C. Atilgan

Elucidating TolC Protein Dynamics: Structural Shifts Facilitate Efflux Mediated β-lactam Resistance

This study investigates TolC protein dynamics in Gram-negative bacteria, identifying structural shifts that facilitate β-lactam efflux and resistance, with implications for antibiotic design.

Allosteric Modulation of Fluorescence Revealed by Hydrogen Bond Dynamics in a Genetically Encoded Maltose Biosensor

The paper uses molecular dynamics simulations to analyze hydrogen bond dynamics in a maltose biosensor, identifying key factors distinguishing its bright and dark states.

Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS

The paper shows that small molecules can disrupt HRASG12D-RAF interaction by mimicking phosphorylation effects on Switch I, as validated by MD simulations and in vitro experiments.

Dynamic Community Composition Unravels Allosteric Communication in PDZ3

The paper uses community composition analysis from molecular dynamics simulations to study how point mutants and ligands affect PDZ3's binding dynamics and selectivity.

Could network structures generated with simple rules imposed on a cubic lattice reproduce the structural descriptors of globular proteins?

The paper generates artificial protein-like structures on a cubic lattice using simple rules and shows they closely resemble real globular proteins in structural descriptors.

N-terminus of the third PDZ Domain of PSD-95 Orchestrates Allosteric Communication for Selective Ligand Binding

This study investigates how mutations in the N-terminus of PDZ3 affect ligand binding selectivity through molecular dynamics simulations and free energy calculations.

High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection

The paper quantifies high-order epistasis in DHFR mutations under trimethoprim selection, revealing complex fitness landscapes and implications for inhibitor design.