DYNAMICS AND UNFOLDING PATHWAYS OF A HYPERTHERMOPHILIC AND A MESOPHILIC RUBREDOXIN

Molecular dynamics simulations in solution are performed for a rubredo xin from the hyperthermophilic archaeon Pyrococcus furiosus (RdPf) and one from the mesophilic organism Desulfovibrio vulgaris (RdDv). The t wo proteins are simulated at four temperatures: 300 K, 373 K, 473 K (t wo sets), and 500 K; the various simulations extended from 200 ps to 1 ,020 ps. At room temperature, the two proteins are stable, remain clos e to the crystal structure, and exhibit similar dynamic behavior; the RMS residue fluctuations are slightly smaller in the hyperthermophilic protein. An analysis of the average energy contributions in the two p roteins is made; the results suggest that the intraprotein energy stab ilizes RdPf relative to RdDv. At 373 K, the mesophilic protein unfolds rapidly (it begins to unfold at 300 ps), whereas the hyperthermophili c does not unfold over the simulation of 600 ps. This is in accord wit h the expected stability of the two proteins. At 373 K, where both pro teins are expected to be unstable, unfolding behavior is observed with in 200 ps and the mesophilic protein unfolds faster than the hyperther mophilic one. At 500 K, both proteins unfold; the hyperthermophilic pr otein does so faster than the mesophilic protein. The unfolding behavi or for the two proteins is found to be very similar. Although the exac t order of events differs from one trajectory to another, both protein s unfold first by opening of the loop region to expose the hydrophobic core. This is followed by unzipping of the beta-sheet. The results ob tained in the simulation are discussed in terms of the factors involve d in flexibility and thermostability.