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Substrate recognition by norovirus polymerase: microsecond molecular dynamics study
K. Maláč, I. Barvík,
Language English Country Netherlands
Document type Journal Article, Research Support, Non-U.S. Gov't
NLK
ProQuest Central
from 1997-01-01 to 2017-12-31
Medline Complete (EBSCOhost)
from 2003-01-01 to 1 year ago
Health & Medicine (ProQuest)
from 1997-01-01 to 2017-12-31
- MeSH
- Cytidine Triphosphate analogs & derivatives metabolism MeSH
- Caliciviridae Infections virology MeSH
- Humans MeSH
- Norovirus enzymology metabolism MeSH
- RNA-Dependent RNA Polymerase metabolism MeSH
- Molecular Dynamics Simulation MeSH
- Molecular Docking Simulation MeSH
- Substrate Specificity MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Molecular dynamics simulations of complexes between Norwalk virus RNA dependent RNA polymerase and its natural CTP and 2dCTP (both containing the O5'-C5'-C4'-O4' sequence of atoms bridging the triphosphate and sugar moiety) or modified coCTP (C5'-O5'-C4'-O4'), cocCTP (C5'-O5'-C4'-C4'') substrates were produced by means of CUDA programmable graphical processing units and the ACEMD software package. It enabled us to gain microsecond MD trajectories clearly showing that similar nucleoside triphosphates can bind surprisingly differently into the active site of the Norwalk virus RNA dependent RNA polymerase. It corresponds to their different modes of action (CTP-substrate, 2dCTP-poor substrate, coCTP-chain terminator, cocCTP-inhibitor). Moreover, extremely rare events-as repetitive pervasion of Arg182 into a potentially reaction promoting arrangement-were captured.
References provided by Crossref.org
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