Two-component system (TCS) signal transduction is the predominant mechanism in bacteria to adapt to environmental changes. Protein conformational dynamics in various proteins (or individual domains) of this signaling system facilitate signal transduction from the exterior to the interior of the cell. A membrane bound histidine kinase (HK) is autophosphorylated at a conserved histidine residue, upon signal recognition in the extracellular domain. A crucial loop region in the ATP-binding catalytic domain (CA) of HK, namely, the ATP-lid loop, is implicated in the autophosphorylation reaction of the HK. Integral to the TCS pathways is a phosphotransfer reaction between HK and a cognate response regulator (RR) protein. The RR protein undergoes conformational changes due to phosphorylation of a conserved aspartate residue. The phosphorylated form of the RR carries out the response by interacting with its targets, typically some gene promoters for downstream regulation. The autophosphorylation and/or RR phosphatase activities of the HK control the level of RR phosphorylation and hence the output response. The key for understanding of the mechanisms of biological signal transduction is to elucidate the conformational dynamics of its signaling proteins, as the activation of a signaling protein is fundamentally a process of conformational transition from an inactive to an active state. Activation of a response regulator protein has been investigated using RR468 as a model system using equilibrium and non equilibrium simulation techniques. Conformational dynamics in the CA domain (of HK) and RR protein are studied here using various computational tools to characterize intermediate states in the process of conformational transition. A protein is likely to have intramolecular interactions that are not present in the experimentally observed stable states but should be there to stabilize intermediates in the process of conformational transition. These non native interactions were identified using molecular dynamics simulations. It is hypothesized that any perturbation in these interaction hotspots can severely impair the process of conformational transition. Identification of metastable intermediates and non native interactions in the CA domain and RR enables us to elucidate the underlying mechanism of signal transmission through the TCS.
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