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Computational study of the IRES subdomain IIa structural plasticity and the ligand binding affinity


Grabar Branilović, Marina; Tomić, Sanja
Computational study of the IRES subdomain IIa structural plasticity and the ligand binding affinity // Chemistry towards Biology 7th Central European Conference - Book of Abstracts / Jarzembek, Krystyna (ur.) (ur.).
Katowice, Poljska, 2014. str. P10-P10 (poster, međunarodna recenzija, sažetak, znanstveni)


Naslov
Computational study of the IRES subdomain IIa structural plasticity and the ligand binding affinity

Autori
Grabar Branilović, Marina ; Tomić, Sanja

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, znanstveni

Izvornik
Chemistry towards Biology 7th Central European Conference - Book of Abstracts / Jarzembek, Krystyna (ur.) - Katowice, Poljska, 2014, P10-P10

Skup
7th Central European Conference Chemistry towards Biology

Mjesto i datum
Katowice, Poljska, 09-12.09.2014.

Vrsta sudjelovanja
Poster

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
HCV inhibitor; IRES subdomain IIa; molecular modelling; MD simulations; QM/MM method

Sažetak
The internal ribosome entry site (IRES) of the hepatitis C virus (HCV) drives noncanonical initiation of protein synthesis necessary for viral replication. In order to fulfill its role in HCV translation its domain II should adopt an L-shaped conformation. We performed detailed molecular dynamics (MD) simulations for the ligand free RNA and its (native and mutated) complexes with the potential HCV inhibitors, with and without the presence of magnesium ions. We have shown that upon ligand removal conformation of the IIa subdomain changed from extended into the L-shaped one during several tens of ns MD simulation. Differently, binding of the benzimidazole translation inhibitors locked IIa in the extended conformation. We also performed MD study for the IIa in complex with newly discovered translation inhibitor diaminopiperidine (DAP) for which is experimentally suggested that locks the IIa RNA switch in the bent conformation and inhibits IRES function perhaps by preventing ribosome releas1. The starting points for our calculations were the three-dimensional structures of the IRES subdomain IIa determined by X-ray diffraction (34 nucleotides) (PDB ID code 3TZR)2 and by NMR spectroscopy (38 nucleotides) (PDB ID code 2KTZ)3. In both of them the subdomain IIa is complexed with a benzimidazole translation inhibitor 2. Since there are no crystallographically determined structure of the complexes with ligand 1, analog 3 and inhibitor DAP, we constructed them and performed molecular modeling calculations. Besides MD, we determined changes in the inhibitor structure and electronic charge distribution at the presence of magnesium cations and RNA using QM/MM approach.

Izvorni jezik
Engleski

Znanstvena područja
Fizika, Kemija, Temeljne medicinske znanosti



POVEZANOST RADA


Projekt / tema
098-1191344-2860 - Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritama (Sanja Tomić, )

Ustanove
Institut "Ruđer Bošković", Zagreb