Giulia Palermo

This paper introduces edge-aware graph attention networks to interpret biophysical mechanisms from molecular dynamics simulations, showing improved prediction and communication network analysis.

This study identifies a cryptic divalent metal binding pocket that regulates Cas9's metal-dependent activity through conformational activation and catalytic efficiency.

This study determines how the I-F3 CRISPR-associated transposase recognizes and pairs transposon ends for transposition using cryo-EM and biochemical analyses.

This study investigates how Ru and Os organometallic agents bind to nucleosome surface and superhelical crevice sites, revealing ligand substitution effects on binding profiles and stability.

This study investigates how AcrIIC1 inhibits GeoCas9 by analyzing structural and dynamic changes in the HNH nuclease domain.

This study identifies design rules for expanding PAM compatibility in CRISPR-Cas9 variants by analyzing structural and functional interactions in VQR, VRER, and EQR variants.

This study investigates differences in cis and trans cleavage efficiency among Cas12a orthologues and identifies REC2-NUC interactions as key determinants of their function.

This study uses deep learning and simulations to uncover the molecular mechanisms of TnsC filament assembly in a CRISPR-associated transposon.

This study reveals the conformational dynamics of the Cas8 protein in the Cascade-TniQ complex, showing how it transitions between open and closed states to facilitate DNA binding and transposition.

This study investigates how xCas9 expands DNA targeting by recognizing alternative PAM sequences through increased flexibility in its PAM-interacting region.

This study investigates how single-atom mutations in the recognition lobe of GeoCas9 affect its structure, dynamics, and guide RNA interactions without altering its functional specificity.

The paper investigates how specific mutations in the Rec3 domain of CRISPR-Cas9 variants affect structural dynamics and allosteric communication to enhance specificity.

This paper develops new CRISPR-Cas13a variants and crRNA design strategies to improve RNA-detection specificity, achieving better discrimination of SARS-CoV-2 strains.

This study elucidates the allosteric activation mechanism of CRISPR-Cas13a using molecular dynamics simulations and experiments, revealing key residues critical for RNA cleavage selectivity.