ObjectiveThe green fluorescent protein (GFP) and its derivatives are widely used in biomedical research. The manipulation of GFP-tagged proteins by GFP-specific binders, e.g. single-domain antibodies (nanobodies), is of increasing significance. It is therefore important to better understand the properties of antiGFP-GFP interaction in order to establish methodological applications. In this work the interaction of superfolder GFP (sfGFP) and its enhancer nanobody (aGFPenh) was characterized further.ResultsPrevious calorimetric experiments demonstrated that the aGFPenhnanobody binds strongly to sfGFP with a nanomolar affinity. Here we show that this interaction results in a substantial structural stabilization of aGFPenhreflected in a significant increase of its melting temperature by almost 30 °C. The thermal stability of the sfGFP-aGFPenhcomplex is close to 85 °C in the pH range 7.0–8.5. For therapeutic applications thermoresistance is often an essential factor. Our results suggest that methodologies based on GFP-aGFP interaction can be applied under a wide range of physicochemical conditions. The aGFPenhnanobody seems to be suitable for manipulating sfGFP-labeled targets even in extreme thermophilic organisms.