Are the native states of proteins kinetic traps?

Leonor Cruzeiro (1) , Paulo Afonso Lopes (2)

1 FCT - Faculdade de Ciências e Tecnologia [Faro]
2 Informática

Four proteins are selected to represent each of the four different CATH classes and, for each protein, three decoys are built with structures that are totally alien to the native state. The decoys are scored against the native state with the help of the AMBER force field, using three measures: the average energy, the average fluctuation and the resistance to a heat pulse. Two sets of simulations are performed, one with explicit solvent and another set with implicit solvent. The overall conclusion is that of these three measures that which is most successful in picking out the native states is the last one since the native structures take a consistently longer time to be destabilized in this manner. But the general conclusion is also that none of measures is completely effective in discriminating all the decoys, a result that supports other studies according to which the native state is reached by a kinetic step.

Mots clés: Physical Sciences

Leonor Cruzeiro, Paulo Afonso Lopes. Are the native states of proteins kinetic traps?. Molecular Physics, 2009, 107 (14), pp.1485-1493. ⟨10.1080/00268970902950386⟩. ⟨hal-00513291⟩