Camilo A. Aponte-Santamaria

Choosing a lipid force field for membrane remodeling: pore formation and membrane mimetics in CHARMM36, AMBER Lipid21 and Slipids

This study compares three lipid force fields for membrane remodeling using molecular dynamics simulations, finding differences in pore formation and stability under enhanced sampling methods.

The Staphylococcus aureus carotenoid staphyloxanthin modifies the structure of phosphatidylglycerol lipid bilayers

This study investigates how staphyloxanthin modifies phosphatidylglycerol lipid bilayers using simulations and experiments, revealing structural changes that enhance membrane stability.

Coarse-grained simulations of long intrinsically disordered proteins: a benchmark of Martini 3 force-fields

The paper benchmarks four Martini 3 force-field variations for simulating long intrinsically disordered proteins up to 809 amino acids and finds that general rescaling of interaction parameters better reproduces experimental compaction levels.

The phosphoproteomic landscape of the DNA damage response

This study profiles the human phosphoproteome in response to eleven DNA damage agents, identifying core phosphorylation sites and DDR signatures, and links proteasome regulation to the DDR via UBE3A.

KIMMDY: a biomolecular reaction emulator

KIMMDY emulates biomolecular reactions using kinetic Monte Carlo and graph neural networks, validated against experimental data and applied to various reaction types.

Coarse-grained Martini 3 model of chondroitin sulfate A

The paper develops a coarse-grained Martini 3 model of chondroitin sulfate A to enable efficient molecular dynamics simulations of its structural and electrostatic properties.

Membrane binding of a cyanobacterial ESCRT-III protein crucially involves the helix α1-3 hairpin conserved in all superfamily members

The paper shows IM30 binds membranes via a conserved helical hairpin, initiating assembly into higher-order structures that mediate membrane remodeling, revealing a conserved mechanism across ESCRT-III superfamily members.

Riboflavin metabolism shapes FSP1-driven ferroptosis resistance

This study identifies riboflavin as a modulator of ferroptosis sensitivity by supporting FSP1 stability and antioxidant recycling, with implications for therapeutic targeting.

Insights into human outer kinetochore assembly and force transmission from a structure-function analysis of the KMN network

The paper presents a structural and functional analysis of the KMN network, revealing key interfaces and their role in stabilizing microtubule binding and force transmission during chromosome segregation.