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Pregled bibliografske jedinice broj: 938009

Časopis

Autori: Kazazić, Saša; Karačić, Zrinka; Sabljić, Igor; Agić, Dejan; Tomin, Marko; Abramić, Marija; Dadlez, Michal; Tomić, Antonija; Tomić, Sanja
Naslov: Conservation of the conformational dynamics and ligand binding within M49 enzyme family
( Conservation of the conformational dynamics and ligand binding within M49 enzyme family )
Izvornik: RSC Advances (2046-2069) 8 (2018), 24; 13310-13322
Vrsta rada: članak
Ključne riječi: dipeptidyl peptidase III ; DPP III ; hydrogen-deuterium exchange ; HDX ; MD simulations ; conformational dynamics
( dipeptidyl peptidase III ; DPP III ; hydrogen-deuterium exchange ; HDX ; MD simulations ; conformational dynamics )
Sažetak:
The hydrogen deuterium exchange (HDX) mass spectrometry combined with molecular dynamics (MD) simulations was employed to investigate conformational dynamics and ligand binding within the M49 family (dipeptidyl peptidase III family). Six dipeptidyl peptidase III (DPP III) orthologues, human, yeast, three bacterial and one plant (moss) were studied. According to the results, all orthologues seem to be quite compact wherein DPP III from the thermophile Caldithrix abyssi seems to be the most compact. The protected regions are located within the two domains core and the overall flexibility profile consistent with semi-closed conformation as the dominant protein form in solution. Besides conservation of conformational dynamics within the M49 family, we also investigated the ligand, pentapeptide tynorphin, binding. By comparing HDX data obtained for unliganded protein with those obtained for its complex with tynorphin it was found that the ligand binding mode is conserved within the family. Tynorphin binds within inter-domain cleft, close to the lower domain β-core and induces its stabilization in all orthologues. Docking combined with MD simulations revealed details of the protein flexibility as well as of the enzyme–ligand interactions.
Projekt / tema: HRZZ-IP-2013-11-7235, FP7-REGPOT- 2012-2013-1
Izvorni jezik: eng
Rad je indeksiran u
bazama podataka:
Current Contents Connect (CCC)
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:
Kemija,Biotehnologija
URL Internet adrese: http://fulir.irb.hr/4315/
http://pubs.rsc.org/en/content/articlelanding/2018/ra/c7ra13059g#!divAbstract
http://pubs.rsc.org/en/content/articlepdf/2018/ra/c7ra13059g
Broj citata:
Altmetric:
DOI: 10.1039/c7ra13059g
URL cjelovitog teksta:
Google Scholar: Conservation of the conformational dynamics and ligand binding within M49 enzyme family
Upisao u CROSBI: Marko Tomin (Marko.Tomin@irb.hr), 14. Svi. 2018. u 04:57 sati



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