Equilibrium simulation of trp-cage in the presence of protein crowders.

Anna Bille, Björn Linse, Sandipan Mohanty, Anders Irbäck

The Journal of chemical physics 2015 Nov 7

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While steric crowders tend to stabilize globular proteins, it has been found that protein crowders can have an either stabilizing or destabilizing effect, where a destabilization may arise from nonspecific attractive interactions between the test protein and the crowders. Here, we use Monte Carlo replica-exchange methods to explore the equilibrium behavior of the miniprotein trp-cage in the presence of protein crowders. Our results suggest that the surrounding crowders prevent trp-cage from adopting its global native fold, while giving rise to a stabilization of its main secondary-structure element, an α-helix. With the crowding agent used (bovine pancreatic trypsin inhibitor), the trp-cage-crowder interactions are found to be specific, involving a few key residues, most of which are prolines. The effects of these crowders are contrasted with those of hard-sphere crowders.

Citation

Anna Bille, Björn Linse, Sandipan Mohanty, Anders Irbäck. Equilibrium simulation of trp-cage in the presence of protein crowders. The Journal of chemical physics. 2015 Nov 7;143(17):175102