E. Shakhnovich

This study shows that metabolons enhance metabolic flux for reaction-limited enzymes but not diffusion-limited ones, suggesting an evolutionary strategy for compensating inefficiency through clustering.

This study investigates how AMP substrate inhibition in adenylate kinase is modulated by domain motions, showing that inhibitory concentrations of AMP increase domain closure and affect catalytic activity.

The paper investigates how disulfide bond formation during translation guides the folding of the SARS-CoV-2 RBD, showing that non-equilibrium mechanisms are required to prevent misfolding.

This study shows phosphorylation sites prevent liquid-solid transitions in FUS condensates by reducing β-sheet propensity and stabilizing liquid-like states.

This study uses simulations to show how multi-domain RNA-binding proteins transition from disordered to ordered, solid-like structures, with implications for disease-related changes.

This study shows RNA promotes phase separation of protein clusters by acting as super-scaffolds, enabling liquid-like dynamics at low protein concentrations.

The paper investigates how point mutations in DHFR affect E. coli metabolism and phenotype by analyzing dTTP levels and enzyme kinetics.

DBFOLD predicts protein folding pathways and transition rates by combining Monte-Carlo simulations with high-temperature unfolding simulations to account for non-native interactions.

This study identifies a compound that inhibits both wild-type and TMP-resistant variants of E. coli DHFR, delaying resistance development through efflux pump duplication.

The paper shows that multi-valent proteins form micro-phase separated droplets through arrested macro-phase separation, which is dynamic and functional, unlike the static macro-phase separation predicted by traditional models.

The paper shows that adaptation to mutational inactivation of an essential E. coli gene converges to a suboptimal fitness peak through specific metabolic and proteomic changes.

This paper shows co-translational folding helps misfolding-prone proteins avoid kinetic traps by optimizing nascent chain lengths and translation rates.

This study reveals that wild-type HγD accelerates aggregation of the cataract-related W42Q variant through a mechanism called interface stealing, where intermolecular domain interactions outcompete native intramolecular stabilization.

The paper shows that mutation rate variability affects resistance fixation in bacterial populations under stress, with low and high stress leading to disproportionate hypermutation effects.

The paper shows that variation in microbial growth traits on a single resource can produce higher-order ecological effects, leading to complex community dynamics.

ProteomeVis explores protein evolution across S. cerevisiae and E. coli proteomes by analyzing structure, sequence, and organismal properties.

This study predicts the evolutionary pathway of norovirus escaping antibodies using a biophysical fitness model, validated by experimental evolution in bulk culture and microfluidics.

The paper uses in silico SELEX to study mutational robustness of an L-Arm binding aptamer, finding two functional genotype neighborhoods with similar binding affinity to the wild-type.