Structural dynamics as a contributor to error-prone replication by an RNA-dependent RNA polymerase.
RNA viruses encoding high- or low-fidelity RNA-dependent RNA polymerases (RdRp) are attenuated. The ability to predict residues of the RdRp required for faithful incorporation of nucleotides represents an essential step in any pipeline intended to exploit perturbed fidelity as the basis for rational design of vaccine candidates. We used x-ray crystallography, molecular dynamics simulations, NMR spectroscopy, and pre-steady-state kinetics to compare a mutator (H273R) RdRp from poliovirus to the wild-type (WT) enzyme. We show that the nucleotide-binding site toggles between the nucleotide binding-occluded and nucleotide binding-competent states. The conformational dynamics between these states were enhanced by binding to primed template RNA. For the WT, the occluded conformation was favored; for H273R, the competent conformation was favored. The resonance for Met-187 in our NMR spectra reported on the ability of the enzyme to check the correctness of the bound nucleotide. Kinetic experiments were consistent with the conformational dynamics contributing to the established pre-incorporation conformational change and fidelity checkpoint. For H273R, residues comprising the active site spent more time in the catalytically competent conformation and were more positively correlated than the WT. We propose that by linking the equilibrium between the binding-occluded and binding-competent conformations of the nucleotide-binding pocket and other active-site dynamics to the correctness of the bound nucleotide, faithful nucleotide incorporation is achieved. These studies underscore the need to apply multiple biophysical and biochemical approaches to the elucidation of the physical basis for polymerase fidelity.
From the Department of Biochemistry and Molecular Biology.
Ibrahim M
IM
Moustafa
From the Department of Biochemistry and Molecular Biology.
Victoria K
VK
Korboukh
From the Department of Biochemistry and Molecular Biology.
Jamie J
JJ
Arnold
From the Department of Biochemistry and Molecular Biology.
Eric D
ED
Smidansky
the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
Laura L
LL
Marcotte
the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
David W
DW
Gohara
the Department of Chemistry.
Xiaorong
X
Yang
the Department of Chemical Engineering, and.
María Antonieta
MA
Sánchez-Farrán
the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
David
D
Filman
the Department of Chemical Engineering, and.
Janna K
JK
Maranas
the Department of Chemistry.
David D
DD
Boehr
the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
James M
JM
Hogle
the Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 and.
Coray M
CM
Colina
From the Department of Biochemistry and Molecular Biology, cec9@psu.edu.
Craig E
CE
Cameron
D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009154:Mutation; D020125:Mutation, Missense; D009711:Nucleotides / Q000737:chemistry; D017955:Poliovirus / Q000201:enzymology*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012367:RNA, Viral / Q000737:chemistry / Q000502:physiology; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry* / Q000235:genetics; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics
D009711:Nucleotides; D012367:RNA, Viral; D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase
Lethal Mutagenesis; Plus-stranded RNA Virus; Poliovirus; Polymerase Fidelity; Population Genetics; RNA Polymerase; RNA Virus; Viral Replication