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Autori: Tomić, Antonija; Abramić, Marija; Smith, David; Tomić, Sanja
Naslov: Molecular dynamics simulations of ligands binding into the active site of human dipeptidyl-peptidases (DPPIII)
( Molecular dynamics simulations of ligands binding into the active site of human dipeptidyl-peptidases (DPPIII) )
Izvornik: Book of Abstracts of the EMBO Young Scientists Forum
Skup: EMBO Young Scientists Forum
Mjesto i datum: Zagreb, Hrvatska, 15.-17.06.2009
Ključne riječi: dipeptidyl-peptidases; molecular dynamics simulations; ligands binding
( dipeptidyl-peptidases; molecular dynamics simulations; ligands binding )
Dipeptidyl-peptidases III (peptidase family M49) are zinc-dependent enzymes that specifically cleave the first two amino acids from the N terminus of different length peptides. This zinc-dependent enzyme has been recently recognized among metallopeptidases, based on the unique structural motif, hexapeptide HELLGH, which harbours the predicted active site residues. Besides its contribution in normal protein catabolism, the regulatory and pathophysiological role for DPPIII was suggested, however molecular mechanism of its action is still unknown. Recently determined crystal structure of human DPPIII (PDB code 3FVY) enabled detailed molecular modelling study. In order to understand mechanism of substrates (Arg-Arg-2naphthylamide and Ala-Ala-2naphthylamide) and inhibitor (Tyr-Phe-hydroxamate) binding into the active site of H-DPPIII we performed molecular modelling study using the Amber10 program suite. The initial structures were built in program Insight II ( and the steered molecular dynamics simulations were performed to determine possible orientations of the ligands in binding site. We have determined similar binding of the ligands (inhibitor and substrates) into the DPPIII active site. Namely the hydrogen bonds formed during molecular dynamics simulations are mostly conserved in all tree complexes. The zinc-binding site is built up by His-450, Glu-451 and His-455 belonging to the first conserved (450HELLGH455) signature motif, Glu-508 which is part of the second conserved motif (507EECRAE512), water molecule and carbonyl group belonging to the ligand second peptide bond from N terminus . Longer simulations aimed to study stability of these complexes and to determine effects of amino acids mutations on ligands binding have been started.
Vrsta sudjelovanja: Poster
Vrsta prezentacije u zborniku: Sažetak
Vrsta recenzije: Nema recenziju
Projekt / tema: 06M1801
Izvorni jezik: eng
Kategorija: Znanstveni
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Upisao u CROSBI: (, 10. Ruj. 2009. u 15:57 sati

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