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Description
  • 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.
  • 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. (en)
Title
  • Substrate recognition by norovirus polymerase: microsecond molecular dynamics study
  • Substrate recognition by norovirus polymerase: microsecond molecular dynamics study (en)
skos:prefLabel
  • Substrate recognition by norovirus polymerase: microsecond molecular dynamics study
  • Substrate recognition by norovirus polymerase: microsecond molecular dynamics study (en)
skos:notation
  • RIV/00216208:11320/13:10190059!RIV14-GA0-11320___
http://linked.open...avai/riv/aktivita
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  • I, P(GA202/09/0193)
http://linked.open...iv/cisloPeriodika
  • 4
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  • 108914
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  • RIV/00216208:11320/13:10190059
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  • ACEMD; CUDA; GPU; NAMD; Chain terminator; Competitive inhibitor; Phosphonate; Molecular dynamics; RNA dependent RNA polymerase; Hepatitis C virus; Norwalk virus (en)
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  • NL - Nizozemsko
http://linked.open...ontrolniKodProRIV
  • [C52D891A21B0]
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  • Journal of Computer-Aided Molecular Design
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  • 27
http://linked.open...iv/tvurceVysledku
  • Barvík, Ivan
  • Maláč, Kamil
http://linked.open...ain/vavai/riv/wos
  • 000320505600007
issn
  • 0920-654X
number of pages
http://bibframe.org/vocab/doi
  • 10.1007/s10822-013-9652-8
http://localhost/t...ganizacniJednotka
  • 11320
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