@article { ISI:000353720700004,
	title = {Distinct molecular features facilitating ice-binding mechanisms in hyperactive antifreeze proteins closely related to an Antarctic sea ice bacterium},
	journal = {Journal of Biomolecular Structure \& Dynamics},
	volume = {33},
	number = {7},
	year = {2015},
	month = {JUL},
	pages = {1424-1441},
	publisher = {TAYLOR \& FRANCIS INC},
	address = {530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA},
	abstract = {<p>Antifreeze proteins or ice-binding proteins (IBPs) facilitate the survival of certain cellular organisms in freezing environment by inhibiting the growth of ice crystals in solution. Present study identifies orthologs of the IBP of Colwellia sp. SLW05, which were obtained from a wide range of taxa. Phylogenetic analysis on the basis of conserved regions (predicted as the {\textquoteleft}ice-binding domain{\textquoteright} [IBD]) present in all the orthologs, separates the bacterial and archaeal orthologs from that of the eukaryotes{\textquoteright}. Correspondence analysis pointed out that the bacterial and archaeal IBDs have relatively higher average hydrophobicity than the eukaryotic members. IBDs belonging to bacterial as well as archaeal AFPs contain comparatively more strands, and therefore are revealed to be under higher evolutionary selection pressure. Molecular docking studies prove that the ice crystals form more stable complex with the bacterial as well as archaeal proteins than the eukaryotic orthologs. Analysis of the docked structures have traced out the ice-binding sites (IBSs) in all the orthologs which continue to facilitate ice-binding activity even after getting mutated with respect to the well-studied IBSs of Typhula ishikariensis and notably, all these mutations performing ice-binding using {\textquoteleft}anchored clathrate mechanism{\textquoteright} have been found to prefer polar and hydrophilic amino acids. Horizontal gene transfer studies point toward a strong selection pressure favoring independent evolution of the IBPs in some polar organisms including prokaryotes as well as eukaryotes because these proteins facilitate the polar organisms to acclimatize to the adversities in their niche, thus safeguarding their existence.</p>},
	keywords = {antifreeze proteins, horizontal gene transfer, ice-recrystallization inhibition, Molecular docking, Phylogenetic analysis},
	issn = {0739-1102},
	doi = {10.1080/07391102.2014.952665},
	author = {Banerjee, Rachana and Chakraborti, Pratim and Bhowmick, Rupa and Mukhopadhyay, Subhasish}
}
@article {46814,
	title = {Differential suitability of reactive oxygen species and the role of glutathione in regulating paradoxical behavior in gliomas: a mathematical perspective},
	journal = {PloS One},
	volume = {15},
	year = {2020},
	month = {JUN},
	pages = {e0235204},
	type = {Article},
	abstract = {<p>Manipulative strategies of ROS in cancer are often exhibited as changes in the redox and thiol ratio of the cells. Cellular responses to oxidative insults are generated in response to these changes which are triggered due to the rerouting of the metabolic framework to maintain survival under stress. However, mechanisms of these metabolic re-routing are not clearly understood and remained debatable. In the present work, we have designed a context-based dynamic metabolic model to establish that the coordinated functioning of glutathione peroxidase (GTHP), glutathione oxidoreductase (GTHO) and NADPH oxidase (NOX) is crucial in determining cancerous transformation, specifically in gliomas. Further, we propose that the puzzling duality of ROS (represented by changes inh(2)o(2)in the present model) in exhibiting varying cellular fates can be determined by considering simultaneous changes innadph/nadp(+)andgsh/gssgthat occur during the reprogramming of metabolic reactions. This will be helpful in determining the pro-apoptotic or anti-apoptotic fate of gliomas and can be useful in designing effective pro-oxidant and/or anti-oxidant therapeutic approaches against gliomas.</p>
},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0235204},
	author = {Bhowmick, Rupa and Sarkar, Ram Rup}
}
