Biology subjects

Oliver, T. A. A.

Publications and source records attributed to Oliver, T. A. A..

5 recordsLinked to original sources

bioRxiv2026

Expanding all-α-helical protein space through rational computational design

De novo protein design is advancing rapidly1,2. This is being driven by AI to generate protein backbones, sequences, and structural models3-7. As a result, de novo designed proteins are becoming larger and more complex8-10, and increasingly explore new protein structures11,12. By contrast, natural proteins have evolved structural and functional complexity by modular combination of recurring protein domains13. Approximately 25% of these natural domains are mostly -helical structures14. Here we show how these can be expanded using rational computational design. Following the domain classification scheme CATH15, we build complex all- de novo proteins hierarchically using sequence-to-structure relationships for helix-helix interactions, systematic rules to connect helices, computational tools to design loops, and in silico evaluation. The pipeline starts with a target architecture of free-standing helices. These are connected into a topology by considering local arrangements of helical bundles using understood sequence-to-structure relationships for helix packing. Single-chain sequences are completed using template- and AI-based methods. Finally, AlphaFold models are assessed to give small numbers of designs for experimental validation. We test 31 designs for 14 different architectures and 25 topologies. 75% of these express as stable, monomeric, water-soluble proteins; and >30% yield X-ray crystal structures matching the designs to atomic accuracy and with new-to-nature structures. Finally, several of the scaffolds are functionalised through one-shot designs to deliver ion, small-molecule and protein binders.

synthetic biology↗

bioRxiv2025

Rapid Assessment of Size, Shape, and Chemical Complementarity of Ligands for Computational Protein Design

Driven by deep-learning approaches, computational protein design is advancing rapidly, and it is now possible to generate many de novo protein structures quickly and robustly. This sets new frontiers for the field, including designing proteins that bind small molecules tightly and specifically, and understanding the non-covalent interactions that underpin such designs to make binding predictable and tunable. Here we address these challenges with a rapid physics-based computational method to generate isosteric and chemically complementary binding pockets for small-molecule targets in de novo designed proteins. We test this experimentally by constructing and characterizing binding proteins for several synthetic and natural chromophores. By evaluating only single-digit numbers of designs, the pipeline delivers stable proteins with pre-organized binding sites confirmed by X-ray crystallography, which bind the targets selectively with micromolar affinities or better. To illustrate the scope and applications of this approach, we incorporate distinct and coupled chromophore-binding sites in a two-domain de novo protein enabling controlled energy transfer between the two sites, and we develop a small de novo binding protein that can be used in live mammalian cells to visualize sub-cellular structures.

biophysics↗

bioRxiv2024

Confinement and Catalysis Within De Novo Designed Peptide Barrels

De novo protein design has advanced such that many peptide assemblies and protein structures can be generated predictably and quickly. The drive now is to bring functions to these structures, for example, small-molecule binding and catalysis. The formidable challenge of binding and orienting multiple small molecules to direct chemistry is particularly important for paving the way to new functionalities. To address this, here we describe the design, characterization, and application of small-molecule:peptide ternary complexes in aqueous solution. This uses -helical barrel (HB) peptide assemblies, which comprise 5 or more -helices arranged around central channels. These channels are solvent accessible, and their internal dimensions and chemistries can be altered predictably. Thus, HBs are analogous to molecular flasks made in supramolecular, polymer, and materials chemistry. Using Forster resonance energy transfer as a readout, we demonstrate that specific HBs can accept two different organic dyes, 1,6-diphenyl-1,3,5-hexatriene and Nile Red in close proximity. In addition, two anthracene molecules can be accommodated within an HB to promote photocatalytic anthracene-dimer formation. However, not all ternary complexes are productive, either in energy transfer or photocatalysis, illustrating the control that can be exerted by judicious choice and design of the HB.

synthetic biology↗

bioRxiv2022

Photovoltaic enzymes by design and evolution

The global energy crisis challenges us to develop more efficient strategies for the sustainable production of energy. Given the excellent efficiency of the natural photosynthetic apparatus, biohybrid photovoltaic devices present an attractive solution for solar energy conversion. However, their composition, stability, and complexity can limit their inclusion into photovoltaic devices. Here, we combined computational design and directed evolution to overcome these limitations and create tailor-made photoenzymes. Photo-biocatalysts were designed by introducing photosensitizer binding sites into heme-containing helical bundle proteins. The designed binding sites were specific for the target photosensitizer and readily transplanted into other helical bundles. The best design was highly evolvable and reached nanomolar ligand affinity after mutagenesis and screening. The evolved enzyme generated 2.6 times higher photocurrents than the photosensitizer alone, primarily driven by increased photostability. Evolvability is a unique advantage of our protein-based approach over abiological photovoltaic and will be critical to developing efficient biohybrid systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/521207v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@2b6031org.highwire.dtl.DTLVardef@1b83f69org.highwire.dtl.DTLVardef@14b39a4org.highwire.dtl.DTLVardef@1b569bb_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2019

Photosynthesis and crop productivity is enhanced by glucose-functionalized fluorescent carbon dots

From global food security to textile production and biofuels, the demands currently made on plant photosynthetic productivity will continue to increase. Enhancing photosynthesis using designer, green and sustainable materials offers an attractive alternative to current genetic-based strategies and promising work with nanomaterials has recently started to emerge. Here we describe in planta use of carbon-based nanoparticles produced by low-cost renewable routes that are bioavailable to mature plants. Uptake of these functionalised nanoparticles from the soil improves photosynthesis and also increases crop production. We show for the first time that glucose-functionalization enhances nanoparticle uptake, photoprotection and pigment production, unlocking enhanced yields. This is demonstrated in Triticum aestivum Apogee (dwarf bread wheat) and results in an 18% increase in grain yield. This establishes the viability of a functional nanomaterial to augment photosynthesis as a route to increased crop productivity.

plant biology↗