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Structural Biology of the Enterovirus Replication-Linked 5'-Cloverleaf RNA and Associated Virus Proteins. Microbiol Mol Biol Rev 2020; 84:84/2/e00062-19. [PMID: 32188627 DOI: 10.1128/mmbr.00062-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although enteroviruses are associated with a wide variety of diseases and conditions, their mode of replication is well conserved. Their genome is carried as a single, positive-sense RNA strand. At the 5' end of the strand is an approximately 90-nucleotide self-complementary region called the 5' cloverleaf, or the oriL. This noncoding region serves as a platform upon which host and virus proteins, including the 3B, 3C, and 3D virus proteins, assemble in order to initiate replication of a negative-sense RNA strand. The negative strand in turn serves as a template for synthesis of multiple positive-sense RNA strands. Building on structural studies of individual RNA stem-loops, the structure of the intact 5' cloverleaf from rhinovirus has recently been determined via nuclear magnetic resonance/small-angle X-ray scattering (NMR/SAXS)-based methods, while structures have also been determined for enterovirus 3A, 3B, 3C, and 3D proteins. Analysis of these structures, together with structural and modeling studies of interactions between host and virus proteins and RNA, has begun to provide insight into the enterovirus replication mechanism and the potential to inhibit replication by blocking these interactions.
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Martel E, Forzono E, Kurker R, Clark BA, Neilan JG, Puckette M. Effect of foot-and-mouth disease virus 3C protease B2 β-strand proline mutagenesis on expression and processing of the P1 polypeptide using a plasmid expression vector. J Gen Virol 2019; 100:446-456. [PMID: 30702422 DOI: 10.1099/jgv.0.001204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The production of experimental molecular vaccines against foot-and-mouth disease virus utilizes the viral encoded 3C protease for processing of the P1 polyprotein. Expression of wild type 3C protease is detrimental to host cells. The molecular vaccine constructs containing the 3C protease L127P mutant significantly reduce adverse effects associated with protease expression while retaining the ability to process and assemble virus-like particles. In published 3C protease crystal structures, the L127 residue is contained within the B2 β-strand as part of the A2-B2 β-sheet. To provide insight into the mechanism by which the L127P mutant alters the properties of the 3C protease, we performed scanning proline mutagenesis of residues 123-128 of the B2 β-strand and monitored expression and P1 processing. Simultaneously, we utilized random mutagenesis of the full 3C sequence to identify additional mutations presenting a phenotype similar to the L127P mutation. Six of the tested mutants enhanced expression over wild type, and the I22P, T100P and V124P mutations surpassed the L127P mutation in certain cell lines. These data areinterpreted in conjunction with published 3C protease crystal structures to provide insight into the mechanism by which these mutations enhance expression.
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Affiliation(s)
- Erica Martel
- 1Oak Ridge Institute for Science and Education, Plum Island Animal Disease Center Research Participation Program, Oak Ridge, TN, USA
| | - Emily Forzono
- 1Oak Ridge Institute for Science and Education, Plum Island Animal Disease Center Research Participation Program, Oak Ridge, TN, USA
- †Present address: Coastal Carolina University, 100 Chanticleer Dr W, Conway, SC 29528, USA
| | - Richard Kurker
- 1Oak Ridge Institute for Science and Education, Plum Island Animal Disease Center Research Participation Program, Oak Ridge, TN, USA
- ‡Present address: Bard High School Early College Baltimore, 2801 N. Dukeland Street, Baltimore, MD 21216, USA
| | - Benjamin A Clark
- 2Leidos, Inc., Plum Island Animal Disease Center, Greenport, NY 11944, USA
| | - John G Neilan
- 3U. S. Department of Homeland Security Science and Technology Directorate, Plum Island Animal Disease Center, Greenport, NY 11944, USA
| | - Michael Puckette
- 3U. S. Department of Homeland Security Science and Technology Directorate, Plum Island Animal Disease Center, Greenport, NY 11944, USA
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Gao FS, Feng L, Jiang P, Li ZB, Gao H, Zhai XX, Zhang ZH, Hu X. Expression, purification, crystallization and preliminary X-ray diffraction analysis of swine leukocyte antigen 2 complexed with a CTL epitope AS64 derived from Asia1 serotype of foot-and-mouth disease virus. BMC Vet Res 2018; 14:407. [PMID: 30563524 PMCID: PMC6299498 DOI: 10.1186/s12917-018-1742-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 12/07/2018] [Indexed: 02/05/2023] Open
Abstract
Background Currently, the structural characteristics of the swine major histocompatibility complex (MHC) class I molecule, also named swine leukocyte antigen class I (SLA-I) molecule need to be further clarified. Results A complex of SLA-I constituted by an SLA-2*HB01 molecule with swine β2-microglobulin and a cytotoxic T lymphocyte (CTL) epitope FMDV-AS64 (ALLRSATYY) derived from VP1 protein (residues 64–72) of Asia 1 serotype of foot-and-mouth disease virus (FMDV) was expressed, refolded, purified and crystallized. By preliminary X-ray diffraction analysis, it was shown that the diffraction resolution of the crystal was 2.4 Å and the space group belonged to P212121 with unit cell parameters a = 48.37, b = 97.75, c = 166.163 Å. Conclusion This research will be in favor of illuminating the structural characteristics of an SLA-2 molecule associated with a CTL epitope derived from Asia1 serotype of FMDV.
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Affiliation(s)
- Feng-Shan Gao
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China.
| | - Lei Feng
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Ping Jiang
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Zi-Bin Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100094, People's Republic of China
| | - Hua Gao
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Xiao-Xin Zhai
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Zong-Hui Zhang
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Xiao Hu
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
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Gao FS, Zhai XX, Jiang P, Zhang Q, Gao H, Li ZB, Han Y, Yang J, Zhang ZH. Identification of two novel foot-and-mouth disease virus cytotoxic T lymphocyte epitopes that can bind six SLA-I proteins. Gene 2018; 653:91-101. [PMID: 29432828 DOI: 10.1016/j.gene.2018.02.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 01/24/2018] [Accepted: 02/08/2018] [Indexed: 10/18/2022]
Abstract
Currently available vaccines from inactivated foot-and-mouth disease virus (FMDV) only protect animals by inducing neutralizing antibodies. A vaccine that contains cytotoxic T lymphocytes (CTL) epitopes to induce strong CTL responses might protect animals more effectively. Herein, we used swine leukocyte antigen class I (SLAI) proteins derived from six different strains of domestic pigs to screen and identify shared FMDV CTL epitopes. Four potential FMDV CTL epitopes (Q01, Q02, AS3, and QA4) were confirmed by mass spectrometry. We also determined the antigenicity of these epitopes to elicit cell-mediated immunoresponse by the ELISPOT and CTL assays. Among the four peptides, Q01 and QA4 were found to bind all six SLA-I proteins with strong affinity and elicit significant activity of CTL (P < 0.01). We conclude that Q01 and QA4 peptides are novel shared epitopes that can be recognized by all six SLA-I molecules on representative CTLs.
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Affiliation(s)
- Feng-Shan Gao
- Department of Bioengineering, College of Life Science and Technology, Dalian University, Dalian, Liaoning 116622, PR China.
| | - Xiao-Xin Zhai
- Department of Bioengineering, College of Life Science and Technology, Dalian University, Dalian, Liaoning 116622, PR China
| | - Ping Jiang
- Department of Bioengineering, College of Life Science and Technology, Dalian University, Dalian, Liaoning 116622, PR China
| | - Qiang Zhang
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzou, Gansu 730046, PR China
| | - Hua Gao
- Department of Bioengineering, College of Life Science and Technology, Dalian University, Dalian, Liaoning 116622, PR China
| | - Zi-Bin Li
- Department of Bioengineering, College of Life Science and Technology, Dalian University, Dalian, Liaoning 116622, PR China; Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, PR China
| | - Yong Han
- Department of Bioengineering, College of Life Science and Technology, Dalian University, Dalian, Liaoning 116622, PR China
| | - Jie Yang
- Department of Bioengineering, College of Life Science and Technology, Dalian University, Dalian, Liaoning 116622, PR China
| | - Zong-Hui Zhang
- Department of Bioengineering, College of Life Science and Technology, Dalian University, Dalian, Liaoning 116622, PR China
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Dauter Z, Jaskolski M. On the helical arrangements of protein molecules. Protein Sci 2017; 27:643-652. [PMID: 29194829 DOI: 10.1002/pro.3356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/22/2017] [Accepted: 11/28/2017] [Indexed: 11/09/2022]
Abstract
Helical structures are prevalent in biology. In the PDB, there are many examples where protein molecules are helically arranged, not only according to strict crystallographic screw axes but also according to approximate noncrystallographic screws. The preponderance of such screws is rather striking as helical arrangements in crystals must preserve an integer number of subunits per turn, while intuition and simple packing arguments would seem to favor fractional helices. The article provides insights into such questions, based on stereochemistry, trigonometry, and topology, and illustrates the findings with concrete PDB structures. Updated statistics of Sohncke space groups in the PDB are also presented.
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Affiliation(s)
- Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, 61-614, Poland.,Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
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Affiliation(s)
- Kimi Azad
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India;,
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India;,
| | - John E. Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037
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