Fuzzy regions in an intrinsically disordered protein impair protein–protein interactions

<jats:p>Despite the partial disorder‐to‐order transition that intrinsically disordered proteins often undergo upon binding to their partners, a considerable amount of residual disorder may be retained in the bound form, resulting in a fuzzy complex. Fuzzy regions flanking molecular recognition elements may enable partner fishing through non‐specific, transient contacts, thereby facilitating binding, but may also disfavor binding through various mechanisms. So far, few computational or experimental studies have addressed the effect of fuzzy appendages on partner recognition by intrinsically disordered proteins. In order to shed light onto this issue, we used the interaction between the intrinsically disordered C‐terminal domain of the measles virus (MeV) nucleoprotein (<jats:styled-content style="fixed-case">N<jats:sub>TAIL</jats:sub></jats:styled-content>) and the X domain (<jats:styled-content style="fixed-case">XD</jats:styled-content>) of the viral phosphoprotein as model system. After binding to <jats:styled-content style="fixed-case">XD</jats:styled-content>, the N‐terminal region of <jats:styled-content style="fixed-case">N<jats:sub>TAIL</jats:sub></jats:styled-content> remains conspicuously disordered, with α‐helical folding taking place only within a short molecular recognition element. To study the effect of the N‐terminal fuzzy region on <jats:styled-content style="fixed-case">N<jats:sub>TAIL</jats:sub></jats:styled-content>/<jats:styled-content style="fixed-case">XD</jats:styled-content> binding, we generated N‐terminal truncation variants of <jats:styled-content style="fixed-case">N<jats:sub>TAIL</jats:sub></jats:styled-content>, and assessed their binding abilities towards <jats:styled-content style="fixed-case">XD</jats:styled-content>. The results revealed that binding increases with shortening of the N‐terminal fuzzy region, with this also being observed with hsp70 (another MeV <jats:styled-content style="fixed-case">N<jats:sub>TAIL</jats:sub></jats:styled-content> binding partner), and for the homologous <jats:styled-content style="fixed-case">N<jats:sub>TAIL</jats:sub></jats:styled-content>/<jats:styled-content style="fixed-case">XD</jats:styled-content> pairs from the Nipah and Hendra viruses. Finally, similar results were obtained when the MeV <jats:styled-content style="fixed-case">N<jats:sub>TAIL</jats:sub></jats:styled-content> fuzzy region was replaced with a highly dissimilar artificial disordered sequence, supporting a sequence‐independent inhibitory effect of the fuzzy region.</jats:p>