Primary Citation PubMed: 23393263
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Structure based identification and characterization of flavonoids that disrupt human papillomavirus-16 E6 function.
(2013) PLoS One 8
PubMed: 24376816 | PubMedCentral: PMC3871595 | DOI: 10.1371/journal.pone.0084506
Starting from the crystal structure of HPV E6 bound to the LXXLL peptide of E6AP (PDB ID: 4GIZ), luteolin ( A ), CAF-24 ( B ) and the acetylated analog of luteolin; Compound 170 (C) were flexibly dock... d into E6 using the induced-fit docking model in Schrödinger Maestro, while allowing protein flexibility within a 10Å radius of each ligand.
( A ) Illustration of E6AP (green helix) binding to HPV16-E6 (PDB ID: 4GIZ).
Docking of flavones into the E6AP binding site on the three dimensional structure of HPV16-E6 Luteolin, CAF-24, and the acetylated luteolin pro-drug were docked as ligands onto the E6 structure (PDB ID: 4GIZ) [ 38 ] using an induced-fit docking model in Schrödinger Maestro [ 49 , 50 ] ( Figure 11 ).
Publication Year: 2013
Elucidating Molecular Interactions of Natural Inhibitors with HPV-16 E6 Oncoprotein through Docking Analysis.
(2014) Genomics Inform 12
PubMed: 25031569 | PubMedCentral: PMC4099350 | DOI: 10.5808/GI.2014.12.2.64
Since the three-dimensional structure of E6 was not available, its structure model was predicted using the Phyre 2 server by taking chain C of the crystal structure of full-length HPV oncoprotein e62 ... n complex with the lxxll peptide of ubiquitin ligase e6ap (PDB ID: 4GIZ) as a structural template.
Publication Year: 2014
PubMed ID is not available.
Published in 2015
This hypothetical model of the complex between PDZbody20 and HPV E6 is based on the crystal structures of HPV16 E6 with the E6AP helix (protein data bank code: 4GIZ) and that of SAP97 PDZ2.
Publication Year: 2015
BLASTp search revealed one putative template (PDB id: 4GIZ, Chain C) of high-label identity and query coverage with the target sequence, as the best template for comparative modeling.
Citation: Mamgain et al , Bioinformation 11(5): 236-242 (2015) References 1 Arundhati B J Nat Sci Biol Med 2012 3 186 23225983 2 GY Ho J Natl Cancer Inst 1995 87 1365 7658497 3 Guan P Int J Cancer 2012 131 2349 22323075 4 Matlashewski G EMBO J 1987 6 1741 3038534 5 Vousden K FASEB J 1993 7 872 8393818 6 Rangarajan A Virology 2001 286 23 11448155 7 Kiyono T Proc Natl Acad Sci U S A 1997 94 11612 9326658 8 Bharti AC Indian J Med Res 2009 130 296 19901439 9 Dubey K Process Biochem 2008 43 251 10 Larkin MA Bioinformatics 2007 23 2947 17846036 11 Goel A Biochem Pharmacol 2008 75 787 17900536 12 Lu Food Chem 2011 124 1500 13 Kuo Life Sciences 2006 78 2550 16337242 14 Batra P Sharma A 3 Biotech 2013 3 439 15 Corcoran MP J Nutr Gerontol Geriatr 2012 31 176 22888837 16 Tamura K Mol Biol Evol 2013 30 2725 24132122 17 Larkin MA Bioinformatics 2007 23 2947 17846036 18 Trott O J Comput Chem 2010 31 455 19499576 19 Laskowski RA J Chem Inf Model 2011 51 2778 21919503 20 Pathak RK Bioinformation 2014 10 428 25187683 21 Ambrish R Nat Protoc 2010 5 725 20360767 Figure 1 Pair-wise sequence alignment of the target protein E6 with C-chain of its template (PDB id: 4GIZ) Figure 2 Homology model of E6 of HPV-16.
During structure prediction, crystal structure of C chain of full-length HPV oncoprotein e62 in complex with lxxll peptide of ubiquitin ligase E6AP (PDB ID, 4GIZ) was taken as structural template by P... yre2 server.
[ 7 ] By combining our previous structures of the E6/LxxLL complex (PDB ID 4GIZ[ 7 ]; Figure 1 a ) and of the E6/PDZ2 complex (PDB ID 2KPL[ 9a ]; Figure 1 b ), we built a tridimensional model of the p... anned PDZ-LxxLL chimera (Figure 1 c and the Supporting Information) and of its expected complex with E6 (Figure 1 d ).
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