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Bacteriophage (phage) T4 has served as an extraordinary model to elucidate biological structures and mechanisms. Recent discoveries on the T4 head (capsid) structure, portal vertex, and genome packaging add a significant body of new literature to phage biology. Head structures in unexpanded and expanded conformations show dramatic domain movements, structural remodeling, and a ~70% increase in inner volume while creating high-affinity binding sites for the outer decoration proteins Soc and Hoc. Small changes in intercapsomer interactions modulate angles between capsomer planes, leading to profound alterations in head length. The in situ cryo-EM structure of the symmetry-mismatched portal vertex shows the remarkable structural morphing of local regions of the portal protein, allowing similar interactions with the capsid protein in different structural environments. Conformational changes in these interactions trigger the structural remodeling of capsid protein subunits surrounding the portal vertex, which propagate as a wave of expansion throughout the capsid. A second symmetry mismatch is created when a pentameric packaging motor assembles at the outer “clip” domains of the dodecameric portal vertex. The single-molecule dynamics of the packaging machine suggests a continuous burst mechanism in which the motor subunits adjusted to the shape of the DNA fire ATP hydrolysis, generating speeds as high as 2000 bp/s.
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Simulations of Phage T7 Capsid Expansion Reveal the Role of Molecular Sterics on Dynamics
Molecular dynamics techniques provide numerous strategies for investigating biomolecular energetics, though quantitative analysis is often only accessible for relatively small (frequently monomeric) systems. To address this limit, we use simulations in combination with a simplified energetic model to study complex rearrangements in a large assembly. We use cryo-EM reconstructions to simulate the DNA packaging-associated 3 nm expansion of the protein shell of an initially assembled phage T7 capsid (called procapsid or capsid I). This is accompanied by a disorder–order transition and expansion-associated externalization displacement of the 420 N-terminal tails of the shell proteins. For the simulations, we use an all-atom structure-based model (1.07 million atoms), which is specifically designed to probe the influence of molecular sterics on dynamics. We find that the rate at which the N-terminal tails undergo translocation depends heavily on their position within hexons and pentons. Specifically, trans-shell displacements of the hexon E subunits are the most frequent and hexon A subunits are the least frequent. The simulations also implicate numerous tail translocation intermediates during tail translocation that involve topological traps, as well as sterically induced barriers. The presented study establishes a foundation for understanding the precise relationship between molecular structure and phage maturation.
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- PAR ID:
- 10233515
- Date Published:
- Journal Name:
- Viruses
- Volume:
- 12
- Issue:
- 11
- ISSN:
- 1999-4915
- Page Range / eLocation ID:
- 1273
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/v12111273
