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As cells and organisms age, their proteins sustain increasing amounts of oxidative damage. It is estimated that half of all proteins are damaged in old organisms, yet the dominant mechanisms by which damage affects proteins and cellular phenotypes are not known. Here, we show that random modification of side chain charge induced by oxidative damage is likely to be a dominant source of protein stability...
The mechanical unfolding of a set of 12 proteins with diverse topologies is investigated using an all-atom constraint-based model. Proteins are represented as polypeptides cross-linked by hydrogen bonds, salt bridges, and hydrophobic contacts, each modeled as a harmonic inequality constraint capable of supporting a finite load before breaking. Stereochemically acceptable unfolding pathways are generated...
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