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Pregled bibliografske jedinice broj: 583274

Časopis

Autori: Tomić, Antonija; Gonzalez, Miguel; Tomić, Sanja
Naslov: The large scale conformational change of the human DPP III – substrate prefers the "closed" form
( The large scale conformational change of the human DPP III – substrate prefers the "closed" form )
Izvornik: Journal of chemical information and modeling (1549-9596) 52 (2012), 6; 1583-1594
Vrsta rada: članak
Ključne riječi: metallo-peptidase; human dipeptidyl peptidase III; large scale conformational changes; molecular dynamic simulations; substrate binding; binding free energy
( metallo-peptidase; human dipeptidyl peptidase III; large scale conformational changes; molecular dynamic simulations; substrate binding; binding free energy )
Sažetak:
Human dipeptidyl peptidase III (DPP III) is a two domain metallo–peptidase from M49 family. The wide inter–domain cleft and broad substrate specificity suggest that this enzyme could experience significant conformational change. Long (> 100 ns) molecular dynamics (MD) simulations of DPP III revealed large range conformational changes of the protein suggesting the pre-existing equilibrium model for a substrate binding. The binding free energy calculations revealed tighter binding of the preferred synthetic substrate Arg–Arg–2–naphtylamide to the "closed" than to the "open" DPP III conformation. Our assumption that Asp372 plays a crucial role in the large scale inter–domain closure was approved by the MD simulations of the Asp372Ala variant. During the same simulation time the variant remained more "open" than the wild type protein. Apparently, Ala was not as efficient as Asp in establishing the inter–domain interactions. According to the MM–PBSA calculations, the electrostatic component of the free energy of solvation turned out to be higher for the "closed" protein than for its less compact form. However, gain in entropy due to water release from the inter–domain cleft nicely balanced this negative effect.
Projekt / tema: 022-0222148-2822, 098-1191344-2860
Izvorni jezik: eng
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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:
Kemija
URL Internet adrese: http://pubs.acs.org/doi/abs/10.1021/ci300141k
Broj citata:
Altmetric:
DOI: 10.1021/ci300141k
URL cjelovitog teksta:
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Upisao u CROSBI: atomic@irb.hr (atomic@irb.hr), 11. Lip. 2012. u 14:00 sati



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