Computational studies on Membrane Proteins (bovine CNGA1 & mouse TSPO)

Around thirty percent of total proteins are present in the membrane and play an important role to communicate intracellular and extracellular region. Their presence in the membrane is one of the limiting steps to determine protein structure and to understand their mechanisms. Hence bioinformatics techniques and computational tools play an important role to overcome these issues in characterizing the structural/functional mechanism of membrane proteins. In this thesis, I have developed and used state of the art computational techniques applied to two different pharmaceutically relevant membrane proteins, Cyclic nucleotide-gated channels (CNG) and translocator membrane protein (TSPO). CNG ion channels are embedded into the neuronal membrane. Till date, the structure and their gating mechanism are subject to interest. Different approaches like electrophysiology, single molecule force spectroscopy, biophysics, etc. have been employed to study these channels. Here I studied the gating mechanism of the CNGA1 ion channel by use of homology modeling and coarse-grained molecular dynamics. TSPO is a key biomarker for the diagnostics of inflammation in the brain. Limited Structural and functional information available on mammalian TSPOs homodimers. Computational studies suggested that the NMR-solved structure is not prone to dimer formation and is not stable in a membrane environment and has been an object of vivid criticism. To address this issue we use homology modeling technique and molecular dynamics approach. Principle results are: 1. I have successfully created homology models for CNGA1 homotetramer and performed coarse-grained simulation in the presence and absence of cGMP molecule and developed the coarse-grained force-field parameters for cGMP. 2. I have proposed a new model of the functionally relevant dimeric form of mTSPO. The model is fully consistent with solid-state NMR spectral data. Our predictions provide for the first time structural insights on this pharmaceutically important target fully consistent with experimental data. 3. During these studies, and in order to optimize the preparation of the systems it was necessary to develop an automated tool for creating the input files for doing coarse-grained simulations. These tools are shared with the community through a publically available online web-server that simplifies the task of generating input files which help in performing simulation and retrieving the result data for small simulations. The web-server, MERMAID is available at MERMAID (http://molsim.sci.univr.it/mangesh/). The application of novel computational approaches in this thesis allowed me to characterize extensively both systems by offering a rational to a huge amount of experimental data on biological relevant systems

MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics

Atomistic molecular dynamics simulations of membrane proteins have been shown to be extremely useful for characterizing the molecular features underlying their function, but require high computational power, limiting the understanding of complex events in membrane proteins, e.g. ion channels gating, GPCRs activation. To overcome this issue, it has been shown that coarse-grained approaches, although requiring less computational power, are still capable of correctly describing molecular events underlying big conformational changes in biological systems. Here, we present the Martini coarse-grained membrane protein dynamics (MERMAID), a publicly available web interface that allows the user to prepare and run coarse-grained molecular dynamics (CGMD) simulations and to analyse the trajectories

Sustainable Concrete by Partially Replacing Coarse Aggregate Using Coconut Shell

A common feature of sustainable buildings is that they drastically reduce emissions, material use and water use and with involvement of economic vitality, environmental, health, and social equity in it. As a whole, the study main concern is the environment and the construction and building technology to enhance natural world as well as building materials. In view to provide new knowledge to the contractors and developers on how to improve the construction industry methods and services by using coconut shells and to sustain good product performance and meet recycling goals, there is need to design a technical specification of concrete using coconut shell as aggregates that will meet the Indian standard requirements in order to help contribute to the industry in saving the environment, to encourage the government to find solutions regarding the disposal to landfills of waste materials and save the environment. The use of coconut by products has been a long time source of income for some people. Recycling of the disposed material is one method of treating the agricultural waste. The used of coconut shell could be a valuable substitute in the formation of composite material that can be used as a housing construction,such as concrete

Fermentation, Isolation, Structure, and antidiabetic activity of NFAT-133 produced by Streptomyces strain PM0324667

Type-2 diabetes is mediated by defects in either insulin secretion or insulin action. In an effort to identify extracts that may stimulate glucose uptake, similar to insulin, a high throughput-screening assay for measuring glucose uptake in skeletal muscle cells was established. During the screening studies to discover novel antidiabetic compounds from microbial resources a Streptomyces strain PM0324667 (MTCC 5543, the Strain accession number at Institute of Microbial Technology, Chandigarh, India), an isolate from arid soil was identified which expressed a secondary metabolite that induced glucose uptake in L6 skeletal muscle cells. By employing bioactivity guided fractionation techniques, a tri-substituted simple aromatic compound with anti-diabetic potential was isolated. It was characterized based on MS and 2D NMR spectral data and identified as NFAT-133 which is a known immunosuppressive agent that inhibits NFAT-dependent transcription in vitro. Our investigations revealed the antidiabetic potential of NFAT-133. The compound induced glucose uptake in differentiated L6 myotubes with an EC50 of 6.3 ± 1.8 μM without activating the peroxisome proliferator-activated receptor-γ. Further, NFAT-133 was also efficacious in vivo in diabetic animals and reduced systemic glucose levels. Thus it is a potential lead compound which can be considered for development as a therapeutic for the treatment of type-2 diabetes. We have reported herewith the isolation of the producer microbe, fermentation, purification, in vitro, and in vivo antidiabetic activity of the compound

DATA MINING USING AGGLOMERATIVE MEAN SHIFT CLUSTERING WITH EUCLIDEAN DISTANCE

Agglomerative clustering is a non parametric clustering technique. In the present paper an approach agglomerative mean shift clustering applied to a text document using a query compression technique Clustering is presented. Here a distance based technique is developed. Two types of distances one for document and one for Query are made use of. Euclidean distance is used for finding query distance between two terms.The results achieved are comparable to other distance methods showing better time and distance accuracy than the existing system. A method entitled ‘Cluster analysis ’ comprises of a grouping of allied techniques which are used to classify objects or cases of a domain into relatively like groups i.e a cluster. Each Object in a cluster tends to be similar in characteristics and different to objects in other clusters. Analysis done on Clusters is called classification analysis and is based on numerical taxonomy.[1

Importance of Gliricidia in soil Fertility management(Marathi Version)

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Preparation and Characterization of Rodent Intestinal Microsomes: Comparative Assessment of Two Methods

Small intestine plays an important role in the first-pass metabolism of orally ingested xenobiotics as a result of expression of both Phase I and Phase II metabolic enzymes, together with associated transporters. Intestinal microsomes thus can be used to study susceptibility of compounds to metabolism in vitro. The present study was undertaken to have a comparative assessment between different methods of preparation of rodent intestinal microsomes. Mouse and rat intestinal microsomes were prepared by two methods, in method A intestines were homogenized, while in method B mucosal cells were scrapped followed by homogenization. Further, microsomes were prepared by centrifugation (10000xg) followed by ultra centrifugation (100000×g) of the homogenates. The prepared microsomes were characterized for protein concentration using Bradford's method and CYP450 content using carbon monoxide bubbling method. The protein concentration and CYP450 content in microsomes prepared by method B was significantly higher than method A. In conclusion, superior quality intestinal microsomes can be obtained from rodents by using scrapped intestinal mucosal cells as compared to the intestinal homogenates

Nutrient Management in Ber (Zizyphus jujube)(Marathi Version)

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Nutrient management in custard apple(Marathi Version)

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Nutrient Management in Aonla(Marathi Version)

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