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Chaperone protein - the most disordered among all protein groups - help RNAsfold into their functional structure by destabilizing misfolded configurationsor stabilizing the functional ones. But disentangling the mechanism underlyingRNA chaperoning is challenging, mostly due to inherent disorder of thechaperones and the transient nature of their interactions with RNA. Inparticular, it is unclear how specific the interactions are and what role isplayed by amino acid charge and polarity patterns. Here, we address thesequestions in the RNA chaperone StpA. We adapted direct coupling analysis (DCA)into the $\alpha\beta$DCA method that can treat in tandem sequences written intwo alphabets, nucleotides and amino acids. With $\alpha\beta$DCA, we couldanalyze StpA-RNA interactions and show consistency with a previously proposedtwo-pronged mechanism: StpA disrupts specific positions in the group I intronwhile globally and loosely binding to the entire structure. Moreover, theinteractions are strongly associated with the charge pattern: negativelycharged regions in the destabilizing StpA N-terminal affect a few specificpositions in the RNA, located in stems and in the pseudoknot. In contrast,positive regions in the C-terminal contain strongly coupled amino acids thatpromote non-specific or weakly-specific binding to the RNA. The present studyopens new avenues to examine the functions of disordered proteins and to designdisruptive proteins based on their charge patterns.

$\alpha\beta$ DCA method identifies unspecific binding but specific disruption of the group I intron by the StpA chaperone