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Chakraborty S.,Tougaloo College | Chakraborty S.,Saroj Mohan Institute of Technology | Levenson A.S.,University of Mississippi Medical Center | Biswas P.K.,Tougaloo College
BMC Structural Biology | Year: 2013

Background: Resveratrol, a naturally occurring stilbene, has been categorized as a phytoestrogen due to its ability to compete with natural estrogens for binding to estrogen receptor alpha (ERα) and modulate the biological responses exerted by the receptor. Biological effects of resveratrol (RES) on estrogen receptor alpha (ERα) remain highly controversial, since both estrogenic and anti-estrogenic properties were observed. Results: Here, we provide insight into the structural basis of the agonist/antagonist effects of RES on ERα ligand binding domain (LBD). Using atomistic simulation, we found that RES bound ERα monomer in antagonist conformation, where Helix 12 moves away from the ligand pocket and orients into the co-activator binding groove of LBD, is more stable than RES bound ERα in agonist conformation, where Helix 12 lays over the ligand binding pocket. Upon dimerization, the agonistic conformation of RES-ERα dimer becomes more stable compared to the corresponding monomer but still remains less stable compared to the corresponding dimer in antagonist conformation. Interestingly, while the binding pocket and the binding contacts of RES to ERα are similar to those of pure agonist diethylstilbestrol (DES), the binding energy is much less and the hydrogen bonding contacts also differ providing clues for the partial agonistic character of RES on ERα. Conclusions: Our Molecular Dynamics simulation of RES-ERα structures with agonist and antagonist orientations of Helix 12 suggests RES action is more similar to Selective Estrogen Receptor Modulator (SERM) opening up the importance of cellular environment and active roles of co-regulator proteins in a given system. Our study reveals that potential co-activators must compete with the Helix 12 and displace it away from the activator binding groove to enhance the agonistic activity. © 2013 Chakraborty et al.; licensee BioMed Central Ltd. Source


Banerjee A.,Jadavpur University | Rahaman F.,Jadavpur University | Jotania K.,M. S. University of Baroda | Sharma R.,P.A. College | Karar I.,Saroj Mohan Institute of Technology
General Relativity and Gravitation | Year: 2013

The Bañados et al. (Phys Rev Lett 69:1849, 1992) solution corresponding to the exterior space-time of a black hole in (2+1) dimensions has been found to be very useful to understand various aspects relating to the gravitational field of a black hole. We present here a class of interior solutions corresponding to the BTZ exterior by making use of a model presented by Finch and Skea (Class Quantum Grav 6:467, 1989) which was earlier found to be relevant for the description realistic stars in (3+1) dimensions. We show physical viability of the model in lower dimensions as well. © 2013 Springer Science+Business Media New York. Source


Chakraborty S.,Saroj Mohan Institute of Technology | Kumar S.,Jadavpur University | Basu S.,Maulana Abul Kalam Azad University of Technology
Neurochemistry International | Year: 2011

BACE1 is a key protease involved in the proteolysis of amyloid precursor protein (APP) that generates a toxic peptide amyloid beta (Aβ), a pathological feature of Alzheimer's disease (AD). The enzyme is believed to possess an open and a closed conformation that corresponds to its free and inhibitor-bound form respectively. Here, we study the dynamic transition of BACE1 employing normal mode analysis (NMA) using a simplified elastic network model (ENM). Estimation of the catalytic cavity volume on the structures of BACE1 encoded by the lowest frequency normal mode reveals the dynamical transition of the enzyme from the open to the closed conformer. Detailed analysis reveals that concerted movement of different loop segments in the active site of the protein, namely flap regions, 10s loop, A loop and F loop, squeeze the catalytic cavity between the N-terminal and C-terminal lobe of the substrate binding domain of BACE1. We also propose that the NMA encoded multiple receptor conformations (MRC) of BACE1 elucidate the pharmacophoric feature necessary to inhibit the enzyme by a polyphenol, myricetin. van der Waals interaction is found to be the main driving force that guides the ligand induced conformational switching to the closed conformer. We suggest that NMA derived MRC of BACE1 is an efficient way to treat the receptor flexibility in docking and thus can be further applied in virtual screening and structure based drug design. © 2011 Elsevier Ltd. Source


Mukherjee B.,Kalna College | Mukherjee M.,Saroj Mohan Institute of Technology
Langmuir | Year: 2011

Fabrication of high-performance organic thin film transistors (OTFTs) with solution processed organic charge transfer complex (TTF-TCNQ) film as bottom contact source-drain electrodes is reported. A novel capillary based method was used to deposit the source-drain electrodes from solution and to create the channel between the electrodes. Both p- and n-type OTFTs have been fabricated with solution deposited organic charge transfer film as contact electrodes. Comparison of the device performances between OTFTs with TTF-TCNQ as source-drain electrodes and those with Au electrodes (both top and bottom contact) indicate that better results have been obtained in organic complex film contacted OTFT. The high mobility, low threshold voltage, and efficient carrier injection in both types of OTFTs implies the potential use of the TTF-TCNQ based complex material as low-cost contact electrodes. The lower work function of the TTF-TCNQ electrode and better contact of the complex film with the organic thin film owing to the organic-organic interface results in efficient charge transfer into the semiconductor yielding high device performance. The present method having organic metal as contact materials promises great potential for the fabrication of all-organics and plastic electronics devices with high throughput and low-cost processing. © 2011 American Chemical Society. Source


Das R.K.,Saroj Mohan Institute of Technology
Ultrasonics Sonochemistry | Year: 2015

The effects of both acid (acetic acid) and base (ammonia) catalysts in varying on the sol-gel synthesis of SiO2 nanoparticles using tetra ethyl ortho silicate (TEOS) as a precursor was determined by ultrasonic method. The ultrasonic velocity was received by pulsar receiver. The ultrasonic velocity in the sol and the parameter ΔT (time difference between the original pulse and first back wall echo of the sol) was varied with time of gelation. The graphs of ln[ln 1/ΔT] vs ln(t), indicate two region - nonlinear region and a linear region. The time corresponds to the point at which the non-linear region change to linear region is considered as gel time for the respective solutions. Gelation time is found to be dependent on the concentration and types of catalyst and is found from the graphs based on Avrami equation. The rate of condensation is found to be faster for base catalyst. The gelation process was also characterized by viscosity measurement. Normal sol-gel process was also carried out along with the ultrasonic one to compare the effectiveness of ultrasonic. The silica gel was calcined and the powdered sample was characterized with scanning electron microscopy, energy dispersive spectra, X-ray diffractogram, and FTIR spectroscopy. © 2014 Elsevier B.V. Source

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