Segmented transition pathway of the signaling protein nitrogen regulatory protein C.

Recent advances in experimental methods provide increasing evidence that proteins sample the conformational substates that are important for function in the absence of their ligands. An example is the receiver domain of nitrogen regulatory protein C, a member of the phosphorylation-mediated signaling family of "two-component systems." The receiver domain of nitrogen regulatory protein C samples both inactive conformation and the active conformation before phosphorylation. Here we determine a possible pathway of interconversion between the active state and the inactive state by targeted molecular dynamics simulations and quasi-harmonic analysis; these methods are used because the experimental conversion rate is in the high microsecond range, longer than those that are easily accessible to atomistic molecular dynamics simulations. The calculated pathway is found to be composed of four consecutive stages described by different progress variables. The lowest quasi-harmonic principal components from unbiased molecular dynamics simulations on the active state correspond to the first stage, but not to the subsequent stages of the transition. The targeted molecular dynamics pathway suggests that several transient nonnative hydrogen bonds may facilitate the transition.

Role of cyclophilin D in the resistance of brain mitochondria to the permeability transition.

The mitochondrial permeability transition (MPT) is involved in both necrosis and apoptosis. Cyclophilin D (CypD) is an important component of the MPT. Brain mitochondria are more resistant to the MPT when compared to heart or liver mitochondria. We found that this increased resistance correlates with low expression of CypD in brain when compared to heart or liver. In newborn rats, sensitivity of brain mitochondria to the MPT and CypD expression are significantly higher than in mature animals. In an in vitro model of neuronal development, mitochondria in differentiated neuronal-like cells exert a higher calcium threshold toward MPT induction and express significantly less CypD when compared to undifferentiated precursor cells. Gain and loss of function experiments confirm the role of CypD in sensitivity to the MPT. Together our data indicate that the increased calcium threshold of brain mitochondria to the MPT correlates with low expression of CypD in brain; and that neuronal cells lose CypD during differentiation and become less sensitive to the MPT induction. This may be a protection mechanism that raises the threshold of brain tissue against injuries.