<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Pagadala, Nataraj Sekhar</style></author><author><style face="normal" font="default" size="100%">Arha, Manish</style></author><author><style face="normal" font="default" size="100%">Reddy, P. S.</style></author><author><style face="normal" font="default" size="100%">Kumar, Ranadheer</style></author><author><style face="normal" font="default" size="100%">Sirisha, V. L.</style></author><author><style face="normal" font="default" size="100%">Prashant, S.</style></author><author><style face="normal" font="default" size="100%">Reddy, K. Janardhan</style></author><author><style face="normal" font="default" size="100%">Khan, Bashir Mohammad</style></author><author><style face="normal" font="default" size="100%">Rawal, S. K.</style></author><author><style face="normal" font="default" size="100%">Kishor, P. B. Kavi</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogenetic analysis, homology modelling, molecular dynamics and docking studies of caffeoyl-CoA-O- methyl transferase (CCoAOMT 1 and 2) isoforms isolated from subabul (Leucaena leucocephala)</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Molecular Modeling</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Caffeoyl-CoA 3-O-methyl transferase</style></keyword><keyword><style  face="normal" font="default" size="100%">docking</style></keyword><keyword><style  face="normal" font="default" size="100%">Modelling</style></keyword><keyword><style  face="normal" font="default" size="100%">S-adenosyl homocysteine</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">FEB</style></date></pub-dates></dates><number><style face="normal" font="default" size="100%">2</style></number><publisher><style face="normal" font="default" size="100%">SPRINGER</style></publisher><pub-location><style face="normal" font="default" size="100%">233 SPRING ST, NEW YORK, NY 10013 USA</style></pub-location><volume><style face="normal" font="default" size="100%">15</style></volume><pages><style face="normal" font="default" size="100%">203-221</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Caffeoyl coenzyme A O-methyltransferase (CCoAOMT) is an important enzyme that participates in lignin biosynthesis especially in the formation of cell wall ferulic esters of plants. It plays a pivotal role in the methylation of the 3-hydroxyl group of caffeoyl CoA. Two cDNA clones that code CCoAOMT were isolated earlier from subabul and in the present study; 3D models of CCoAOMT1 and CCoAOMT2 enzymes were built using the MODELLER7v7 software to find out the substrate binding sites. These two proteins differed only in two amino acids and may have little or no functional redundancy. Refined models of the proteins were obtained after energy minimization and molecular dynamics in a solvated water layer. The models were further assessed by PROCHECK, WHATCHECK, Verify_3D and ERRAT programs and the results indicated that these models are reliable for further active site and docking analysis. The refined models showed that the two proteins have 9 and 10 alpha-helices, 6 and 7 beta-sheets respectively. The models were used for docking the substrates CoA, SAM, SAH, caffeoyl CoA, feruloyl CoA, 5-hydroxy feruloyl CoA and sinapyl CoA which showed that CoA and caffeoyl CoA are binding with high affinity with the enzymes in the presence and absence of SAM. It appears therefore that caffeoyl CoA is the substrate for both the isoenzymes. The results also indicated that CoA and caffeoyl CoA are binding with higher affinity to CCoAOMT2 than CCoAOMT1. Therefore, CCoAOMT2 conformation is thought to be the active form that exists in subabul. Docking studies indicated that conserved active site residues Met58, Thr60, Val63, Glu82, Gly84, Ser90, Asp160, Asp162, Thr169, Asn191 and Arg203 in CCoAOMT1 and CCoAOMT2 enzymes create the positive charge to balance the negatively charged caffeoyl CoA and play an important role in maintaining a functional conformation and are directly involved in donor-substrate binding.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom3><style face="normal" font="default" size="100%">Foreign</style></custom3><custom4><style face="normal" font="default" size="100%">1.871</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sonawane, Prashant</style></author><author><style face="normal" font="default" size="100%">Patel, Krunal</style></author><author><style face="normal" font="default" size="100%">Vishwakarma, Rishi Kishore</style></author><author><style face="normal" font="default" size="100%">Srivastava, Sameer</style></author><author><style face="normal" font="default" size="100%">Singh, Somesh</style></author><author><style face="normal" font="default" size="100%">Gaikwad, Sushama M.</style></author><author><style face="normal" font="default" size="100%">Khan, Bashir Mohammad</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Probing the active site of cinnamoyl CoA reductase 1 (Ll-CCRH1) from Leucaena leucocephala</style></title><secondary-title><style face="normal" font="default" size="100%">International Journal of Biological Macromolecules</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Chemical modification</style></keyword><keyword><style  face="normal" font="default" size="100%">Cinnamoyl CoA reductase 1</style></keyword><keyword><style  face="normal" font="default" size="100%">Docking simulations</style></keyword><keyword><style  face="normal" font="default" size="100%">homology modeling</style></keyword><keyword><style  face="normal" font="default" size="100%">Site directed mutagenesis</style></keyword><keyword><style  face="normal" font="default" size="100%">Substrate protection</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">SEP</style></date></pub-dates></dates><publisher><style face="normal" font="default" size="100%">ELSEVIER SCIENCE BV</style></publisher><pub-location><style face="normal" font="default" size="100%">PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS</style></pub-location><volume><style face="normal" font="default" size="100%">60</style></volume><pages><style face="normal" font="default" size="100%">33-38</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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.&lt;/p&gt;</style></abstract><custom3><style face="normal" font="default" size="100%">Foreign</style></custom3><custom4><style face="normal" font="default" size="100%">3.096
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