Simulations of MTERF1 show how flexibility supports a fast DNA search mode, then shifts into tight recognition. A stable non-specific complex forms on B-DNA while the protein diffuses along the helix, highlighting dynamics-driven targeting.
All-atom modeling maps how spike structure shifts across pH, separating stable regimes from extreme acid/base responses. pH-sensitive regions, especially in receptor-binding architecture, dominate the structural deviations.
Fibrinogen adsorption to hydrophobic surfaces can trigger misfolding and αC-domain untethering, enabling new intermolecular linkages. The pathway connects surface contact to multilayer growth and thick fiber formation, guiding anti-thrombogenic design.
We combine surface experiments and mechanistic reasoning to explain how the P12 peptide disrupts fibrinogen fiber growth on hydrophobic polymers, shifting morphology toward smaller aggregates while preserving endothelial attachment and biocompatibility.
We map ion–protein interactions with all-atom MD and connect them to aggregation by tracking binding sites, residence times, and whether ions bind directly (partly dehydrated) or remain water-mediated via contact maps and hydration-shell metrics.