@article { ISI:000348265400007,
	title = {Genome-wide identification and structure-function studies of proteases and protease inhibitors in cicer arietinum (chickpea)},
	journal = {Computers in Biology and Medicine},
	volume = {56},
	year = {2015},
	month = {JAN},
	pages = {67-81},
	publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
	address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
	abstract = {<p>Background: Proteases are a family of enzymes present in almost all living organisms. In plants they are involved in many biological processes requiring stress response in situations such as water deficiency, pathogen attack, maintaining protein content of the cell, programmed cell death, senescence, reproduction and many more. Similarly, protease inhibitors (PIs) are involved in various important functions like suppression of invasion by pathogenic nematodes, inhibition of spores-germination and mycelium growth of Alternaria alternata and response to wounding and fungal attack. As much as we know, no genome-wide study of proteases together with proteinaceous PIs is reported in any of the sequenced genomes till now. Methods: Phylogenetic studies and domain analysis of proteases were carried out to understand the molecular evolution as well as gene and protein features. Structural analysis was carried out to explore the binding mode and affinity of PIs for cognate proteases and prolyl oligopeptidase protease with inhibitor ligand. Results: In the study reported here, a significant number of proteases and PIs were identified in chickpea genome. The gene expression profiles of proteases and Pis in five different plant tissues revealed a differential expression pattern in more than one plant tissue. Molecular dynamics studies revealed the formation of stable complex owing to increased number of protein-ligand and inter and intramolecular protein-protein hydrogen bonds. Discussion: The genome-wide identification, characterization, evolutionary understanding, gene expression, and structural analysis of proteases and Pis provide a framework for future analysis when defining their roles in stress response and developing a more stress tolerant variety of chickpea. (C) 2014 Elsevier Ltd. All rights reserved.</p>},
	keywords = {Domain, Gene expression, Genome analysis, Homology modelling, Molecular docking, molecular dynamics simulation, Motif, Orthologs, Phylogeny},
	issn = {0010-4825},
	doi = {10.1016/j.compbiomed.2014.10.019},
	author = {Sharma, Ranu and Suresh, C. G.}
}
@article {47070,
	title = {Molecular characterization of the beta(2)-like octopamine receptor of helicoverpa armigera},
	journal = {Journal of Membrane Biology},
	volume = {254},
	year = {2021},
	month = {JUN},
	type = {Article},
	abstract = {<p>Helicoverpa armigera is a devastating polyphagous and cosmopolitan crop pest. There are reports of this insect being resistant to a variety of pesticides raising concern worldwide. The Octopamine (OA) binding beta(2)-like receptor (OAR), a GPCR, is widely distributed in the nervous system of the insect and plays essential roles in the physiology and development and thus is an important target for insecticides. Yet, the molecular characterization of the H. armigera OAR (HarmOAR) and rational design of compounds based on this receptor is lacking. As a first step, we performed multiple sequence alignment of all insect OARs, which revealed that the sequences contained all conserved class A GPCR motifs. Phylogenetic studies showed clade-specific variations in the protein sequences primarily arising owing to differences in the ICL3 loop region. Further, a structural model of HarmOAR was built using the inactive human beta(2)AR as a template. 0.9 mu s atomistic simulations revealed conserved inter helical contacts and water molecules of HarmOAR. The detailed binding of octopamine was studied using molecular docking and 0.3 mu s atomistic simulations. Twenty-two insecticides active against octopamine receptors of other insects were compiled and docked to HarmOAR followed by rescoring with binding free energies to prioritize them for H. armigera. Our study suggests alpha-terpineol to be a good candidate as an insecticide or insect repellent for Helicoverpa armigera.</p>
},
	keywords = {docking, Helicoverpa armigera, Insecticides, molecular dynamics, Octopamine receptor, Phylogeny},
	issn = {0022-2631},
	doi = {10.1007/s00232-021-00172-3, Early Access Date = FEB 2021},
	author = {Gujar, Nidhi and Nikte, V, Siddhanta and Joshi, Rakesh S. and Joshi, Manali}
}
