O'Shea, J. M. | bioRxiv Science

bioRxiv2023

Computational Design of Periplasmic Binding Protein Biosensors Guided by Molecular Dynamics

Periplasmic binding proteins (PBPs) are bacterial proteins commonly used as scaffolds for substrate-detecting biosensors. In such biosensors, effector proteins, for example circularly permuted green fluorescent protein (cpGFP), are inserted into a PBP such that the effector proteins output changes upon PBP-substate binding. The insertion site is often determined by comparison of PBP apo/holo crystal structures, but random insertion libraries have shown that this can miss the best sites. Here, we present a PBP biosensor design method based on residue contact analysis from molecular dynamics. This computational method identifies the best previously known insertion sites in the maltose binding PBP, and suggests further previously unknown sites. We experimentally characterise cpGFP insertions at these new sites, finding they too give functional biosensors. Our method is sufficiently flexible to both suggest insertion sites compatible with a variety of effector proteins and be applied to binding proteins beyond PBPs.

synthetic biology↗

bioRxiv2021

Generation of photocaged nanobodies for in vivo applications using genetic code expansion and computationally guided protein engineering

Nanobodies are becoming increasingly popular as tools for manipulating and visualising proteins in vivo. The ability to control nanobody/antigen interactions using light could provide precise spatiotemporal control over protein function. We develop a general approach to engineer photo-activatable nanobodies using photocaged amino acids that are introduced into the target binding interface by genetic code expansion. Guided by computational alanine scanning and molecular-dynamics simulations, we tune nanobody/target binding affinity to eliminate binding before uncaging. Upon photo-activation, binding is restored. We use this approach to generate improved photocaged variants of two anti-GFP nanobodies. These variants exhibit photo-activatable binding triggered by illumination with 365nm light. We demonstrate that the photocaged nanobodies we have created are highly robust and function in a complex cellular environment. We apply them to control subcellular protein localisation in the nematode worm C. elegans. Our approach provides a rare example of computationally designed proteins being directly applied in living animals and demonstrates the importance of accounting for in vivo effects on protein-protein interactions.

synthetic biology↗