E. I. Shakhnovich

This study simulates condensate coalescence using metadynamics and finds that sticker-spacer polymers undergo kinetic arrest or entropy-driven fusion depending on sticker exchange dynamics and density.

This paper develops a biophysical model to predict the fitness of SARS-CoV-2 variants based on RBD binding thermodynamics and epistatic interactions.

The paper develops a method to map protein conformations to phenotypes by systematically analyzing disulfide bonds in proteins.

This study replaces a helical segment in DHFR with sequences from unrelated proteins, showing that while chimeras fold, their activity and stability are reduced, highlighting limits to sub-domain modularity.

This study identifies myo-inositol as a chemical chaperone that suppresses lens crystallin aggregation, suggesting its potential as a therapeutic target for age-related cataracts.

This study simulates protein evolution to show how native structure influences cotranslational folding, finding that low contact order proteins are more likely to fold cotranslationally.

The paper derives that single mutation effects on protein stability follow a Gaussian distribution using statistical mechanics and supports it with computational and experimental data.

The paper shows that mutations increasing protein stability in E. coli adenylate kinase lead to substrate inhibition by AMP, reducing enzyme activity and fitness.

The paper introduces a first-principles free-energy landscape to predict protein-folding transition-path statistics without requiring dynamical data, showing agreement with simulations and experiments.

The paper shows wild-type human γD crystallin catalyzes aggregation of its W42Q variant through disulfide bond transfer, revealing a redox mechanism relevant to protein aggregation in oxidizing environments.

The paper shows that Shine-Dalgarno sequence accessibility affects N-terminal codon bias in E. coli by modulating translation initiation efficiency.

The paper models microbial growth phases to show how tradeoffs between growth, lag time, and yield lead to frequency-dependent and non-transitive selection.

This study examines how mutations in E. coli's Adenylate Kinase affect growth phases, revealing that catalytic capacity optimizes lag time while growth rates are less affected.

The paper shows that evolutionary selection for folding stability maintains protein structure despite sequence divergence, but allows rare structural innovations over longer timescales.