Structural analysis of H1N1 and H7N9 influenza A virus PA in the absence of PB1

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Moen, Spencer O ^a,b   Abendroth, Jan ^a,b   Fairman, James W ^a,b   Baydo, Ruth O ^a,b   Bullen, Jameson ^a,b   Kirkwood, Jennifer L ^a,b   Barnes, Steve R ^a,b   Raymond, Amy C ^a,b   Begley, Darren W ^a,b   Henkel, Greg ^c   McCormack, Ken ^c   Tam, Vincent C ^d   Phan, Isabelle ^a,d   Staker, Bart L ^a,d   Stacy, Robin ^a,d   Myler, Peter J ^a,d,e   Lorimer, Don ^a,b   Edwards, Thomas E ^a,b  

^a Seattle Structural Genomics Center for Infectious Disease SSGCID   (United States)

^b Beryllium   (United States)

^c Arisan Therapeutics   (United States)

^d Seattle BioMed   (United States)

^e UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INFLUENZA VIRUS POLYMERASE BASIC PROTEIN 1; PA PROTEIN, INFLUENZA VIRUSES; PROTEIN BINDING; RECOMBINANT PROTEIN; RNA DIRECTED RNA POLYMERASE; VIRAL PROTEIN;

AMINO ACID SEQUENCE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME STABILITY; ENZYMOLOGY; ESCHERICHIA COLI; GENE EXPRESSION; GENETICS; INFLUENZA A VIRUS (H1N1); INFLUENZA A VIRUS (H7N9); METABOLISM; MOLECULAR GENETICS; PHYSIOLOGY; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; VIRUS REPLICATION; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ENZYME STABILITY; ESCHERICHIA COLI; GENE EXPRESSION; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA A VIRUS, H7N9 SUBTYPE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; RNA REPLICASE; VIRAL PROTEINS; VIRUS REPLICATION;

EID: 84905454525     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep05944     Document Type: Article

References (35)

1. Resa-Infante, P., Jorba, N., Coloma, R. & Ortin, J. The influenza virus RNA synthesis machine: advances in its structure and function. RNA Biol. 8, 207-215 (2011).
2. Nagata, K., Kawaguchi, A. & Naito, T. Host factors for replication and transcription of the influenza virus genome. Rev. Med. Virol. 18, 247-260 (2008). (Pubitemid 352018848)
3. Sivasubramanian, N. & Nayak, D. P. Sequence analysis of the polymerase 1 gene and the secondary structure prediction of polymerase 1 protein of human influenza virus A/WSN/33. J. Virol. 44, 321-329 (1982). (Pubitemid 12020924)
4. Steitz, T. A. A mechanism for all polymerases. Nature 391, 231-232 (1998).
5. Binh, N. T., Wakai, C., Kawaguchi, A. & Nagata, K. The N-terminal region of influenza virus polymerase PB1 adjacent to the PA binding site is involved in replication but not transcription of the viral genome. Frontiers in Microbiol. 4, 398 (2013).
6. Hemerka, J. N. et al. Detection and characterization of influenza A virus PA-PB2 interaction through a bimolecular fluorescence complementation assay. J. Virol. 83, 3944-3955 (2009).
7. Shi, M. et al. Evolutionary conservation of the PA-X open reading frame in segment 3 of influenza A virus. J. Virol. 86, 12411-12413 (2012).
8. Dias, A. et al. The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit. Nature 458, 914-918 (2009).
9. Yuan, P. et al. Crystal structure of an avian influenza polymerase PA(N) reveals an endonuclease active site. Nature 458, 909-913 (2009).
10. Zhao, C. et al. Nucleoside monophosphate complex structures of the endonuclease domain from the influenza virus polymerase PA subunit reveal the substrate binding site inside the catalytic center. J. Virol. 83, 9024-9030 (2009).
11. Bauman, J. D. et al. Crystallographic fragment screening and structure-based optimization yields a new class of influenza endonuclease inhibitors. ACS Chem. Biol. 8, 2501-2508 (2013).
12. Kowalinski, E. et al. Structural analysis of specific metal chelating inhibitor binding to the endonuclease domain of influenza pH1N1 (2009) polymerase. PLoS Pathog. 8, e1002831 (2012).
13. He, X. et al. Crystal structure of the polymerase PA(C)-PB1(N) complex from an avian influenza H5N1 virus. Nature 454, 1123-1126 (2008).
14. Obayashi, E. et al. The structural basis for an essential subunit interaction in influenza virus RNA polymerase. Nature 454, 1127-1131 (2008).
15. Sugiyama, K. et al. Structural insight into the essential PB1-PB2 subunit contact of the influenza virus RNA polymerase. EMBO J. 28, 1803-1811 (2009).
16. Chen, E. et al. Computation-guided discovery of influenza endonuclease inhibitors. ACS Med. Chem. Lett. 5, 61-64 (2014).
17. Chase, G., Wunderlich, K., Reuther, P. & Schwemmle, M. Identification of influenza virus inhibitors which disrupt of viral polymerase protein-protein interactions. Methods 55, 188-191 (2011).
18. Wunderlich, K. et al. Identification of high-affinity PB1-derived peptides with enhanced affinity to the PA protein of influenza A virus polymerase. Antimicrob. Agents Chemother. 55, 696-702 (2011).
19. Muratore, G. et al. Small molecule inhibitors of influenza A and B viruses that act by disrupting subunit interactions of the viral polymerase. Proc. Natl. Acad. Sci. USA 109, 6247-6252 (2012).
20. Pagano, M. et al. The fight against the influenza A virus H1N1: synthesis, molecular modeling, and biological evaluation of benzofurazan derivatives as viral RNA polymerase inhibitors. ChemMedChem 9, 129-150 (2014).
21. Tintori, C. et al. High-throughput docking for the identification of new influenza A virus polymerase inhibitors targeting the PA-PB1 protein-protein interaction. Bioorg. Med. Chem. Lett. 24, 280-282 (2014).
22. Lorimer, D. et al. Gene composer: database software for protein construct design, codon engineering, and gene synthesis. BMC Biotechnol. 9, 36 (2009).
23. Raymond, A. et al. Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer. BMC Biotechnol. 9, 37 (2009).
24. Niesen, F. H., Berglund, H. & Vedadi, M. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nature Protoc. 2, 2212-2221 (2007). (Pubitemid 351565860)
25. Mehle, A., Dugan, V. G., Taubenberger, J. K. & Doudna, J. A. Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. J. Virol. 86, 1750-1757 (2012).
26. Armour, B. L. et al. Multi-target parallel processing approach for gene-to-structure determination of the influenza polymerase PB2 subunit. J. Vis. Exp. June 26, 76; DOI: 10.3791/4225 (2013).
27. Smith, E. R. et al. The Protein Maker: an automated system for high-throughput parallel purification. Acta Cryst. F 67, 1015-1021 (2011).
28. Yamada, S. et al. Biological and structural characterization of a host-adapting amino acid in influenza virus. PLoS Pathog. 6, e1001034 (2010).
29. Gorrec, F. The MORPHEUS protein crystallization screen. J Appl. Crystallogr. 42, 1035-1042 (2009).
30. Kabsch, W. Xds. Acta Crystallogr D Biol Crystallogr 66, 125-132 (2010).
31. McCoy, A. J. et al. Phaser crystallographic software. J Appl Crystallogr 40, 658-674 (2007). (Pubitemid 47080256)
32. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structuresbythe maximum-likelihood method. Acta Cryst.D53, 240-255 (1997). (Pubitemid 27235885)
33. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Cryst. D 60, 2126-2132 (2004). (Pubitemid 41742764)
34. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Cryst. D 66, 12-21 (2010).
35. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. D 66, 213-221 (2010).