Reactivity of Viral Proteins with Free Chlorine: Structural Insights and Implications for Virus Inactivation

Viruses exhibit diverse susceptibility to free chlorine
inactivation,
but the underlying mechanisms that drive these differences are poorly
understood. To investigate this, we applied a multiplex and cost-effective
tandem mass tag-based quantitative proteomics to characterize peptide
decay kinetics and reactions in three model viruses, namely, MS2,
PhiX174, and T4, when they were treated with free chlorine. Strong
correlations were observed between peptide decay rate constants and
both solvent-accessible surface areas (SASAs) of methionine residues
(Pearson's r = 0.78, p <
0.0001)
and SASAs per residue in methionine-lacking peptides (Pearson's r = 0.81, p < 0.0001). A multiple linear
regression model fitted using these two independent structural variables
accurately predicted peptide decay rate constants in the three viruses
(R2 = 0.91 for MS2 peptides, R2 = 0.72 for PhiX174 peptides, and R2 = 0.86 for T4 peptides). Notably, the peptide decay kinetics
in viral proteins responsible for host attachment and genome injection
better predicted virus resistance than that in other viral proteins.
Furthermore, peptides containing methionine sulfoxide, 3-chlorotyrosine,
and nonspecific peptide bond cleavages were detected in chlorine-treated
viruses. This study combines proteomics and structural analysis, providing
new insights into protein reactivity and virus inactivation by free
chlorine.