Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State

Abstract

By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion.IMPORTANCE When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productiveinfection events.KEYWORDS 80S, VHH, cryo-electron microscopy, expanded virus, poliovirus, singledomain antibodies, three-dimensional structure P oliovirus (PV) is a small, nonenveloped, positive-sense, single-stranded RNA (ssRNA) virus that is a member of the enterovirus genus of the picornavirus family (1, 2). The virus consists of an RNA genome that is surrounded by a protein shell. The shell is formed by an icosahedrally symmetric arrangement of 60 copies each of 3 large proteins (VP1, VP2, and VP3), each of which has a wedge-shaped beta barrel core (3), and the small myristoylated protein VP4 (4), which is located on the inner surface of the capsid. To infect its natural host (human epithelial cells in the gut), poliovirus must solve the problem of getting its genome through the host's protective cellular membrane. Details of how this is accomplished are now gradually emerging (5, 6).

Interacting motif networks located in hotspots associated with RNA release are conserved in Enterovirus capsids

“…Specifically, in comparison to full virus capsids, the first 60 amino acids in the N terminus of VP1 of the early RNArelease structures were disordered [7][8][9][10][11]34]. While in a more recent study of Poliovirus, the VP1 N terminus was observed to be rearranged [18]. Three of the seven enteroviruses mapped in this study correspond to structures in these previous studies, including Enterovirus 71 [7], Coxsackievirus A9 [20] and Rhinovirus A2 [23].…”

“…The externalisation of the N terminus of VP1 and complete loss of VP4 was observed in all RNA-release intermediates reported. While in a more recent study of Poliovirus, the VP1 N terminus was observed to be rearranged [18]. While in a more recent study of Poliovirus, the VP1 N terminus was observed to be rearranged [18].…”

“…The viral RNA then exits the capsid, and infects the host cell. In particular, the N terminus of VP1 was observed as partially rearranged [18]. However, the mechanism is not fully understood.…”

“…In earlier studies neither the VP1 N terminus nor the VP4 protein were captured in RNA-release structures and the polypeptide chains that become disordered have only recently been distinguished from those which are rearranged in Poliovirus. In particular, the N terminus of VP1 was observed as partially rearranged [18].…”

Nanobodies Targeting Norovirus Capsid Reveal Functional Epitopes and Potential Mechanisms of Neutralization

“…Trapping the particles in a particular conformation or otherwise inhibiting capsid "breathing" is a common antiviral strategy shared by many neutralizing mAbs, Nanobodies, and drugs against HIV, flaviviruses, picornaviruses, influenza, and others [54][55][56][57][58][59][60]. For example, several neutralizing Nanobodies against poliovirus and respiratory syncytial virus were shown to specifically stabilize either the native or expanded conformation of capsid, preventing it from further rearrangement necessary for the infection process [30,61]. It is plausible that in the case of norovirus Nanobodies described here, binding resulted in a stabilization of the particular P domain conformation, thus reducing the mobility and influencing the position on the S domain.…”