Cryo EM Analysis Reveals Inherent Flexibility of Authentic Murine Papillomavirus Capsids

Abstract

Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. However, studies have been hampered due to restricted tropism that makes production and purification of high titer virus problematic. This issue has been overcome by developing alternative HPV production methods such as virus-like particles (VLPs), which are devoid of a native viral genome. Structural studies have been limited in resolution due to the heterogeneity, fragility, and stability of the VLP capsids. The mouse papillomavirus (MmuPV1) presented here has provided the opportunity to study a native papillomavirus in the context of a common laboratory animal. Using cryo EM to solve the structure of MmuPV1, we achieved 3.3 Å resolution with a local symmetry refinement method that defined smaller, symmetry related subparticles. The resulting high-resolution structure allowed us to build the MmuPV1 asymmetric unit for the first time and identify putative L2 density. We also used our program ISECC to quantify capsid flexibility, which revealed that capsomers move as rigid bodies connected by flexible linkers. The MmuPV1 flexibility was comparable to that of a HPV VLP previously characterized. The resulting MmuPV1 structure is a promising step forward in the study of papillomavirus and will provide a framework for continuing biochemical, genetic, and biophysical research for papillomaviruses.

Equilibrium dynamics of a biomolecular complex analyzed at single-amino acid resolution by cryo-electron microscopy

“…If these conformations are sufficiently different from the minimum free energy conformation and from each other, structural models for different, inter-converting conformations may be obtained from the corresponding electron density maps, and compared to identify highly dynamic regions. In addition, sophisticated computational approaches have been applied to investigate dynamics from a continuous distribution of heterogeneities in data from an ensemble of individual cryo-EM images (Bonomi, Pellarin, & Vendruscolo, 2018; Doerschuk, Gong, Xu, Domitrovic, & Johnson, 2016; Hartmann et al, 2021; Liao, Hashem, & Frank, 2015; Oide, Kato, Oroguchi, & Nakasako, 2020; Penczek, Kimmel, & Spahn, 2011; Tang et al, 2014; Q. Wang et al, 2013).…”