D. S. Tawfik

The impact of molecular variants, crystallization conditions and space group on structure-ligand complexes: A case study on Bacterial Phosphotriesterase Variants and complexes

This study examines how molecular variants, crystallization conditions, and space group affect the visualization of ligand-bound protein structures, using bacterial phosphotriesterase as a case study.

Widespread Utilization of Diverse Organophosphate Pollutants by Marine Bacteria

Marine bacteria utilize diverse organophosphate pollutants as a phosphorus source, offering potential for bioremediation.

A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

The paper identifies a counter-enzyme complex in Bacillus subtilis that regulates glutamate metabolism by inhibiting GudB activity, essential for growth under varying glutamate conditions.

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

This study uses directed evolution to identify Cfr variants that enhance rRNA methylation, revealing structural insights into antibiotic resistance mechanisms.

Polyamines Mediate Folding of Primordial Hyper-Acidic Helical Proteins

This study shows polyamines induce folding of a hyper-acidic ancestral protein, suggesting they may have functioned as chemical chaperones in early life.

On the Emergence of P-Loop NTPase and Rossmann Enzymes from a Beta-Alpha-Beta Ancestral Fragment

This paper investigates the evolutionary relationship between P-loop NTPases and Rossmann enzymes, suggesting they may share a common ancestral beta-alpha-beta fragment.

On the evolution of chaperones and co-chaperones and the expansion of proteomes across the Tree of Life

The paper analyzes proteome complexity across the Tree of Life, showing significant expansion in protein numbers, size, and fold diversity, accompanied by the evolution of chaperone systems to manage protein quality.

Determining the interaction status and evolutionary fate of duplicated homomeric proteins

The paper systematically analyzes duplicated homomeric proteins in yeast and bacteria to determine their interaction status and evolutionary fate, finding significant differences between species.

Primordial emergence of a nucleic acid binding protein via phase separation and statistical ornithine to arginine conversion

This study demonstrates a transition from phase-separating polypeptides to dsDNA-binding proteins through statistical ornithine-to-arginine conversion and sequence duplication.

A mixture of three engineered phosphotriesterases enables rapid detoxification of the entire spectrum of known threat nerve agents

This paper describes a mixture of three phosphotriesterase variants that detoxify all known threat nerve agents.

Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases

The paper elucidates the catalytic mechanism of chalcone isomerases, showing how an arginine residue activates substrates via Bronsted and Lewis acid interactions, and highlights structural differences between type-1 and type-2 enzymes.

Chance and pleiotropy dominate genetic diversity in complex bacterial environments

The paper examines how environmental complexity influences the evolutionary fate of mutations in Bacillus subtilis, finding that pleiotropy and chance dominate over selection in heterogeneous environments.

Rescue of Conformational Dynamics in Enzyme Catalysis by Directed Evolution

This study uses directed evolution to identify mutations that restore catalytic activity in a mutant enzyme, revealing how conformational dynamics are shaped by evolutionary selection.

Evolution of chalcone isomerase from a non-catalytic ancestor

This study shows chalcone isomerase evolved from a non-catalytic ancestor through four founder mutations with weak epistasis, enabling enantioselective activity.