Are the native states of proteins kinetic traps?

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Abstract

Four proteins were selected to represent each of the four different CATH classes and, for each protein, threedecoys were constructed with structures totally alien to the native state. The decoys were scored against the nativestate with the help of the AMBER force field, using three measures: the average energy, the average fluctuationand the resistance to a heat pulse. Two sets of simulations were performed, one with explicit solvent and the otherwith implicit solvent. The overall conclusion is that, of these three measures, the most successful in picking outthe native states was the last one, since the native structures take a consistently longer time to be destabilized inthis manner. However, the general conclusion is also that none of the measures is completely effective indiscriminating all the decoys, a result that supports other studies, according to which the native state is reachedby a kinetic step.
Original languageUnknown
Pages (from-to)1485-1493
JournalMolecular Physics
Volume107
Issue number14
DOIs
Publication statusPublished - 1 Jan 2009

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