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Capsid Anatomy

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Welcome to the Capsid Anatomy project! Diana Y. Lee is leading the project as part of the Luque lab. Diana is a candidate in the Computational Science program at San Diego State University (SDSU). There are other memebers of the lab involved in the project: Caitlin Bartels, Colin Brown, Brandon Ricafrente, Aurora Vogel, and Jessica Vogt. The project is supervised by the lab’s principal investigator, Antoni (Toni) Luque, Ph.D. Toni is an associate professor in the Department of Mathematics & Statistics, Viral Information Institute, and Computational Science Research Center at SDSU. Don’t hesitate in contacting Toni (aluque@sdsu.edu) if you have any questions, comments, or interests about the project.

What

This project aims to establish gold standard practices to describe and compare the structural anatomy of viral capsids. The current main focus is developing an automatic pipeline that identifies the icosahedral architecture of a capsid and generates visuals comparing the geometrical model and the capsid’s molecular structure. Explore our online documentation to know more our findings (Output and Impact), and the take home message of what we’ve learned so far (Synthesis).

Why

Viruses are the most abundant biological entity on Earth. They usually form a protein shell to protect the viral infective genome, and the majority of viral capsids display mesmerizing icosahedral symmetries. However, we have just start scratching the surface on the possible icosahedral architectures that viruses can built. New quantitative methods and computational pipelines are needed to faciliate the characterization and comparison of these viral capsids. Explore our online documentation to know more about the project’s motivation (Background).

How

Here is the approach’s cornerstone: An icosahedral architecture is considered an adequate characterizatio of a viral capsid if the capsid proteins organize in clusters that are compatible with the geometrical tiles of the proposed architecture. The logical flow is the following: Given a viral capsid, the number of proteins forming the capsid selects plausible architectures based on the eight Archimedean lattices capable of generating icosahedral capsids. The geometrical model candidates are generated with the hkcage tool in the molecular visualization software UCSF Chimera X. The potential geometrical architectures are ranked based on the ability of the constitutive tiles to enclose the capsid protein clusters. High-quality visuals are generated to make a final qualitatively judgement of the best choice. Explore our online documentation to know more about the methods developed and applied in the project (Approach).

The ability of viruses to make icosahedral capsids is a fascinating topic. Learn more about icosahedral capsids in the popular VIPERdb and Viral Zone websites. The lab has extensively contributed to this topic from a geometric, thermodynamic, kinetic, mechanical, ecological, and evolutionary angles. The lab has received funding from the National Science Foundation to progress on this topic. Here are some of the references:

  • NSF Award #1951678, Characterization and Prediction of Viral Capsid Geometries, $300,000.00, September 1, 2020, to August 31, 2023.
  • Luque, Antoni, et al. “The missing tailed phages: prediction of small capsid candidates.” Microorganisms, 8(12):1944 (2020). https://doi.org/10.3390/microorganisms8121944.
  • Twarock, Reidun, and Antoni Luque. “Structural puzzles in virology solved with an overarching icosahedral design principle.” Nature Communications, 10(1):1-9 (2019). https://doi.org/10.1038/s41467-019-12367-3.
  • Hernando-Pérez, Mercedes, et al. “The interplay between mechanics and stability of viral cages.” Nanoscale, 6(5):2702-2709 (2014). https://doi.org/10.1039/C3NR05763A.
  • Luque, Antoni, and David Reguera. “Theoretical studies on assembly, physical stability and dynamics of viruses.” structure and physics of viruses. In Mauricio Mateu (eds) Structure and Physics of Viruses. Subcellular Biochemistry, vol 68. Springer, Dordrecht: 553-595 (2013). https://doi.org/10.1007/978-94-007-6552-8_19.
  • Luque, Antoni, et al. “Physics of shell assembly: Line tension, hole implosion, and closure catastrophe.” The Journal of Chemical Physics, 136(18):184507 (2012). https://doi.org/10.1063/1.4712304.
  • Aznar, Maria, Antoni Luque, and David Reguera. “Relevance of capsid structure in the buckling and maturation of spherical viruses.” Physical Biology, 9(3):036003 (2012). https://doi.org/10.1088/1478-3975/9/3/036003.
  • Carrasco, Carolina, A. Luque, M. Hernando-Pérez, Roberto Miranda, Jose L. Carrascosa, P. A. Serena, M. De Ridder et al. “Built-in mechanical stress in viral shells.” Biophysical Journal, 100(4): 1100-1108 (2011). https://doi.org/10.1016/j.bpj.2011.01.008.
  • Luque, Antoni, and David Reguera. “The structure of elongated viral capsids.” Biophysical Journal, 98(12):2993-3003 (2010). https://doi.org/10.1016/j.bpj.2010.02.051.
  • Luque, Antoni, Roya Zandi, and David Reguera. “Optimal architectures of elongated viruses.” Proceedings of the National Academy of Sciences, 107(12):5323-5328 (2010). https://doi.org/10.1073/pnas.0915122107.