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Article

Simulations of Phage T7 Capsid Expansion Reveal the Role of Molecular Sterics on Dynamics

1
Department of Physics, Northeastern University, Boston, MA 02115, USA
2
Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115, USA
3
Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47906, USA
4
Department of Biochemistry and Structural Biology, The University of Texas Health Center, San Antonio, TX 78229-3900, USA
*
Author to whom correspondence should be addressed.
Received: 26 October 2020 / Revised: 4 November 2020 / Accepted: 4 November 2020 / Published: 7 November 2020
(This article belongs to the Special Issue In Memory of Michael Rossmann)
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. View Full-Text
Keywords: bacteriophage T7; disorder; DNA packaging; molecular dynamics simulation; protein dynamics bacteriophage T7; disorder; DNA packaging; molecular dynamics simulation; protein dynamics
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MDPI and ACS Style

Whitford, P.C.; Jiang, W.; Serwer, P. Simulations of Phage T7 Capsid Expansion Reveal the Role of Molecular Sterics on Dynamics. Viruses 2020, 12, 1273. https://0-doi-org.brum.beds.ac.uk/10.3390/v12111273

AMA Style

Whitford PC, Jiang W, Serwer P. Simulations of Phage T7 Capsid Expansion Reveal the Role of Molecular Sterics on Dynamics. Viruses. 2020; 12(11):1273. https://0-doi-org.brum.beds.ac.uk/10.3390/v12111273

Chicago/Turabian Style

Whitford, Paul C., Wen Jiang, and Philip Serwer. 2020. "Simulations of Phage T7 Capsid Expansion Reveal the Role of Molecular Sterics on Dynamics" Viruses 12, no. 11: 1273. https://0-doi-org.brum.beds.ac.uk/10.3390/v12111273

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