@article { ISI:000313165500067, title = {Functional characterization, homology modeling and docking studies of beta-glucosidase responsible for bioactivation of cyanogenic hydroxynitrile glucosides from Leucaena leucocephala (subabul)}, journal = {Molecular Biology Reports}, volume = {40}, number = {2}, year = {2013}, month = {FEB}, pages = {1351-1363}, publisher = {SPRINGER}, address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS}, abstract = {

Glycosyl hydrolase family 1 beta-glucosidases are important enzymes that serve many diverse functions in plants including defense, whereby hydrolyzing the defensive compounds such as hydroxynitrile glucosides. A hydroxynitrile glucoside cleaving beta-glucosidase gene (Llbglu1) was isolated from Leucaena leucocephala, cloned into pET-28a (+) and expressed in E. coli BL21 (DE3) cells. The recombinant enzyme was purified by Ni-NTA affinity chromatography. The optimal temperature and pH for this beta-glucosidase were found to be 45 A degrees C and 4.8, respectively. The purified Llbglu1 enzyme hydrolyzed the synthetic glycosides, pNPGlucoside (pNPGlc) and pNPGalactoside (pNPGal). Also, the enzyme hydrolyzed amygdalin, a hydroxynitrile glycoside and a few of the tested flavonoid and isoflavonoid glucosides. The kinetic parameters K (m) and V (max) were found to be 38.59 mu M and 0.8237 mu M/mg/min for pNPGlc, whereas for pNPGal the values were observed as 1845 mu M and 0.1037 mu M/mg/min. In the present study, a three dimensional (3D) model of the Llbglu1 was built by MODELLER software to find out the substrate binding sites and the quality of the model was examined using the program PROCHEK. Docking studies indicated that conserved active site residues are Glu 199, Glu 413, His 153, Asn 198, Val 270, Asn 340, and Trp 462. Docking of rhodiocyanoside A with the modeled Llbglu1 resulted in a binding with free energy change (Delta G) of -5.52 kcal/mol on which basis rhodiocyanoside A could be considered as a potential substrate.

}, keywords = {Glycosyl hydrolase family 1, homology modeling, Leucaena leucocephala, Molecular docking}, issn = {0301-4851}, doi = {10.1007/s11033-012-2179-6}, author = {Shaik, Noor M. and Misra, Anurag and Singh, Somesh and Fatangare, Amol B. and Ramakumar, Suryanarayanarao and Rawal, Shuban K. and Khan, Bashir Mohammad} } @article { ISI:000324842900004, title = {Probing the active site of cinnamoyl CoA reductase 1 (Ll-CCRH1) from Leucaena leucocephala}, journal = {International Journal of Biological Macromolecules}, volume = {60}, year = {2013}, month = {SEP}, pages = {33-38}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

Lack of three dimensional crystal structure of cinnamoyl CoA reductase (CCR) limits its detailed active site characterization studies. Putative active site residues involved in the substrate/NADPH binding and catalysis for Leucaena leucocephala CCR (Ll-CCRH1; GenBank: DQ986907) were identified by amino acid sequence alignment and homology modeling. Putative active site residues and proximal H215 were subjected for site directed mutagenesis, and mutated enzymes were expressed, purified and assayed to confirm their functional roles. Mutagenesis of S136, Y170 and K174 showed complete loss of activity, indicating their pivotal roles in catalysis. Mutant S212G exhibited the catalytic efficiencies less than 10\% of wild type, showing its indirect involvement in substrate binding or catalysis. R51G, D77G, F30V and I31N double mutants showed significant changes in K-m values, specifying their roles in substrate binding. Finally, chemical modification and substrate protection studies corroborated the presence Ser, Tyr, Lys, Arg and carboxylate group at the active site of Ll-CCRH1. (c) 2013 Elsevier B.V. All rights reserved.

}, keywords = {Chemical modification, Cinnamoyl CoA reductase 1, Docking simulations, homology modeling, Site directed mutagenesis, Substrate protection}, issn = {0141-8130}, doi = {10.1016/j.ijbiomac.2013.05.005}, author = {Sonawane, Prashant and Patel, Krunal and Vishwakarma, Rishi Kishore and Srivastava, Sameer and Singh, Somesh and Gaikwad, Sushama M. and Khan, Bashir Mohammad} } @article { ISI:000368702300006, title = {Molecular interaction of selected phytochemicals under the charged environment of Plasmodium falciparum chloroquine resistance transporter (PfCRT) model}, journal = {Journal of Biomolecular Structure \& Dynamics}, volume = {34}, number = {2}, year = {2016}, month = {FEB}, pages = {290-303}, publisher = {TAYLOR \& FRANCIS INC}, address = {530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA}, abstract = {

Phytochemicals of Catharanthus roseus Linn. and Tylophora indica have been known for their inhibition of malarial parasite, Plasmodium falciparum in cell culture. Resistance to chloroquine (CQ), a widely used antimalarial drug, is due to the CQ resistance transporter (CRT) system. The present study deals with computational modeling of Plasmodium falciparum chloroquine resistance transporter (PfCRT) protein and development of charged environment to mimic a condition of resistance. The model of PfCRT was developed using Protein homology/analogy engine (PHYRE ver 0.2) and was validated based on the results obtained using PSI-PRED. Subsequently, molecular interactions of selected phytochemicals extracted from C. roseus Linn. and T. indica were studied using multiple-iterated genetic algorithm-based docking protocol in order to investigate the translocation of these legends across the PfCRT protein. Further, molecular dynamics studies exhibiting interaction energy estimates of these compounds within the active site of the protein showed that compounds are more selective toward PfCRT. Clusters of conformations with the free energy of binding were estimated which clearly demonstrated the potential channel and by this means the translocation across the PfCRT is anticipated.

}, keywords = {homology modeling, molecular dynamics, Plasmodium falciparum chloroquine, resistance transporter model}, issn = {0739-1102}, doi = {10.1080/07391102.2015.1028449}, author = {Patel, Saumya K. and Khedkar, Vijay M. and Jha, Prakash C. and Jasrai, Yogesh T. and Pandya, Himanshu A. and George, Linz-Buoy and Highland, Hyacinth N. and Skelton, Adam A.} } @article {47391, title = {Molecular phylogeny, structure modeling and in silico screening of putative inhibitors of aerolysin of Aeromonas hydrophila EUS112}, journal = {Journal of Biomolecular Structure \& Dynamics}, volume = {40}, year = {2022}, month = {JUN}, type = {Article}, abstract = {

Aeromonas hydrophila, a Gram-negative bacterium, causes diseases in fish, resulting in excessive loss to the aquaculture industry. Aeromonas is a highly heterogeneous group of bacteria, and the heterogeneity of the genus is attributed to variation and diversity in the virulence factors and toxins among various Aeromonas strains. One of the major toxins aerolysin, secreted by the bacterium, causes hemorrhagic-septicemia and diarrhea and can serve as a drug target. Here, we describe characterization, molecular phylogeny, and homology modeling of the aerolysin of A. hydrophila strain EUS112 (Ah(EUS112)) cloned in our lab. The encoded aerolysin is 485 amino acids long with an N-terminal signal sequence of 23 amino acids. Phylogenetic analysis of the aerolysin of Ah(EUS112) revealed that it belongs to a diverse group of toxins, showing maximum similarity with aerolysins of other Aeromonas strains followed by Vibrio toxin. The homology model of the mature aerolysin of Ah(EUS112) was generated using the crystal structure of a mutant aerolysin (PDB\#3g4n) as the template, which showed that the encoded aerolysin exists as a channel protein. Validation of the generated model using bioinformatics tool confirmed it to be a good quality model that can be used for drug design. Molecular dock analysis revealed that drugs, aralia-saponin I, cyclamin, ardisiacrispin B, and aralia-saponin II bind to aerolysin with a higher affinity as compared to other drugs and at functionally important amino acids of aerolysin. Hence, these molecules can act as an effective therapeutics for inhibiting the aerolysin pore formation and curtail the severity of Aeromonas infection. Communicated by Ramaswamy H. Sarma

}, keywords = {Aerolysin, homology modeling, Molecular docking, Molecular dynamic simulation, phylogenetic tree}, issn = {0739-1102}, doi = {10.1080/07391102.2021.1918254, Early Access Date = APR 2021}, author = {Yadav, Sunita Kumari and Panwar, Deepak and Singh, Ankita and Tellis, Meenakshi B. and Joshi, Rakesh Shamsunder and Dixit, Aparna} }