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Substrate recognition by norovirus polymerase: microsecond molecular dynamics study

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Abstract

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.

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Acknowledgments

This work was supported by the Grant Agency of the Czech Republic (202/09/0193). The access to computing and storage facilities owned by parties and projects contributing to the National Grid Infrastructure MetaCentrum, provided under the programme “Projects of Large Infrastructure for Research, Development, and Innovations” (LM2010005) is highly acknowledged.

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  1. Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, Prague 2, 121 16, Czech Republic

    Kamil Maláč & Ivan Barvík

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  1. Kamil Maláč
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Correspondence to Ivan Barvík.

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10822_2013_9652_MOESM1_ESM.tif

Figure S1: NV RdRp in complex with nucleic acids (PDB id: 3BSO [3-4]). NV RdRp has a typical structure of polymerases resembling the right hand (palm—grey, thumb—blue, fingers—red). In RdRps, thumb and fingers are bound, and hence not allowed to change conformation independently (TIFF 2797 kb)

10822_2013_9652_MOESM2_ESM.tif

Figure S2: CTP in the active site of NV RdRp shown in the context of Primer and Template RNA. Mg2+ ions are bound by conserved aspartic acids (Asp344, Asp343, Asp242) in the palm domain of NV RdRp (TIFF 14913 kb)

10822_2013_9652_MOESM3_ESM.tif

Figure S2: CTP in the active site of NV RdRp shown in the context of Primer and Template RNA. Mg2+ ions are bound by conserved aspartic acids (Asp344, Asp343, Asp242) in the palm domain of NV RdRp (TIFF 11186 kb)

Figure S3: Structure of CTP, 2dCTP, coCTP and cocCTP (TIFF 128 kb)

Figure S4: Point charges (TIFF 293 kb)

Figure S5: Force constants for modified parts of CTP analogs (DOC 5 kb)

Figure S6: Time evolution of the total energy within MD simulations (TIFF 6371 kb)

Figure S7: Time evolution of RMSD for NV RdRp and nucleic acids (EPS 55 kb)

10822_2013_9652_MOESM9_ESM.eps

Figure S8: Time evolution of Mg1 2+–Mg2 2+, Mg1 2+—ligand and Mg2 2+—ligand distances in the NV RdRp active site. Mg1 2+ ligands (see Figure S2b) are distinguished in charts by the following color code: water molecule (red line), 3′ RNA terminus (green), α-phosphate/phosphonate group of CTP/2dCTP/coCTP/cocCTP (blue), Asp344 (magenta), Asp343 (cyan), Asp242 (yellow). Mg2 2+ ligands are distinguished in charts by the following color code: α-phosphate/phosphonate group of CTP/2dCTP/coCTP/cocCTP (red), β-phosphate group (green), γ-phosphate group (blue), Tyr243 (magenta), Asp242 (cyan), Asp343 (yellow) (EPS 32060 kb)

Figure S9: Time evolution of distances between RNA_primer_C2′ and C1′_xCTP atoms (EPS 455 kb)

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Maláč, K., Barvík, I. Substrate recognition by norovirus polymerase: microsecond molecular dynamics study. J Comput Aided Mol Des 27, 373–388 (2013). https://doi.org/10.1007/s10822-013-9652-8

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