Bacterial chemotaxis is one of the best understood signaling systems in biology. It is one of a large number of two component sensory systems in bacteria that use two proteins, a histidine auto kinase (CheA) and the response regulator proteins (CheY and CheB) that are the kinase substrates that are phosphorylated on aspartate residues. Phosphorylation of the response regulator domain modulates its interactions with its target domain(s) resulting in increased or decreased affinity for the other domain, depending on the system. We propose to use modern nuclear magnetic resonance techniques and other physical methods to answer questions in two specific aims: (1) What is the structural basis for the modulation of the kinase activity of CheA. CheA forms a hetero-trimeric complex with the transmembrane chemotaxis receptors and the coupling protein CheW. The receptors compare the current environment by binding attractant ligands to a memory of the recent past stored as methylation of certain glutamate resides in the receptors. How do the receptors make that comparison? How do they transmit that information to CheA to modulate its activity. (2) Phosphorylated CheY, produced by CheA, controls the sense of rotation of the bacterial rotary flagellar motors. The first step in the process is the binding to a recognition sequence in FliM, a protein of the switch complex made up of three proteins (FliM, FliG and FliN) located on the rotor of the motor. How does this binding event result in a change in the sense of rotation of the motor? How does the CheY-FliM complex communicate this information to the rest of the components of the motor?