Liam M. Longo

This study investigates the emergence of two key cofactor-binding protein folds by analyzing their metabolic roles, structural organization, and folding mechanisms.

This paper reconstructs the historical emergence of enzymatic folds using metabolic reaction networks, finding that enzyme evolution is embedded in metabolic interdependencies and that β-proteins dominated early metabolism.

This paper introduces CLSS, a contrastive learning model that co-embeds protein sequences and structures, revealing evolutionary relationships and structural transitions.

This study investigates the evolutionary remodelling of isoleucyl-tRNA synthetase C-terminal domains in prokaryotes, finding that such remodelling enhances aminoacylation rates.

This paper discovers a universal polyphosphate kinase capable of phosphorylating all eight common ribonucleotides, enabling efficient in vitro transcription.

This study investigates how peptides interact with mineral surfaces and lipid vesicles, showing acidic residues bind minerals and arginine enhances phosphate mobilization, while different amino acid alphabets affect vesicle stability.

This paper challenges the evolutionary model that the Walker A motif was a seed for early P-loop NTPases by showing that disembodied Walker A peptides do not form stable phosphate-binding nests.

The paper models ancient metabolic networks to show purine synthesis was a bottleneck in metabolic evolution, requiring non-autocatalytic phosphoryl agents and leading to coenzyme emergence.

This study reconstructs the evolutionary history of Class I aminoacyl-tRNA synthetases, finding that early AARSs were generalists capable of charging a wide range of amino acids, suggesting statistical translation evolved before specialized, accurate translation.

The paper investigates the evolutionary origins of β-trefoil proteins by identifying sequence and structural motifs in unrelated lineages, proposing a 'peptide budding' mechanism from an IgG-like β-sandwich.

This study demonstrates that simple polypeptides with P-loop motifs can exhibit helicase-like activities, suggesting they may represent early precursors to complex P-loop NTPases.