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Pregled bibliografske jedinice broj: 525058

Mechanism and thermodynamics of ligand binding to auxin amidohydrolase

Šimunović, Mijo; Žagrović, Bojan; Tomić, Sanja
Mechanism and thermodynamics of ligand binding to auxin amidohydrolase // Journal of molecular recognition, 24 (2011), 5; 854-861 doi:10.1002/jmr.1128 (međunarodna recenzija, članak, znanstveni)

Mechanism and thermodynamics of ligand binding to auxin amidohydrolase

Šimunović, Mijo ; Žagrović, Bojan ; Tomić, Sanja

Journal of molecular recognition (0952-3499) 24 (2011), 5; 854-861

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

Ključne riječi
Auxin amidohydrolase; auxin conjugate; binding affinity; BrILL2; conformational change; M20; molecular dynamics

BrILL2 is catalytically the most efficient auxin amidohydrolase from Brassica rapa, playing a key role in auxin metabolism by catalyzing its release from amino acid conjugates. Auxins, with the most abundant representative indole-acetic acid ([1H-indol-3-yl]-acetic acid, IAA), are a group of plant hormones that in very small concentrations regulate ubiquitin-mediated degradation of transcription regulators. Kinetic studies on BrILL2 showed that it hydrolyzes alanine conjugates of IAA and of its larger analogues, indole-propionic acid (3-[1H-indol-3-yl]-propionic acid, IPA) and indole-butyric acid (4-[1H-indol-3-yl]-butyric acid, IBA). Structurally, BrILL2 belongs to the largest known family of metallopeptidases (M20) that share a recognizable 3D structure, characterized by two perpendicular domains. Its members have been implicated in numerous biochemical processes and have been found across all species sequenced to date. Here, molecular dynamics simulations were carried out to study structural and thermodynamic properties of ligand binding to BrILL2. A conformational change was captured in multiple copies of 10 ns long simulations, described by a rigid body movement of the two domains, and its associated key interactions between residues were examined. For the three substrates, complexes in two possible binding modes were recreated, along with a single binding mode for the putative substrate tryptophanyl–alanine (Trp–Ala), which were subsequently simulated in multiple copies of 10 ns long simulations. Thermodynamic calculations were used to assess their binding affinities and explain the selectivity toward the longer ligands. Based on the results, a possible route for the reaction is proposed.

Izvorni jezik

Znanstvena područja
Fizika, Kemija


Projekt / tema
022-0222148-2822 - Modeliranje i međudjelovanje kompleksa prijelaznih metala i bioliganada (Jasmina Sabolović, )
098-1191344-2860 - Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritama (Sanja Tomić, )
177-1770495-0476 - Razvoj i primjene principa maksimalne proizvodnje entropije (Davor Juretić, )

Institut za medicinska istraživanja i medicinu rada, Zagreb,
Institut "Ruđer Bošković", Zagreb,
Prirodoslovno-matematički fakultet, Split

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