Colin J. Jackson

The paper shows how SARS-CoV-2 variants, particularly Omicron, evolved proteolytic controls at the Spike furin cleavage site to enhance transmission while reducing lower respiratory tract pathogenicity.

The paper identifies a small molecule inhibitor of AtSAL1, demonstrating its ability to modulate PAP signaling and enhance stress tolerance in Arabidopsis without genetic pleiotropy.

This study identifies nanobodies that target Plasmodium adhesins, blocking receptor engagement and inhibiting parasite invasion of red blood cells.

This study investigates how functional and conformational substates change during enzyme evolution using single-molecule kinetic assays and simulations, showing coordinated shifts in substate equilibria that optimize catalytic efficiency.

This study investigates the molecular basis and evolutionary constraints of organophosphate resistance in dipteran carboxylesterases, revealing sequence context-dependent success of a mutation and trade-offs between affinity and turnover.

This study uses fragment-based drug design to identify novel heparanase inhibitors, resulting in compounds with improved potency for potential therapeutic applications.

This study maps the sequence space of bacterial chitinases to show how domain composition and catalytic core evolve differently based on functional roles.

The paper presents analyses to assess selection dynamics in multi-round protein selection experiments, offering insights into diversity, coverage, and reproducibility.

This study evaluates ML architectures for protein fitness prediction using simulated and empirical landscapes, identifying landscape ruggedness as a key determinant of accuracy.

The paper introduces a sequence analysis pipeline that improves exploration of protein sequence space through hierarchical clustering and alternative homology metrics, demonstrating scalability and utility in analyzing large datasets.

This study uses ancestral sequence reconstruction to explore PET-degrading cutinase sequence space, revealing diverse evolutionary pathways and the effectiveness of LASE in mapping fitness landscapes.

This paper describes a F420-dependent chemogenetic tool that induces and releases protein dimerization by exploiting a mycobacterial oxidoreductase.

The paper introduces a graph-based measure of protein fitness landscape ruggedness and shows it concentrates at regions where dominant constraints change.

The paper examines how thermodynamic binding strategies in proteins evolved in response to temperature changes, showing a shift from entropy-driven to enthalpy-driven binding over time.

The paper shows ribosomal synthesis generates a noncanonical 3-nitrotyrosine building block used in nonribosomal peptide synthesis of rufomycin.

This study isolates and characterizes a bacterial strain capable of detoxifying malachite green, identifying an azoreductase responsible for its degradation.

This paper introduces LASE, a method using ancestral sequence reconstruction to train protein language models with higher accuracy and faster computation than large models.

This paper introduces 4-cyano-tryptophan (4-CN-Trp) as a fluorescent amino acid that preserves protein structure and enables detection of ligand binding sites through fluorescence changes.

This study presents high-resolution structures of C. albicans Cdr1 in multiple states and uses simulations and evolutionary analysis to elucidate its transport mechanism and drug resistance.

The paper identifies that CsoSCA, a carboxysomal carbonic anhydrase in cyanobacteria, is allosterically activated by RuBP, revealing a regulatory mechanism in CO2 fixation.

The paper identifies and characterizes a bacterial periplasmic solute-binding protein that specifically binds L-amino acid amides, revealing structural and functional insights into bacterial nutrient uptake.

The paper investigates how active site mutations in FDOR enzymes affect stereoselectivity and reveals that a Tyr-Met mutation reverses stereoselectivity and alters hydrogenation mode.

The paper performs a comprehensive phylogenetic analysis of ribonucleotide reductase (RNR) family to identify an ancestral clade and trace evolutionary diversification through insertions and extensions.

This study constructs a comprehensive phylogeny of 6000 serpin sequences across all kingdoms of life, showing convergent evolution rather than horizontal gene transfer for the central hub proteins.

This study shows that LTP induces astroglial withdrawal, increasing glutamate spillover and inter-synaptic communication.

This study identifies mutations in Mycobacterium tuberculosis that confer resistance to nitroimidazole antibiotics, highlighting the need for monitoring these mutations to manage antibiotic use.

This study identifies five mutations that enable the evolution of a xenobiotic-degrading enzyme and shows that higher-order epistasis shapes its adaptive landscape and substrate specificity.

The paper revises the biosynthetic pathway for the cofactor F420 in bacteria by identifying the correct substrate for guanylyltransferases and elucidating the role of the C-terminal domain of FbiB.

This study shows how an enzyme evolved from a solute-binding protein through structural and catalytic changes, highlighting mechanisms of de novo enzyme emergence.