Screening and structural characterization of a nanobody targeting the thermostable green fluorescent protein

Nanobody-fluorescent protein pairs are powerful tools in imaging, protein purification, and structural biology studies. While thermostable GFP (TGP) offers improved characteristics over conventional GFP, nanobodies that specifically recognize TGP remain relatively limited. Here, we report the screening and identification of a synthetic nanobody, Sb32, that binds TGP with nanomolar affinity using the ribosome technique. The crystal structure of the Sb32-TGP complex, solved at 1.82 [A] resolution, revealed an unusual binding mode in which Complementarity Determining Region 2 (CDR2) provides the major contribution, rather than the typically dominant CDR3. Moreover, the interface is stabilized by an extensive hydration network, which compensates for relatively few direct contacts and may explain the fast association and dissociation kinetics observed for this complex. These findings expand the repertoire of TGP-specific nanobodies and highlight an alternative strategy by which nanobodies achieve high affinity. Sb32 provides a new reagent for TGP-based applications, with potential utility in membrane protein purification and structural studies.