Norovirus RNA‐dependent RNA polymerase: A computational study of metal‐binding preferences

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2017-08, Vol.85 (8), p.1435-1445
• Main Authors: Shaik, Md Munan, Bhattacharjee, Nicholus, Feliks, Mikolaj, Ng, Kenneth K.‐S., Field, Martin J.
• Format: Article
• Language: English
• Subjects: Amino Acid Motifs; Antiviral agents; Binding energy; Binding Sites; Catalytic Domain; Cations; Cations, Divalent; Cobalt; Cobalt - chemistry; Computer applications; Computer simulation; Copper - chemistry; Crystallization; Crystallography; Crystallography, X-Ray; DNA-directed RNA polymerase; Enzymes; Gastroenteritis; Genomes; Iron; Iron - chemistry; Kinetics; Manganese; Manganese - chemistry; Manganese ions; metal binding; Metals; Molecular Dynamics Simulation; Nickel; Nickel - chemistry; norovirus; Norovirus - chemistry; Norovirus - enzymology; Oligoribonucleotides - chemistry; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Proteins; quantum chemical/molecular mechanical hybrid potentials; Quantum chemistry; Quantum Theory; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; Replicating; Ribonucleic acid; RNA; RNA polymerase; RNA Replicase - chemistry; RNA Replicase - genetics; RNA Replicase - metabolism; RNA-directed RNA polymerase; RNA‐dependent RNA polymerase; Substrate Specificity; Thermodynamics; Tracking; Translocation; Viral Proteins - chemistry; Viral Proteins - genetics; Viral Proteins - metabolism; Viruses; X-ray crystallography; Zinc; Zinc - chemistry
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.25304

ABSTRACT Norovirus (NV) RNA‐dependent RNA polymerase (RdRP) is essential for replicating the genome of the virus, which makes this enzyme a key target for the development of antiviral agents against NV gastroenteritis. In this work, a complex of NV RdRP bound to manganese ions and an RNA primer‐template duplex was investigated using X‐ray crystallography and hybrid quantum chemical/molecular mechanical simulations. Experimentally, the complex crystallized in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back‐tracked state of the enzyme, in which the 3′‐end of the primer occupies the position expected for the post‐incorporated nucleotide before translocation. Computationally, it is found that the complex can accept a range of divalent metal cations without marked distortions in the active site structure. The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt. Proteins 2017; 85:1435–1445. © 2017 Wiley Periodicals, Inc.