A simple simulation model can reproduce the thermodynamic folding intermediate of apoflavodoxin

Abstract

Flavodoxins are single domain proteins with an alpha/beta structure, whose function and folding have been well studied. Detailed experiments have shown that several members of this protein family present a stable intermediate, which accumulates along the folding process. In this work, we use a coarse-grained model for protein folding, whose interactions are based on the topology of the native state, to analyze the thermodynamic characteristics of the folding of Anabaena apoflavodoxin. Our model shows evidence for the existence of a thermodynamic folding intermediate, which reaches a significant population along the thermal transition. According to our simulation results, the intermediate is compact, well packed, and involves distortions of the native structure similar to those experimentally found. These mainly affect the long loop in the protein surface comprising residues 120–139. Although the agreement between simulation and experiment is not perfect, something impossible for a crude model, our results show that the topology of the native state is able to dictate a folding process which includes the presence of an intermediate for this protein.