Mamalis, D. | bioRxiv Science

bioRxiv2022

Stereoretentive Post-Translational Protein Editing

Chemical post-translational methods now allow convergent side-chain editing of proteins as a form of direct chemical mutagenesis without needing to resort to genetic intervention. Current approaches that allow the creation of constitutionally native side-chains via C-C formation using off-protein carbon-centred C* radicals added to unnatural amino acid radical acceptor SOMOphile tags such as dehydroalanine are benign and wide-ranging. However, they also typically create epimeric mixtures of D-/L-residues. Here we describe a light-mediated desulfurative method that, through the creation and reaction of stereoretained on-protein L-alanyl C{beta}* radicals, allows C{beta}-H{gamma}, C{beta}-O{gamma}, C{beta}-Se{gamma}, C{beta}-B{gamma} and C{beta}-C{gamma} bond formation to flexibly generate site-selectively edited proteins with full retention of native stereochemistry under mild conditions from a natural amino acid. This methodology shows great potential to explore protein side-chain diversity and construct useful bioconjugates. Table of Contents Image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=32 SRC="FIGDIR/small/504816v1_ufig1.gif" ALT="Figure 1"> View larger version (7K): org.highwire.dtl.DTLVardef@1ccd60corg.highwire.dtl.DTLVardef@f8ca72org.highwire.dtl.DTLVardef@1b33835org.highwire.dtl.DTLVardef@12f32e9_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2022

Gluebodies improve crystal reliability and diversity through transferable nanobody mutations that introduce constitutive crystal contacts

The design of proteins that may assemble in a manner that is transferable and modular remains an enduring challenge. In particular, obtaining well-diffracting protein crystals suitable for characterizing ligands or drug candidates and understanding different protein conformations remains a bottleneck for structural studies. Using nanobodies as crystallization chaperones is one strategy to address the problem, but its reliability is uncharacterized and, in this study, we observed it to have a limited success rate. Here we show that by exploring and testing the nanobody-nanobody interfaces predominant in >200 combinations of surface mutations in multiple iterations we can engineer robust crystallization behaviour into the nanobody scaffold. Strikingly, this survey yielded multiple polymorphs, all mediated by the same interface. The resulting Gluebodies (Gbs) provide far superior resolution and reliability of diffraction and can be routinely generated for chaperone experiments. We furthermore show that Gbs cannot rescue intrinsically non-crystallizing proteins, but instead are a powerful approach to improve the packing and resolution limit of poorly diffracting crystals. The discovery of an engineered, preferred nanobody interface that arises under kinetic control - trapped here by irreversible crystallization - embodies a protein assembly strategy that could prove even more broadly useful for modular assembly trapped by other irreversible methods.

biochemistry↗