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Pregled bibliografske jedinice broj: 489936

Časopis

Autori: Tomić, Antonija; Abramić, Marija; Špoljarić, Jasminka; Agić, Dejan; Smith, David M.; Tomić, Sanja
Naslov: Human Dipeptidyl Peptidase III: Insights into Ligand Binding from a Combined Experimental and Computational Approach
( Human Dipeptidyl Peptidase III: Insights into Ligand Binding from a Combined Experimental and Computational Approach )
Izvornik: Journal of molecular recognition (0952-3499) 24 (2011), 5; 804-814
Vrsta rada: članak
Ključne riječi: dipeptidyl peptidase III; molecular modelling; binding affinity; catalytic affinity
( dipeptidyl peptidase III molecular modelling; binding affinity; catalytic affinity )
Sažetak:
Human dipeptidyl peptidase III (DPP III) is a zinc-exopeptidase with implied roles in protein catabolism, pain modulation and defense against oxidative stress. To understand the mode of ligand binding into its active site, we performed molecular modeling, site-directed mutagenesis and biochemical analyses. Using the recently determined crystal structure of the human DPP III we built complexes between both, the wild type protein and its mutant H568N with the preferred substrate Arg-Arg-2-naphthylamide (RRNA) and a competitive inhibitor Tyr-Phe-hydroxamate (Tyr-Phe-NHOH). The mutation of the conserved H1099-1352is568, structurally equivalent to catalytically important His231 in thermolysin, to Asn, resulted in a 1300-fold decrease of kcat for RRNA hydrolysis and in significantly lowered affinity for the inhibitor. Molecular dynamics (MD) simulations revealed the key protein ligand interactions as well as the ligand induced reorganization of the binding site and its partial closure. Simultaneously, the non catalytic domain was observed to stretch and the opening at the wide side of the inter-domain cleft became enhanced. The driving force for these changes was the formation of the hydrogen bond between Asp372 and the bound ligand. The structural and dynamical differences, found for the ligand binding to the wild-type enzyme and the H568N mutant, and the calculated binding free energies, agree well with the measured affinities. On the basis of the obtained results we suggest a possible reaction mechanism. In addition, this work provides a foundation for further site-directed mutagenesis experiments, as well as for modeling the reaction itself.
Projekt / tema: 098-1191344-2860, 098-1191344-2938, 098-0982933-2937, 022-0222148-2822
Izvorni jezik: eng
Rad je indeksiran u
bazama podataka:
Current Contents Connect (CCC)
MEDLINE
Scopus
SCI-EXP, SSCI i/ili A&HCI
Science Citation Index Expanded (SCI-EXP) (sastavni dio Web of Science Core Collectiona)
Kategorija: Znanstveni
Znanstvena područja:
Fizika,Kemija,Biologija
URL Internet adrese: http://onlinelibrary.wiley.com/doi/10.1002/jmr.1115/abstract
Broj citata:
Altmetric:
DOI: 10.1002/jmr.1115
URL cjelovitog teksta:
Google Scholar: Human Dipeptidyl Peptidase III: Insights into Ligand Binding from a Combined Experimental and Computational Approach
Upisao u CROSBI: tomic@irb.hr (tomic@irb.hr), 5. Stu. 2010. u 11:19 sati



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