@article { ISI:000323584400008, title = {Structural modelling of substrate binding and inhibition in penicillin V acylase from pectobacterium atrosepticum}, journal = {Biochemical and Biophysical Research Communications}, volume = {437}, number = {4}, year = {2013}, month = {AUG}, pages = {538-543}, publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE}, address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA}, abstract = {

Penicillin V acylases (PVAs) and bile salt hydrolases (BSHs) have considerable sequence and structural similarity; however, they vary significantly in their substrate specificity. We have identified a PVA from a Gram-negative organism, Pectobacterium atrosepticum (PaPVA) that turned out to be a remote homolog of the PVAs and BSHs reported earlier. Even though the active site residues were conserved in PaPVA it showed high specificity towards penV and interestingly the penV acylase activity was inhibited by bile salts. Comparative modelling and docking studies were carried out to understand the structural differences of the binding site that confer this characteristic property. We show that PaPVA exhibits significant differences in structure, which are in contrast to those of known PVAs and such enzymes from Gram-negative bacteria require further investigation. (C) 2013 Elsevier Inc. All rights reserved.

}, keywords = {Bile salt hydrolase, docking, Homology modelling, Inhibition, Pectobacterium, Penicillin acylase}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2013.06.109}, author = {Avinash, Vellore Sunder and Panigrahi, Priyabrata and Suresh, C. G. and Pundle, Archana V. and Ramasamy, Sureshkumar} } @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 = {

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.

}, 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 {44651, title = {Cloning and characterization of trehalase: a conserved glycosidase from oriental midge, Chironomus ramosus}, journal = {3 Biotech}, volume = {8}, year = {2018}, month = {AUG}, pages = {352}, abstract = {

Insect trehalase is a multiferous enzyme, crucial for normal physiological functions as well as under stress conditions. In this report, we present a fundamental study of the trehalase gene segment (1587 bp) from Chironomus ramosus (CrTre) encoding for 529 amino acids, using appropriate bioinformatics tools. C. ramosus, a tropical midge is an emerging animal model to investigate the consequences of environmental stresses. We observed that CrTre belongs to GH family 37 in the CAZy database and possess 57-92\% identity to dipteran trehalases. In silico characterization provided information regarding the structural, functional and evolutionary aspects of midge trehalase. In the phylogenetic tree, CrTre clustered with the soluble dipteran trehalases. Moreover, domain functional characterization of the deduced protein sequence by InterProScan (IPR001661), ProSite (PS00927 and PS00928) and Pfam (PF01204) indicated presence of highly conserved signature motifs which are important for the identification of trehalase superfamily. Furthermore, the instability index of CrTre was predicted to be \< 40 suggesting its in vivo stability while, the high aliphatic index indicated towards its thermal stability (index value 71-81). The modelled 3D tertiary structure of CrTre depicts a (alpha/alpha)(6) barrel toroidal core. The catalytic domain of the enzyme comprised Glu424 and Asp226 as the putative active site residues. Interestingly, the conserved motifs were observed to be formed by the flexible loopy regions in the tertiary structure. This study revealed essential sequence features of the midge trehalase and offers better insights into the structural aspects of this enzyme which can be correlated with its function.

}, keywords = {Conserved motifs, Homology modelling, Midges, Secondary structure, trehalose}, issn = {2190-572X}, doi = {10.1007/s13205-018-1376-y}, author = {Shukla, Ekta and Thorat, Leena and Bendre, Ameya D. and Jadhav, Santosh and Pal, Jayanta K. and Nath, Bimalendu B. and Gaikwad, Sushama M.} }