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Statements

Subject Item
n2:RIV%2F61388971%3A_____%2F13%3A00423430%21RIV14-MSM-61388971
rdf:type
skos:Concept n11:Vysledek
dcterms:description
An all atomic, non-restrained molecular dynamics (MD) simulation in explicit water was used to study in detail the structural features of the highly conserved glycine-rich loop (GRL) of the a-subunit of the yeast mitochondrial processing peptidase (MPP) and its importance for the tertiary and quaternary conformation of MPP. Wild-type and GRL-deleted MPP structures were studied using non-restrained MD simulations, both in the presence and the absence of a substrate in the peptidase active site. Targeted MD simulations were employed to study the mechanism of substrate translocation from the GRL to the active site. We demonstrate that the natural conformational flexibility of the GRL is crucial for the substrate translocation process from outside the enzyme towards the MPP active site. We show that the a-helical conformation of the substrate is important not only during its initial interaction with MPP (i.e. substrate recognition), but also later, at least during the first third of the substrate translocation trajectory. Further, we show that the substrate remains in contact with the GRL during the whole first half of the translocation trajectory and that hydrophobic interactions play a major role. Finally, we conclude that the GRL acts as a precisely balanced structural element, holding the MPP subunits in a partially closed conformation regardless the presence or absence of a substrate in the active site An all atomic, non-restrained molecular dynamics (MD) simulation in explicit water was used to study in detail the structural features of the highly conserved glycine-rich loop (GRL) of the a-subunit of the yeast mitochondrial processing peptidase (MPP) and its importance for the tertiary and quaternary conformation of MPP. Wild-type and GRL-deleted MPP structures were studied using non-restrained MD simulations, both in the presence and the absence of a substrate in the peptidase active site. Targeted MD simulations were employed to study the mechanism of substrate translocation from the GRL to the active site. We demonstrate that the natural conformational flexibility of the GRL is crucial for the substrate translocation process from outside the enzyme towards the MPP active site. We show that the a-helical conformation of the substrate is important not only during its initial interaction with MPP (i.e. substrate recognition), but also later, at least during the first third of the substrate translocation trajectory. Further, we show that the substrate remains in contact with the GRL during the whole first half of the translocation trajectory and that hydrophobic interactions play a major role. Finally, we conclude that the GRL acts as a precisely balanced structural element, holding the MPP subunits in a partially closed conformation regardless the presence or absence of a substrate in the active site
dcterms:title
A Computational Study of the Glycine-Rich Loop of Mitochondrial Processing Peptidase A Computational Study of the Glycine-Rich Loop of Mitochondrial Processing Peptidase
skos:prefLabel
A Computational Study of the Glycine-Rich Loop of Mitochondrial Processing Peptidase A Computational Study of the Glycine-Rich Loop of Mitochondrial Processing Peptidase
skos:notation
RIV/61388971:_____/13:00423430!RIV14-MSM-61388971
n11:predkladatel
n12:ico%3A61388971
n3:aktivita
n17:I n17:S n17:P
n3:aktivity
I, P(EE2.3.20.0055), P(EE2.3.30.0003), P(GBP208/12/G016), S
n3:cisloPeriodika
9
n3:dodaniDat
n9:2014
n3:domaciTvurceVysledku
n8:6261817 n8:5649854 n8:2389924 n8:5934915 n8:8171890
n3:druhVysledku
n18:J
n3:duvernostUdaju
n14:S
n3:entitaPredkladatele
n13:predkladatel
n3:idSjednocenehoVysledku
58534
n3:idVysledku
RIV/61388971:_____/13:00423430
n3:jazykVysledku
n7:eng
n3:klicovaSlova
ALPHA-SUBUNIT; BETA-SUBUNIT; CRYSTAL-STRUCTURES
n3:klicoveSlovo
n16:CRYSTAL-STRUCTURES n16:BETA-SUBUNIT n16:ALPHA-SUBUNIT
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[50F82784B88A]
n3:nazevZdroje
PLoS ONE
n3:obor
n19:EE
n3:pocetDomacichTvurcuVysledku
5
n3:pocetTvurcuVysledku
6
n3:projekt
n10:EE2.3.30.0003 n10:GBP208%2F12%2FG016 n10:EE2.3.20.0055
n3:rokUplatneniVysledku
n9:2013
n3:svazekPeriodika
8
n3:tvurceVysledku
Otyepka, M. Janata, Jiří Samad, Abdul Kučera, Tomáš Matušková, Anna Kutejová, Eva
n3:wos
000324408400082
s:issn
1932-6203
s:numberOfPages
13
n15:doi
10.1371/journal.pone.0074518