Capsid Geometrical Anatomy (Luque lab)

October 27, 2021

Zoom session

• Public recording with integrated audio transcript.

Access to workshop files

• Folder in the Athena GitHub repo.
• Online content provided by GitHub pages is based on the standard lab’s public documentation system.
• Our approach to share knowledge steams from our Athena initiative.

Temporary Athena site for the Capsid Anatomy project:

• GitHub research repo: https://github.com/luquelab/auto-lattice
• Accessible online site: https://luquelab.github.io/auto-lattice

Part 1: Capsid anatomy

Capsid molecular composition

• Stoichiometry: Major capsid, minor capsid, scaffold, reinforcemen, and decoration proteins.
• Functions other than major capsid protein are usually fuzzy!

Capsid physical properties

• Diameter, surface, volume, and sphericity (internal and external).
  • Chimera: Icosahedron surface.
• Elasticity and brittleness.
  • No standard approach.

Capsid geometric architecture

• T-number and icosahedral lattice; Q-number for elongated structures.
• Generalized T-numbers: Twarock and Luque, Nature Communications, 2019.
• Chimera X: hkcage command and hkcage bundle.
• First used in Luque et al. Microorganisms, 2020.

How to assign T-numbers

Molecular approach: Correspondence between geometric tiles and protein clusters.

• Example: Bacteriophage P22 (PDB 5uu5)
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• Observation: Challenge assigning minor capsid protein function:

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• Observation: The HK97-fold sliding hypothesis:

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  • More examples in https://luquelab.github.io/auto-lattice/output/.

Mechanical approach: Correspondence between quasi-rigid regions and geometrical tiles.

• Elastic analysis of capsids
  • Perturbation analysis of alpha-carbon capsid models.
  • Example: Small tobacco necrosis virus (PDB 1A34):
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  • Computational challenge: large capsids.

Part 2: Molecular approach (Diana Lee)

Part 3: Mechanical approach (Colin Brown)