Biology subjects

Buchel, F.

Publications and source records attributed to Buchel, F..

3 recordsLinked to original sources

bioRxiv2026

Learning the structural diversity in random protein sequence space

The universe of possible protein sequences is astronomically large, yet our understanding of the sequence-structure relationship is confined to the infinitesimal fraction used currently by life. Determining whether "foldable" architectures are rare singularities or accessible solutions is critical for understanding protein evolution and designing novel proteins. Here, we map the structural landscape of random sequence space by screening one million synthetic proteins using a high-throughput in vivo FRET biosensor. We reveal that this space is structurally heterogeneous, populated not only by disordered chains and stress-inducing aggregates but also by "benign" compact structures that resemble globular proteins and evade cellular chaperone responses. By training machine learning models on these phenotypes, we show that structural potential is learnable and generalizes to natural proteomes. These findings demonstrate that biology-like folds are accessible from random sequences with surprising frequency, providing data required to expand generative protein design beyond evolutionary priors.

synthetic biology↗

bioRxiv2024

High-throughput selection of human de novo-emerged sORFs with high folding potential

De novo genes emerge from previously non-coding stretches of the genome. Their en-coded de novo proteins are generally expected to be similar to random sequences and, accordingly, with no stable tertiary fold and high predicted disorder. However, structural properties of de novo proteins and whether they differ during the stages of emergence and fixation have not been studied in depth and rely heavily on predictions. Here we generated a library of short human putative de novo proteins of varying lengths and ages and sorted the candidates according to their structural compactness and disorder propensity. Using Forster resonance energy transfer (FRET) combined with Fluorescence-activated cell sorting (FACS) we were able to screen the library for most compact protein structures, as well as most elongated and flexible structures. Compact de novo proteins are on average slightly shorter and contain lower predicted disorder than less compact ones. The predicted structures for most and least compact de novo proteins correspond to expectations in that they contain more secondary structure content or higher disorder content, respectively. Our experiments indicate that older de novo proteins have higher compactness and structural propensity compared to young ones. We discuss possible evolutionary scenarios and their implications underlying the age-dependencies of compactness and structural content of putative de novo proteins.

evolutionary biology↗

bioRxiv2022

Experimental characterisation of de novoproteins and their unevolved random-sequencecounterparts

De novo gene emergence provides a route for new proteins to be formed from previously non-coding DNA. Proteins born in this way are considered random sequences, and typically assumed to lack defined structure. While it remains unclear how likely a de novo protein is to assume a soluble and stable tertiary structure, intersecting evidence from random-sequence and de novo-designed proteins suggests that native-like biophysical properties are abundant in sequence space. Taking putative de novo proteins identified in human and fly, we experimentally characterise a library of these sequences to assess their solubility and structure propensity. We compare this library to a set of synthetic random proteins with no evolutionary history. Bioin-formatic prediction suggests that de novo proteins may have remarkably similar distributions of biophysical properties to unevolved random sequences of a given length and amino acid composition. However, upon expression in vitro, de novo proteins exhibit higher solubility which is further induced by the DnaK chaperone system. We suggest that while synthetic ran-dom sequences are a useful proxy for de novo proteins in terms of structure propensity, de novo proteins may be better integrated in the cellular system given their higher solubility.

evolutionary biology↗