Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation

Abstract

Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with <2 nm epitope-label displacement. For this, we introduced cysteines at specific positions in the nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target.

DOI: http://dx.doi.org/10.7554/eLife.11349.001

eLife digest

Antibodies not only protect humans and other animals against disease-causing bacteria and viruses. They can also be used as tools for medical diagnostics and basic research. Conventional antibodies consist of light and heavy protein chains, and both are required to bind to target molecules (or antigens). Alpacas, llamas and camels, however, possess simpler antibodies that lack light chains and bind to antigens via a single protein domain. Such domains can be produced in "re-programmed" bacteria and are then called nanobodies. Compared to normal antibodies, nanobodies are 10-fold smaller, which is of great advantage in virtually all practical applications.

Pleiner et al. made nanobodies against the nuclear pore complex (or NPC for short) – a nanoscopic machine for transporting large biological molecules in and out of the cell’s nucleus. These nanobodies can be linked to dyes called fluorophores and then used to stain NPCs so that they can be observed under a microscope.

When fluorophores were attached, in the traditional way, via the amino acid lysine, all tested nanobodies performed poorly in fluorescence microscopy - pointing to a systematic problem. Pleiner et al. therefore explored an alternative, namely to label nanobodies via engineered cysteines. This was counterintuitive, because nanobodies contain already two other cysteines that must not be modified and that normally form a stabilizing “disulfide” bond. Pleiner et al. found, however, that the labeling reaction is absolutely specific for the engineered surface cysteines when it is performed at low temperature. This strategy consistently yielded imaging reagents that could effectively deliver fluorophores as close as 1-2 nanometers to their antigens. Nanobodies labeled in this way are therefore ideal to exploit the full potential of super-resolution microscopy.

The engineered surface cysteines proved also useful as "position sensors" to report which region of an antigen is actually contacted by a given nanobody.

Nanobodies are also used to purify protein complexes from crude cell extracts by a method called affinity chromatography. Previously, nanobodies were chemically attached to an insoluble matrix, and bound protein complexes were released under conditions that destroy interactions between proteins. Pleiner et al. now replaced the destructive step with a step that uses an enzyme to cut a bond and gently detach the nanobody (along with any bound protein complex) from the matrix. Bound protein complexes thus stay intact and can be studied further. In the future, this strategy can be applied to nanobodies that recognize tags commonly added to proteins (i.e. GFP) to isolate virtually any protein complex for functional assays or structural analyses.

DOI: http://dx.doi.org/10.7554/eLife.11349.002