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Masuda T, Kotani O, Yokoyama M, Abe Y, Kawai G, Sato H. Cis-Allosteric Regulation of HIV-1 Reverse Transcriptase by Integrase. Viruses 2022; 15:31. [PMID: 36680070 PMCID: PMC9864105 DOI: 10.3390/v15010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Reverse transcriptase (RT) and integrase (IN) are encoded tandemly in the pol genes of retroviruses. We reported recently that HIV-1 RT and IN need to be supplied as the pol precursor intermediates, in which RT and IN are in fusion form (RTIN) to exert efficient reverse transcription in the context of HIV-1 replication. The mechanism underlying RTIN's effect, however, remains to be elucidated. In this study, we examined the effect of IN fusion on RT during reverse transcription by an in vitro cell-free assay, using recombinant HIV-1 RTIN (rRTIN). We found that, compared to recombinant RT (rRT), rRTIN generated significantly higher cDNAs under physiological concentrations of dNTPs (less than 10 μM), suggesting increased affinity of RTIN to dNTPs. Importantly, the cleavage of RTIN with HIV-1 protease reduced cDNA levels at a low dose of dNTPs. Similarly, sensitivities against RT inhibitors were significantly altered in RTIN form. Finally, analysis of molecular dynamics simulations of RT and RTIN suggested that IN can influence the structural dynamics of the RT active center and the inhibitor binding pockets in cis. Thus, we demonstrated, for the first time, the cis-allosteric regulatory roles of IN in RT structure and enzymatic activity.
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Affiliation(s)
- Takao Masuda
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima, 1-5-45 Bunkyo-ku, Tokyo 113-8519, Japan
| | - Osamu Kotani
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Gakuen, 4-7-1, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Masaru Yokoyama
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Gakuen, 4-7-1, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Yuya Abe
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima, 1-5-45 Bunkyo-ku, Tokyo 113-8519, Japan
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan
| | - Hironori Sato
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Gakuen, 4-7-1, Musashimurayama-shi, Tokyo 208-0011, Japan
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Kotani O, Suzuki Y, Saito S, Ainai A, Ueno A, Hemmi T, Sano K, Tabata K, Yokoyama M, Suzuki T, Hasegawa H, Sato H. Structure-Guided Creation of an Anti-HA Stalk Antibody F11 Derivative That Neutralizes Both F11-Sensitive and -Resistant Influenza A(H1N1)pdm09 Viruses. Viruses 2021; 13:v13091733. [PMID: 34578314 PMCID: PMC8473006 DOI: 10.3390/v13091733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/05/2022] Open
Abstract
The stalk domain of influenza virus envelope glycoprotein hemagglutinin (HA) constitutes the axis connecting the head and transmembrane domains, and plays pivotal roles in conformational rearrangements of HA for virus infection. Here we characterized molecular interactions between the anti-HA stalk neutralization antibody F11 and influenza A(H1N1)pdm09 HA to understand the structural basis of the actions and modifications of this antibody. In silico structural analyses using a model of the trimeric HA ectodomain indicated that the F11 Fab fragment has physicochemical properties, allowing it to crosslink two HA monomers by binding to a region near the proteolytic cleavage site of the stalk domain. Interestingly, the F11 binding allosterically caused a marked suppression of the structural dynamics of the HA cleavage loop and flanking regions. Structure-guided mutagenesis of the F11 antibody revealed a critical residue in the F11 light chain for the F11-mediated neutralization. Finally, the mutagenesis led to identification of a unique F11 derivative that can neutralize both F11-sensitive and F11-resistant A(H1N1)pdm09 viruses. These results raise the possibility that F11 sterically and physically disturbs proteolytic cleavage of HA for the ordered conformational rearrangements and suggest that in silico guiding experiments can be useful to create anti-HA stalk antibodies with new phenotypes.
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Affiliation(s)
- Osamu Kotani
- Center for Pathogen Genomics, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (M.Y.); (H.S.)
- Correspondence: (O.K.); (S.S.)
| | - Yasushi Suzuki
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.S.); (H.H.)
| | - Shinji Saito
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
- Correspondence: (O.K.); (S.S.)
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
| | - Akira Ueno
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
| | - Takuya Hemmi
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
| | - Kaori Sano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
| | - Koshiro Tabata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Hokkaido 001-0020, Japan
| | - Masaru Yokoyama
- Center for Pathogen Genomics, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (M.Y.); (H.S.)
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
| | - Hideki Hasegawa
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.S.); (H.H.)
| | - Hironori Sato
- Center for Pathogen Genomics, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (M.Y.); (H.S.)
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