Recognition of the PS

The CTD may primalrily detect the PS

How to study functionally important domains of NP

Recognition of the packaging signal - models

(pmid: 31505321) The two candidates for a viral molecular partner that recognizes the PS are the N protein and the M protein.

N and M molecules associate with each other via their respective carboxy termini. domain N3 the sole region of N that interacts with M protein (Hurst et al., 2005; Verma et al., 2006; Kuo et al., 2016a).

Genetic and biochemical analyses have localized critical residues in both N (Hurst et al., 2005; Verma et al., 2006) and M (Escors et al., 2001; Kuo and Masters, 2002; Verma et al., 2007) that are essential for these assembly interactions. In virion ultrastructural studies, the N-M interaction has been visualized as what has been described as thread-like connections between the two proteins (Bárcena et al., 2009; Neuman et al., 2011). M is the most abundant virion structural protein, present in a roughly 1.4:1 molar ratio to N protein (recomputed from Sturman et al., 1980). Thus, in principle, there are sufficient M endodomain tails on the internal surface of the virion membrane to accommodate an interaction with every domain N3 in the nucleocapsid. However, there is structural evidence that virion M endodomains actually exist in two conformations, compact and elongated, with only the latter making contact with the nucleocapsid (Neuman et al., 2011).

N - specific recognition of PS

(pmid: 31505321) Although N protein must possess broadly nonspecific RNA-binding activity in order to coat the entire viral genome, efforts have been made to identify sequence-specific RNA substrates that may be relevant to packaging or other functions. Molenkamp and Spaan (1997)

others showed no higher specificity for TS

The presence in the coronavirus N protein of two distinct RNAbinding domains, the NTD and the CTD, is an unusual characteristic for an RNA virus nucleocapsid protein (Chang et al., 2014).

M - specific binding to PS

(pmid: 31505321) Studies indicating M protein is the principal, and possibly sole, PS recognition element

M protein (possibly with the assistance of E) is the viral component that recognizes and binds to the PS, and that formation of a nucleocapsid with N protein is not required for packaging specificity.

M or N??

(pmid: 31505321) studies implicated both the N protein CTD and domain N3 as major determinants of PS recognition, a conclusion markedly in contrast with that of prior studies that suggested the primary role for M protein. To date, genetic evidence has not been obtained that could either rule in or rule out participation of the M protein in PS recognition, in part because the M protein endodomain is much less tolerant to mutational alteration than is the N protein (Kuo et al., 2016a).