Inomata et al. suggested that protein folding of ubiquitin in HeLa cells is destabilised, partly due to interactions with endogenous interacting proteins. This result was a challenge to the general belief that protein folding inside cells is stabilised through macromolecular crowding and macromolecular confinement effects. Later, in vitro NMR experiments demonstrated that protein crowders can be mildly destabilising proteins by non-specific interactions, which was confirmed by recent molecular dynamics simulation studies. Here we briefly review these recent findings on the relationship between protein structure, dynamics and stability in intracellular environments.
Hydrogenases play crucial roles in the hydrogen metabolism by catalyzing the production and decomposition of H2. The membrane-bound [NiFe]-hydrogenase is a representative member of O2-tolerant hydrogenases, but the mechanism of which is poorly understood. Recently, we and other groups have reported the crystal structures of membrane-bound [NiFe]-hydrogenases, which revealed an unprecedented structure of one of three iron-sulfur clusters in the enzyme. Together with the spectroscopic study that shows the unique iron-sulfur cluster takes three oxidation states under physiological redox potentials, we concluded that the iron-sulfur cluster plays a key role in the O2-tolerant mechanism of the membrane-bound [NiFe]-hydrogenase.
Biological systems can operate robustly even with substantial stochasticity in their components. One possible but not yet proven mechanism to implement robust operation with noisy components is that relevant information for robust control is embedded in apparently stochastic signals. In this work, by employing Bayesian theory, we theoretically show that intracellular reactions with specific structures can implement statistically optimal dynamics to decode (extract) the relevant information embedded (encoded) within the apparently noisy signal. We also demonstrate that the decoding dynamics is related to a noise-induced transition, implying that optimal dynamics to suppress noise behaves as if exploiting noise for signal amplification.
Formation of synaptic connections between nerve cells is the key to understanding neuronal development. Despite the wealth of in vitro information, fundamental questions regarding how synapses are formed in the mammalian brain remain unanswered. Glutamate receptor (GluR) δ2 selectively expressed in cerebellar Purkinje cells is essential for synaptic formation in vivo. We showed that the trans-synaptic interaction of postsynaptic GluRδ2 and presynaptic neurexins through secreted cerebellin precursor protein 1 (Cbln1) mediates cerebellar synapse formation. We also demonstrated that GluRδ2 triggers synapse formation by tetramerization of neurexins through Cbln1. These finding provide a molecular insight into the mechanism of synapse formation in the brain.
Energy-conversion systems mediated by bacterial metabolism have recently attracted much attention, and therefore, demands for tuning of bacterial metabolism are increasing. It is widely recognized that intracellular redox atmosphere is one of the important factors influencing on bacterial metabolism. Although intracellular redox atmosphere had been conventionally tuned by dissolved oxygen concentration or by appropriate selection of an electron acceptor for respiration, we are developing novel method based on electrochemical technique for on-line (dynamic) tuning. Here we review our recent studies on electrochemical tuning of intracellular redox environment toward the control of bacterial metabolic pathway and activity.