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

ABSTRACT: 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 desi

SUBMITTER: Whitford PC 

PROVIDER: S-EPMC7695174 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature