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Twórca:

Sarzyńska J.

Typ zasobu:

artykuł

Współtwórca:

Mickiewicz A., Miłostan M., Łukasiak P., Błażewicz J., Figlerowicz M., Kuliński T.

Abstrakt:

Dicer is an enzyme responsible for processing double-stranded RNAs and plays a key role in an RNAi mechanism. Structural insight into the Dicer is provided by the crystal structure of eukaryotic Dicer from Giardia intestinalis. It has been proposed that the structure has three structurally rigid regions that are connected by the flexible hinges. Flexibility of the Dicer is believed to be a critical feature for its function. Spatial arrangement of the RNA-recognition and the catalytic regions is crucial for producing small RNAs of defined length. It has been suggested that in the Giardia Dicer a Platform domain may help in specific arrangement of these regions. To learn more about the role of the Platform domain in Giardia Dicer, we have performed molecular dynamics (MD) simulations of the whole Dicer (WT Dicer) and the Dicer with a deleted platform domain (ΔPlf Dicer). The MD simulations were carried out in an implicit solvent model with two implementations of analytic Generalized Born (GB) solvation model in CHARMM: GBMV (Generalized Born using Molecular Volume) and GBSW (Generalized Born with simple Switching). To detect the key global motions of the Dicer, a principal component analysis (PCA) of the obtained MD trajectories has been used. To further explore the motion of the Dicer, we performed a domain motion analysis with the DYNDOM program. The simulations show that both WT Dicer and ΔPlf Dicer display flexibility which can be described as a movement of two or three domains. The removal of the Platform substantially changed the flexibility and arrangement of these domains. During the MD simulations of ΔPlf Dicer an large movement of the RNA-recognition domain was observed.

Miejsce wydania:

Poznań

Wydawca:

OWN

Data akceptacji:

2010.03.10

Data złożenia:

2009.12.14

Data wydania:

2010.05.19

Data modyfikacji:

2010.03.02

Format:

application/pdf

Identyfikator zasobu:

oai:lib.psnc.pl:717

Język:

eng

Temat i słowa kluczowe:

implicit solvent model, principal component analysis, molecular dynamics, domain motions, Giardia Dicer

Kolekcje, do których przypisany jest obiekt:

Data ostatniej modyfikacji:

2014-08-19

Data dodania obiektu:

2014-06-27

Liczba wyświetleń treści obiektu:

177

Wszystkie dostępne wersje tego obiektu:

https://lib.psnc.pl/publication/899

Wyświetl opis w formacie RDF:

RDF

Wyświetl opis w formacie OAI-PMH:

OAI-PMH

Nazwa wydania Data
Flexibility of Dicer Studied by Implicit Solvent Molecular Dynamics Simulations 2014-08-19

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Brak tytułu

Sarzyńska J. Kuliński T.

artykuł

Brak tytułu

Sarzyńska J. Kulińska K., Kuliński T.

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Dane kontaktowe

Adres

Poznańskie Centrum Komputerowo-Sieciowe
ul. Jana Pawła II 10
61-139 Poznań
Polska

Telefon

(+48 61) 858-20-01
(+48 61) 852-59-54

E-Mail

dlibra@psnc.pl

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