Comprehensive Analysis of the Relationship Between Triangulation Number, Baltimore Classification, Hosts, Point Arrays, and Gauge Points of Each Type of Spherical Virus

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Authors
Roof, Danielle A.
Issue Date
2020-11-01
Type
Thesis
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en_US
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Abstract
Viruses are complex nucleic acid-filled capsids that are completely dependent on their host cells’ machinery to reproduce and survive. Their self-assembling outer structural shells are called capsids, which enclose the genetic material. Spherical viruses follow icosahedral symmetry and their capsids have geometric constraints with protruding features on the great circles. Triangulation Number is used to classify spherical viruses’ capsids while the 7 Baltimore Classification classes describe the internal genetic material. Using Triangulation Number, Baltimore Classification, best-fit Point Array(s), corresponding Gauge Point(s), and the host of each type of spherical virus, this study aimed to reveal a relationship and possible dependency among viruses’ characteristics. All data were extracted from the VIPER database (VIPERdb). MATLAB, Terminal, and VMD were used to determine Point Arrays, Gauge Points, and visual representations of the asymmetric unit. This comprehensive analysis confirmed there is no relationship between TNumber and Baltimore Classification alone. Many spherical viruses with Gauge Point 1 are either T3/pT3, Baltimore Classification I/IV/V. It also exposed that many viruses do not have Gauge Points on their 3’ or 2’ axes, suggesting this axis to be the most restrictive. None of the 144 known spherical virus structures used in this analysis had Gauge Point 6 as their best fit. Gauge Points 10, 11, 12, 13, 14, 15, 16, and 17 are only used by RNA viruses. Gauge Point 1 is almost always used by viruses with larger TNumbers, suggesting that Gauge Point 1 has the least constraints and is the most easily accessible for large viruses. For further research, some interesting data analysis with Gauge Points would be host type, antibody location, and changes throughout maturation.
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v, 117 p.
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Kalamazoo College
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U.S. copyright laws protect this material. Commercial use or distribution of this material is not permitted without prior written permission of the copyright holder.
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