R. Potestio

Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations

This study uses coarse-grained simulations to investigate the kinetics of DNA double-strand breaks, finding a linear correlation between DSB distance and energy, and an exponential dependence of rupture times on DSB distance.

In search of a dynamical vocabulary: a pipeline to construct a basis of shared traits in large-scale motions of proteins

The paper introduces a pipeline to quantify large-scale protein dynamics using native structures, showing it can generalize to homologous proteins not in the initial dataset.

Structural Basis of Mutation-Dependent p53 Tetramerization Deficiency

This study investigates how mutations in p53's tetramerization domain affect its structure and function using simulations and yeast assays, showing destabilizing effects and altered transactivation.

Membrane binding of pore-forming γ-hemolysin components studied at different lipid compositions

This paper uses molecular dynamics simulations to study how lipid composition affects the membrane binding of γ-hemolysin components LukF and Hlg2, providing insights into their interaction mechanisms.

How Communication Pathways Bridge Local and Global Conformations in an IgG4 Antibody: a Molecular Dynamics Study

This paper uses molecular dynamics simulations to show that the conformation of pembrolizumab correlates with its CDR, mediated by the hinge region, suggesting a communication network within antibodies.

Searching the optimal folding routes of a Complex Lasso protein

This study uses molecular dynamics to simulate the folding of a complex lasso protein, identifying optimal folding pathways that avoid kinetic traps by locking the cysteine bridge after topology formation.