slower than the bulk signifying a restricted motion as often found in protein hydration layer. (C) 2014 AIP Publishing LLC.

Covalent assembly-disassembly of poly(ether imine) dendritic macromolecular monomers and megamers

Poly(ether imine) dendritic macromolecules were undertaken to study the reversible dendrimer monomer-megamer assembly-disassembly in aqueous solutions. Synthesis of thiol functionalized poly(ether imine) (PETIM) dendrimers and their covalent aggregation behavior in the aqueous solution of ethanol/water (2:1) is demonstrated. The dendritic megamers were characterized using microscopic techniques. Kinetics of the aggregation behavior was followed using turbidity measurements, light-scattering and atomic force microscopic techniques. Inherent luminescence behavior of PETIM dendrimer monomers was retained in the dendrimer megamers also, which allowed visualization of the megamers through confocal microscopy. Extent of thiol functionalities that remained after the megamer assembly was estimated through Ellman's assay. Subsequent to megamer assembly, disassembly of megamers to dendrimer monomers was conducted, using dithiothreitol reagent. Water-insoluble sudan I dye was encapsulated in dendrimer megamer and subsequent release profile was assessed during the disassembly in aqueous solutions. The studies were conducted using first, second and third generations, representing 4, 8 and 16 sulfhydryl groups at their peripheries of dendrimers, respectively. (C) 2014 Elsevier Ltd. All rights reserved.