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Kadam K.,University of Pune | Prabhakar P.,Dr Dy Patil Biotechnology And Bioinformatics Institute | Jayaraman V.K.,University of Pune
Protein and Peptide Letters | Year: 2012

Bacterial lipoproteins play critical roles in various physiological processes including the maintenance of pathogenicity and numbers of them are being considered as potential candidates for generating novel vaccines. In this work, we put forth an algorithm to identify and predict ligand-binding sites in bacterial lipoproteins. The method uses three types of pocket descriptors, namely fpocket descriptors, 3D Zernike descriptors and shell descriptors, and combines them with Support Vector Machine (SVM) method for the classification. The three types of descriptors represent shape-based properties of the pocket as well as its local physio-chemical features. All three types of descriptors, along with their hybrid combinations are evaluated with SVM and to improve classification performance, WEKA-InfoGain feature selection is applied. Results obtained in the study show that the classifier successfully differentiates between ligand-binding and non-binding pockets. For the combination of three types of descriptors, 10 fold cross-validation accuracy of 86.83% is obtained for training while the selected model achieved test Matthews Correlation Coefficient (MCC) of 0.534. Individually or in combination with new and existing methods, our model can be a very useful tool for the prediction of potential ligand-binding sites in bacterial lipoproteins. © 2012 Bentham Science Publishers.

Grace S.V.,Dr Dy Patil Biotechnology And Bioinformatics Institute | Murab S.,Indian Institute of Technology Delhi | Krupadam R.J.,Indian National Environmental Engineering Research Institute
Journal of Hazardous, Toxic, and Radioactive Waste | Year: 2012

A polymer adsorbent specific for 17β-estradiol (E2) was prepared by using a molecular imprinting technique. E2 is a female hormone (i.e., estrogen) and it has been recently reported in drinking water resources. In this paper, the writers present a method for the remediation of E2 in ground water by using a molecularly imprinted polymer (MIP) adsorbent. The molecular modeling software (HyperChem 8.0) was used to select best polymer precursors for polymer preparation on the basis of interaction energy scorings. The scanning electron microscopy (SEM) and transmission electron microscopy (TEM) micrographs revealed the existence of nanopores (0.65 to 0.8 nm in diameter) in the polymer because of imprinting. The Fourier transform infrared (FT-IR) spectra of the MIP and non-imprinted polymer (NIP) further confirmed an H-bond formation between the carboxylic acid group of methacrylic acid (MAA) and E2, which was responsible for the selective adsorption of E2. The adsorption capacity and binding affinity of the MIP were determined by using Langmuir and Freundlich isotherm models. The adsorption capacity of the MIP was 96.75 mg/g this value is twice that of the commercially used activated carbon. The effect of environmental parameters [such as total dissolved solids (TDS) and pH] on the adsorption removal of E2 was studied for water and for groundwater samples collected from industrial areas. In this study, the writer report, for the first time, the reusability of an MIP adsorbent that retains its adsorption capacity for more than eight cycles. High adsorption capacity and resistance to environmental parameters such as TDS and pH demonstrated the merits of MIP over the single use of activated carbon for the remediation of E2-contaminated water. © 2012 American Society of Civil Engineers.

Karthikeyan M.,CSIR - National Chemical Laboratory | Vyas R.,Dr Dy Patil Biotechnology And Bioinformatics Institute
Methods in Molecular Biology | Year: 2012

Efficient storage and retrieval of chemical structures is one of the most important prerequisite for solving any computational-based problem in life sciences. Several resources including research publications, text books, and articles are available on chemical structure representation. Chemical substances that have same molecular formula but several structural formulae, conformations, and skeleton framework/scaffold/functional groups of the molecule convey various characteristics of the molecule. Today with the aid of sophisticated mathematical models and informatics tools, it is possible to design a molecule of interest with specified characteristics based on their applications in pharmaceuticals, agrochemicals, biotechnology, nanomaterials, petrochemicals, and polymers. This chapter discusses both traditional and current state of art representation of chemical structures and their applications in chemical information management, bioactivity- and toxicity-based predictive studies. © 2012 Springer Science+Business Media, LLC.

Purushe S.,University of Pune | Prakash D.,University of Pune | Nawani N.N.,Dr Dy Patil Biotechnology And Bioinformatics Institute | Dhakephalkar P.,Agharkar Research Institute | Kapadnis B.,University of Pune
Bioresource Technology | Year: 2012

The present study is focused on dextranase from Streptomyces sp. NK458 with potential to remove dextran formed during sugar manufacture. The dextranase had molecular weight of 130kDa and hydrolyzed 15-25 and 410kDa dextran. Dextranase production was optimized using statistical designs and the enzyme was purified 1.8-fold with 55.5% recovery. It displayed maximum activity at pH 9.0 and 60°C and was stable over a wide range of pH from 5.0 to 10.0. The k m and V max values were 3.05mM and 17.97mmol/ml/h, respectively. Ten units of dextranase could reduce dextran content by 67% in 24h and 56% in 72h from sugarcane juice of cane variety CoS 86032. The enzyme was stable up to 3days at 30°C beyond which its activity decreased and dextran removal could be retained by supplementation of 5U of dextranase. These properties make it a promising biocatalyst for sugar industry. © 2012 Elsevier Ltd.

Namde H.,Dr Dy Patil Biotechnology And Bioinformatics Institute | Wani M.,Dr Dy Patil Biotechnology And Bioinformatics Institute
Research Journal of Pharmaceutical, Biological and Chemical Sciences | Year: 2014

Tecoma stans is a tropical flowering plant which is used in herbal medicine treatment for diabetes, digestive problems etc. The present investigation was carried out to study the effect of different plant growth regulators on callus induction from Tecoma leaves and to compare the antioxidant activity from the leaves and in vitro generated callus. Qualitative analysis of phytochemicals from the leaves of T. stans were done using different solvents. Callus culture were initiated from leaf explants on Murashige and Skoog medium supplemented with different concentrations and combinations of hormones like 2,4-D, NAA, BAP and Kinetin for rapid initiation of callus and biomass production. To study the antioxidant activity the effect of leaf extract on 2, 2-diphenyl-1-picrylhdrazyl (DPPH) free radical was measured. The best efficiency of callusing was observed when 2,4-D and BAP in 2mg/l concentration each were used which was followed by 2,4-D and Kinetin. Methanolic and ethanolic leaf extract indicated higher antioxidant activity than the callus extract. In vitro studies and production of biomass and extraction of bioactive compounds may contribute in conservation management of naturally grown plants.

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