Siddhartha Banerjee

Bio: Siddhartha Banerjee is an academic researcher from University of Nebraska Medical Center. The author has contributed to research in topics: Lipid bilayer & Bilayer. The author has an hindex of 11, co-authored 28 publications receiving 360 citations. Previous affiliations of Siddhartha Banerjee include Indian Association for the Cultivation of Science.

Nanoscale Dynamics of Amyloid β-42 Oligomers As Revealed by High-Speed Atomic Force Microscopy

Abstract: Amyloid β-protein (Aβ) oligomers are emerging as potent neurotoxic species in Alzheimer's disease pathogenesis. Detailed characterization of oligomer structure and dynamics is necessary to develop oligomer-specific therapeutic agents. However, oligomers exist transiently, which complicates their structural analysis. One approach to mitigate these problems has been photochemical cross-linking of native oligomers. In these states, the oligomers can be isolated and purified for physical and chemical studies. Here we characterized the structure of isolated cross-linked Aβ42 trimers, pentamers, and heptamers with atomic force microscopy (AFM) imaging and probed their dynamics in solution using time-lapse high-speed AFM. This technique enables visualization of the structural dynamics of the oligomers at nanometer resolution on a millisecond time scale. Results demonstrate that cross-linked pentamers and heptamers are very dynamic fluctuating between a compact single-globular and multiglobular assemblies. Trimers remain in their single-globular geometry that elongates adopting an ellipsoidal shape. Biological significance of oligomers dynamics is discussed.

Ethyl(hydroxyethyl)cellulose stabilized polyaniline dispersions and destabilized nanoparticles therefrom

Abstract: Ethyl(hydroxyethyl)cellulose (EHEC) has been used as a stabilizer for the dispersion polymerization of aniline in water and in aqueous ethanols. An increasingly greater amount of aniline could be used to prepare the dispersion as the ethanol concentration increased in the medium over the range 50−70 vol %. EHEC incorporation in the particles increases and particle size decreases with an increase in the ethanol concentration under otherwise identical experimental conditions. Particles prepared in aqueous ethanols and containing less than ca. 8 wt % EHEC are easily disintegrated to nanoparticles (∼20 nm) using ultrasound. These nanoparticles are unstabilized and undergo fractal aggregation even in a medium that contains a substantial amount of EHEC. This fact suggests that in the dispersion polymerization the real stabilizer is not the homopolymer EHEC but could be its graft copolymer. The fractal dimension (D) of the aggregates lies in the range 1.69−1.89. These values agree well with the theoretically det...

A novel pathway for amyloids self-assembly in aggregates at nanomolar concentration mediated by the interaction with surfaces.

Abstract: A limitation of the amyloid hypothesis in explaining the development of neurodegenerative diseases is that the level of amyloidogenic polypeptide in vivo is below the critical concentration required to form the aggregates observed in post-mortem brains. We discovered a novel, on-surface aggregation pathway of amyloidogenic polypeptide that eliminates this long-standing controversy. We applied atomic force microscope (AFM) to demonstrate directly that on-surface aggregation takes place at a concentration at which no aggregation in solution is observed. The experiments were performed with the full-size Aβ protein (Aβ42), a decapeptide Aβ(14-23) and α-synuclein; all three systems demonstrate a dramatic preference of the on-surface aggregation pathway compared to the aggregation in the bulk solution. Time-lapse AFM imaging, in solution, show that over time, oligomers increase in size and number and release in solution, suggesting that assembled aggregates can serve as nuclei for aggregation in bulk solution. Computational modeling performed with the all-atom MD simulations for Aβ(14-23) peptide shows that surface interactions induce conformational transitions of the monomer, which facilitate interactions with another monomer that undergoes conformational changes stabilizing the dimer assembly. Our findings suggest that interactions of amyloidogenic polypeptides with cellular surfaces play a major role in determining disease onset.

Nanoscale dynamics of centromere nucleosomes and the critical roles of CENP-A.

Abstract: In the absence of a functioning centromere, chromosome segregation becomes aberrant, leading to an increased rate of aneuploidy. The highly specific recognition of centromeres by kinetochores suggests that specific structural characteristics define this region, however, the structural details and mechanism underlying this recognition remains a matter of intense investigation. To address this, high-speed atomic force microscopy was used for direct visualization of the spontaneous dynamics of CENP-A nucleosomes at the sub-second time scale. We report that CENP-A nucleosomes change conformation spontaneously and reversibly, utilizing two major pathways: unwrapping, and looping of the DNA; enabling core transfer between neighboring DNA substrates. Along with these nucleosome dynamics we observed that CENP-A stabilizes the histone core against dissociating to histone subunits upon unwrapping DNA, unique from H3 cores which are only capable of such plasticity in the presence of remodeling factors. These findings have implications for the dynamics and integrity of nucleosomes at the centromere.

Dielectric dispersion and ac conductivity in—Iron particles loaded—polymer composites

Abstract: Polymer composites of an epoxy resin matrix with randomly dispersed Iron micro-particles in various amounts were prepared and their dielectric spectra were measured in the frequency range 5 Hz–13 MHz and temperature interval from ambient to 140 °C. Obtained data were analysed by means of electric modulus formalism. Interfacial or Maxwell-Wagner-Sillars relaxation process was revealed in the frequency range and temperature interval of the measurements, which was found to follow the Cole-Davidson approach for the distribution of relaxation times. The examined systems exhibit strong dispersion with frequency. At low frequencies ac conductivity tends to be constant, while at higher becomes frequency dependent varying as a power of frequency. Conductivity increases with temperature in the low frequency regime, remaining almost unaffected at higher frequencies.

Hopping conductivity in polymer matrix–metal particles composites

Abstract: Charge transport properties, such as the temperature dependent dc conductivity and the frequency dependent conductance, of polymer matrix–metal particles composites, are investigated in the present study. Dc and ac conductivity is examined with varying parameters the filler content, temperature and the frequency in the case of ac field. The examined systems, though they are characterized as dielectrics, exhibit considerable conductivity, which alters by several orders of magnitude with temperature and frequency. The temperature and frequency dependence of conductivity gives evidence for the charge carriers transport mechanism via the occurred agreement of experimental results with the employed hopping models (variable range hopping model and random free-energy barrier model).

Preparation of Polyaniline Nanoparticles in Micellar Solutions as Polymerization Medium

Abstract: Chemical oxidative polymerization of aniline was studied in a conventional aqueous solution and in micellar solutions of sodium dodecyl sulfate (SDS, anionic surfactant) and nonylphenol ethoxylate(9) (NP-9, nonionic surfactant) to investigate the effect of molecular structure of surfactants on the polymerization kinetics and particle size. The polymerization kinetics in NP-9 micellar solution were very slow, and this result was explained based on the structural characteristics of surfactant. SDS micellar solutions resulted in a highly transparent solution without any precipitates, whereas some precipitates were visually observed in the NP-9 micellar solution after the reaction finished. The electrical conductivities of polyaniline pellets formed with particles prepared in SDS and NP-9 micellar solutions and aqueous solution showed about 20, 4, and 4 S/cm, respectively. The highest electrical conductivity of particles from SDS micellar solution might be due to the smallest size of particles and the highest...