The ability to perceive the environment, an essential attribute in living organisms, is linked to the evolution of signalling proteins that recognize specific signals and execute predetermined responses. Such proteins constitute concerted systems that can be as simple as a unique protein, able to recognize a ligand and exert a phenotypic change, or extremely complex pathways engaging dozens of different proteins which act in coordination with feedback loops and signal modulation. To understand how cells sense their surroundings and mount specific adaptive responses, we need to decipher the molecular workings of signal recognition, internalization, transfer and conversion into chemical changes inside the cell. Protein allostery and dynamics play a central role. Here, we review recent progress on the study of two- component systems, important signalling machineries of prokaryotes and lower eukaryotes. Such systems implicate a sensory histidine-kinase and a separate response regulator protein. Both components exploit protein flexibility to effect specific conformational rearrangements, modulating protein:protein interactions, and ultimately transmitting information accurately. Recent work has revealed how histidine-kinases switch between discrete functional states according to the presence or absence of the signal, shifting key amino acid positions that define their catalytic activity. In concert with the cognate response regulator’s allosteric changes, the phosphoryl-transfer flow during the signalling process is exquisitely fine-tuned for proper specificity, efficiency and directionality.