WikiJournal of Science/Structural Model of Bacteriophage T4

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Article information

Author: Victor Padilla-Sanchez[a][i]ORCID iD.svg 

Victor Padilla-Sanchez (5 August 2021), "Structural Model of Bacteriophage T4", WikiJournal of Science, 4 (1): 5, doi:10.15347/WJS/2021.005, ISSN 2470-6345, Wikidata Q100272642





Abstract

Bacteriophage T4 is a virus that infects Escherichia coli, having dimensions of 90 nm in width and 200 nm in length (head and tail in extended form).[1] It is a quite common model organism that has been studied for a century by many important virologists, and even Watson and Crick after their elucidation of DNA. Structural characterisation of the bacteriophage’s individual proteins began in the 1980s,[2] and complexes of multiple proteins in the 1990s.[3] However, it has not yet been possible to structurally characterise the complete phage in atomic detail (though some have begun to come closer)[4] with multiple overall schematic models published.[5]

The increasing power of computers and the RCSB structural database have made possible the construction of a single combined model of the entire bacteriophage T4 organism with atomic resolution components as described here.


Introduction

T4 Bacteriophage.gif

 Bacteriophage T4 Structural Model


The complete structural model for bacteriophage T4 has been constructed thanks to the determination of the structures of single proteins that constitute the virus as well as various parts of the virus. First, the capsid (head) of the virus was constructed using a 3D cryoEM reconstruction where each individual protein was fitted into the EM density: soc in orange, hoc in blue, gp23 in green, gp24 in magenta, and gp20 in red (though gp20 is hidden between the head and tail). A similar procedure was followed for the construction of the tail and tail fibers.[6][7] Although each of the component proteins has been described in detail during decades of research, this combined structural model, whilst not perfect, is the best reconstruction of the entire organism that we have today as of 2021.

Reconstruction

This reconstruction largely used the molecular visualization software UCSF Chimera[8] in a personal computer, and where necessary for some tasks, in supercomputers like Bridges for Pittsburgh and Frontera from Texas. This combined structural model has been constructed and updated over time my work in Catholic University of America (where I started in 2007) as new structures of the components have been solved by other researchers, and therefore is the accumulated work of many years of research.

There are approximately 50 structural proteins that assemble the virus which is constructed with protein databank (PDB) structures and one cryoEM reconstruction from the Electron Microscopy Data Bank (EMDB) corresponding to the brown ring between head and tail. This structure can be used for teaching at any level of education and research because is accurate at atomic resolution and therefore can be used to derive hypotheses (e.g., how antigen-display technology could be used with bacteriophage T4). The protein colours are chosen to differentiate between them and make contrast as well as showing art in science, but some colours are the same for different proteins (e.g., soc in the head and gp18 in the tail). As a reference for further publications, you can look at Bacteriophage T4 in Wikipedia where each protein is described in different research articles.

List of PDB and EMDB structures

  • Head: hoc (PDB: 3shs​ - blue), soc (PDB: 5vf3​ - orange), gp23 (PDB: 5vf3​ - dark green), gp24 (PDB: 5vf3​ - dark magenta), gp20 (PDB: 6uzc​ - dark red)
  • Collar: brown (EM density from EMDB: 1075​)
  • Wac fibres: PDB: 2bsg​ - dark green
  • Neck: brown gp13 and gp14 are represented by an EM density from EMDB: 1075
  • Tail:[7] gp15 (PDB: 3j2m​ - orange), gp18 (PDB: 3j2m​ - orange/red)
  • Tail base plate:[7] (PDB: 5iv5​ - dark green/blue/dark red/purple)
  • Long Tail Fibers:[1] composites of gp37 (PDB: 2xgf​) and gp34 (PDB: 4uxf​) repeated to form the long tail fibre.

Note: same protein colours do not necessarily define same proteins.

Additional information

Acknowledgements

  1. This work used the Extreme Science and Engineering Discovery Environment (XSEDE),[9] which is supported by National Science Foundation grant number ACI-1548562. Specifically, it used the Bridges system,[10] which is supported by NSF award number ACI-1445606, at the Pittsburgh Supercomputing Center (PSC).
  2. Stanzione, Dan; West, John; Evans, R. Todd; Minyard, Tommy; Ghattas, Omar; Panda, Dhabaleswar K. (2020-07-26). "Frontera: The Evolution of Leadership Computing at the National Science Foundation". Practice and Experience in Advanced Research Computing (PEARC '20) (New York, NY, USA: Association for Computing Machinery): 106–111. doi:10.1145/3311790.3396656. ISBN 978-1-4503-6689-2. https://dl.acm.org/doi/10.1145/3311790.3396656. 

Competing interests

The author declares no competing interests.

References

  1. 1.0 1.1 Yap, Moh Lan; Rossmann, Michael G (2014-12). "Structure and function of bacteriophage T4". Future Microbiology 9 (12): 1319–1327. doi:10.2217/fmb.14.91. ISSN 1746-0913. PMID 25517898. PMC PMC4275845. https://www.futuremedicine.com/doi/10.2217/fmb.14.91. 
  2. Weaver, L.H.; Matthews, B.W. (1987-01). "Structure of bacteriophage T4 lysozyme refined at 1.7 Å resolution". Journal of Molecular Biology 193 (1): 189–199. doi:10.1016/0022-2836(87)90636-X. https://linkinghub.elsevier.com/retrieve/pii/002228368790636X. 
  3. Hunt, John F; van der Vies, Saskia M; Henry, Lisa; Deisenhofer, Johann (1997-07). "Structural Adaptations in the Specialized Bacteriophage T4 Co-Chaperonin Gp31 Expand the Size of the Anfinsen Cage". Cell 90 (2): 361–371. doi:10.1016/S0092-8674(00)80343-8. https://linkinghub.elsevier.com/retrieve/pii/S0092867400803438. 
  4. Chen, Zhenguo; Sun, Lei; Zhang, Zhihong; Fokine, Andrei; Padilla-Sanchez, Victor; Hanein, Dorit; Jiang, Wen; Rossmann, Michael G. et al. (2017-09-26). "Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses". Proceedings of the National Academy of Sciences 114 (39): E8184–E8193. doi:10.1073/pnas.1708483114. ISSN 0027-8424. PMID 28893988. PMC PMC5625921. http://www.pnas.org/lookup/doi/10.1073/pnas.1708483114. 
  5. Leiman, P. G.; Kanamaru, S.; Mesyanzhinov, V. V.; Arisaka, F.; Rossmann, M. G. (2003-11-01). "Structure and morphogenesis of bacteriophage T4". Cellular and Molecular Life Sciences (CMLS) 60 (11): 2356–2370. doi:10.1007/s00018-003-3072-1. ISSN 1420-682X. http://link.springer.com/10.1007/s00018-003-3072-1. 
  6. Mesyanzhinov, V. V.; Leiman, P. G.; Kostyuchenko, V. A.; Kurochkina, L. P.; Miroshnikov, K. A.; Sykilinda, N. N.; Shneider, M. M. (2004-11). "Molecular architecture of bacteriophage T4". Biochemistry (Moscow) 69 (11): 1190–1202. doi:10.1007/s10541-005-0064-9. ISSN 0006-2979. http://link.springer.com/10.1007/s10541-005-0064-9. 
  7. 7.0 7.1 7.2 Taylor, Nicholas M. I.; Prokhorov, Nikolai S.; Guerrero-Ferreira, Ricardo C.; Shneider, Mikhail M.; Browning, Christopher; Goldie, Kenneth N.; Stahlberg, Henning; Leiman, Petr G. (2016-05). "Structure of the T4 baseplate and its function in triggering sheath contraction". Nature 533 (7603): 346–352. doi:10.1038/nature17971. ISSN 0028-0836. http://www.nature.com/articles/nature17971. 
  8. Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.; Couch, Gregory S.; Greenblatt, Daniel M.; Meng, Elaine C.; Ferrin, Thomas E. (2004-10). "UCSF Chimera—A visualization system for exploratory research and analysis". Journal of Computational Chemistry 25 (13): 1605–1612. doi:10.1002/jcc.20084. ISSN 0192-8651. http://doi.wiley.com/10.1002/jcc.20084. 
  9. Towns, John; Cockerill, Timothy; Dahan, Maytal; Foster, Ian; Gaither, Kelly; Grimshaw, Andrew; Hazlewood, Victor; Lathrop, Scott et al. (2014-09). "XSEDE: Accelerating Scientific Discovery". Computing in Science & Engineering 16 (5): 62–74. doi:10.1109/MCSE.2014.80. ISSN 1521-9615. https://ieeexplore.ieee.org/document/6866038/. 
  10. Nystrom, Nicholas A.; Levine, Michael J.; Roskies, Ralph Z.; Scott, J. Ray (2015). "Bridges: a uniquely flexible HPC resource for new communities and data analytics". Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure (in en). St. Louis, Missouri: ACM Press. pp. 1–8. doi:10.1145/2792745.2792775. ISBN 978-1-4503-3720-5. http://dl.acm.org/citation.cfm?doid=2792745.2792775.