Napredna pretraga

Pregled bibliografske jedinice broj: 776537

Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding


Tomić, Antonija; Berynskyy, Mykhaylo; Wade, Rebecca C.; Tomić, Sanja
Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding // Molecular biosystems, 11 (2015), 3068-3080 doi:10.1039/c5mb00465a (međunarodna recenzija, članak, znanstveni)


Naslov
Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding

Autori
Tomić, Antonija ; Berynskyy, Mykhaylo ; Wade, Rebecca C. ; Tomić, Sanja

Izvornik
Molecular biosystems (1742-206X) 11 (2015); 3068-3080

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
Dipeptidyl peptidase III ; molecular dynamics simulations ; accelerated molecular dynamics simulations ; coarse grained simulation

Sažetak
The experimentally determined structures of human dipeptidyl peptidase III (DPP III) for the wild-type protein and for the complex of its E451A mutant with the peptide substrate, tynorphin, differ significantly in their overall shape. The two domains of the enzyme are separated by a wide cleft in the structure of the ligand-free enzyme, while in the ligand-bound mutant they are very close to each other, and the protein structure is extremely compact. Here, we applied a range of molecular dynamics simulation techniques to investigate the DPP III conformational landscape and the influence of ligand binding on the protein structure and dynamics. We used conventional, accelerated and steered methods to simulate DPP III and its complexes with tynorphin and with the preferred, synthetic, substrate Arg-Arg-2-naphthylamide. We found that DPP III can adopt a number of different forms in solution. The compact forms are more stable, but the open and partially closed states, spanning a wide range of conformations, can more effectively recognize the substrate which preferentially binds to the five-stranded β-core of the lower DPP III domain. The simulations indicated the existence of a dynamic equilibrium between open and semi-closed states and revealed two ways that the protein can close, leading to two distinct compact structures. The way in which the protein closes depends on the presence of the ligand.

Izvorni jezik
Engleski

Znanstvena područja
Kemija



POVEZANOST RADA


Projekt / tema
HRZZ-IP-2013-11-7235 - Povezanost fleksibilnosti, aktivnosti i strukture u porodici dipeptidil-peptidaza III (Sanja Tomić, )

Ustanove
Institut "Ruđer Bošković", Zagreb

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


Citati