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Computational simulations of ABP1 and its interactions with auxin-related molecules


Bertoša, Branimir; Wade, Rebecca; Kojić-Prodić, Biserka; Tomić, Sanja
Computational simulations of ABP1 and its interactions with auxin-related molecules // The 2th Opatija Meeting on Computational Solutions in the Life Sciences / Babić, Darko ; Došlić, Nađa ; David, Smith ; Tomić, Sanja ; Kristijan, Vlahovićek (ur.).
Zagreb: Institut Ruđer Bošković, 2007. str. 30-30 (predavanje, nije recenziran, sažetak, znanstveni)


Naslov
Computational simulations of ABP1 and its interactions with auxin-related molecules

Autori
Bertoša, Branimir ; Wade, Rebecca ; Kojić-Prodić, Biserka ; Tomić, Sanja

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

Izvornik
The 2th Opatija Meeting on Computational Solutions in the Life Sciences / Babić, Darko ; Došlić, Nađa ; David, Smith ; Tomić, Sanja ; Kristijan, Vlahovićek - Zagreb : Institut Ruđer Bošković, 2007, 30-30

ISBN
978-953-6690-69-5)

Skup
The 2th Opatija Meeting on Computational Solutions in the Life Sciences

Mjesto i datum
Opaija, Hrvatska, 04.- 09.09.2007

Vrsta sudjelovanja
Predavanje

Vrsta recenzije
Nije recenziran

Ključne riječi
Auxin; molecular dynamics; computational simulations; RAMD simulations; ABP1

Sažetak
Auxins are plant hormons that controle and regulate plant growth and development through complex signalling pathways. There are at least two proteins for which auxin receptor function has been experimentaly evidenced: TIR1 and ABP1. Crystal structure of Auxin Binding Protein 1 (ABP1) has been known for several years and it eneabled investigation of auxin binding to ABP1 by computational simulations. In order to understand molecular mechanism of ABP1 activity series of Molecular Dynamics (MD) simulations of ABP1 and its complexes with auxin-related compounds have been made. Beside the standard MD simulations at room temperature, simulations in which temperature was shortly increased at 500 K have also been made (altogether 70 ns of MD simulations was accomplished). Results of MD simulations showed that ABP1 can adopt two conformations differing primarily in the position of the C-terminus and that one of them is stabilised by auxin binding. This is in agreement with experimental evidence that auxin induces changes at the ABP1 C-terminus. Antoher interesting thing, which was noticed during all MD simulations, is formation of network of hydrogen-bonded water molecules leading from the bulk water to the zinc-coordinated ligands in the ABP1 binding site. This finding indicated possible role of water molecules in ABP1 mecahanism. Hypothesis about ABP1 molecular mechanism was completed by Random Acceleration Molecular Dynamics (RAMD) symulations which have revealed three main routes by which auxin molecules enter and leave the ABP1 binding site. Considering assumed orientation of ABP1 to the membrane, one of them leads into membrane and the other two to the ABP1 sourandings

Izvorni jezik
Engleski

Znanstvena područja
Kemija



POVEZANOST RADA


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

Ustanove
Institut "Ruđer Bošković", Zagreb