title: Integrating computational modeling and functional assays to decipher the structure-function relationship of influenza virus PB1 protein.
abstract: The influenza virus PB1 protein is the core subunit of the heterotrimeric polymerase complex (PA, PB1 and PB2) in which PB1 is responsible for catalyzing RNA polymerization and binding to the viral RNA promoter. Among the three subunits, PB1 is the least known subunit so far in terms of its structural information. In this work, by integrating template-based structural modeling approach with all known sequence and functional information about the PB1 protein, we constructed a modeled structure of PB1. Based on this model, we performed mutagenesis analysis for the key residues that constitute the RNA template binding and catalytic (TBC) channel in an RNP reconstitution system. The results correlated well with the model and further identified new residues of PB1 that are critical for RNA synthesis. Moreover, we derived 5 peptides from the sequence of PB1 that form the TBC channel and 4 of them can inhibit the viral RNA polymerase activity. Interestingly, we found that one of them named PB1(491-515) can inhibit influenza virus replication by disrupting viral RNA promoter binding activity of polymerase. Therefore, this study has not only deepened our understanding of structure-function relationship of PB1, but also promoted the development of novel therapeutics against influenza virus.
authors.affiliation: 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China.
authors.forename: Chunfeng
authors.initials: C
authors.lastname: Li
authors.affiliation: 1] Suzhou Institute of Systems Medicine, Suzhou. 215123, China [2] Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China.
authors.forename: Aiping
authors.initials: A
authors.lastname: Wu
authors.affiliation: College of Computer Science and Electronic Engineering, Hunan University, Changsha. 410082, China.
authors.forename: Yousong
authors.initials: Y
authors.lastname: Peng
authors.affiliation: Suzhou Institute of Systems Medicine, Suzhou. 215123, China.
authors.forename: Jingfeng
authors.initials: J
authors.lastname: Wang
authors.affiliation: MOH Key Laboratory of Systems Biology of Pahogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, 100730, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China.
authors.forename: Zhigao
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China.
authors.forename: Yongqiang
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China.
authors.forename: Jiuhong
authors.initials: J
authors.lastname: Dong
authors.affiliation: Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China.
authors.forename: Lulan
authors.initials: L
authors.lastname: Wang
authors.affiliation: 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China.
authors.forename: F Xiao-Feng
authors.initials: FX
authors.lastname: Qin
authors.affiliation: 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China [3] Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.
authors.forename: Genhong
authors.initials: G
authors.lastname: Cheng
authors.affiliation: MOH Key Laboratory of Systems Biology of Pahogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, 100730, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Deng
authors.affiliation: 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China [3] Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China.
authors.forename: Taijiao
authors.initials: T
authors.lastname: Jiang
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D004789:Enzyme Activation; D004795:Enzyme Stability; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000502:physiology*; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012367:RNA, Viral / Q000737:chemistry* / Q000648:ultrastructure; D020539:Sequence Analysis, Protein / Q000379:methods; D013329:Structure-Activity Relationship; D018511:Systems Integration; D014764:Viral Proteins / Q000737:chemistry* / Q000378:metabolism* / Q000648:ultrastructure
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins; C077346:influenza virus polymerase basic protein 1