Another caution in using mutants is that changing one gene may have unintended consequences on the Doramapimod greater photosynthetic apparatus. For instance, knocking out PsbS as in npq4 could change the properties of the thylakoid membrane, which affect more processes than just qE. PsbS has been shown to affect the stacking

of the grana membranes (Kiss et al. 2008) and to affect the distance between PSII centers upon illumination (Betterle et al. 2009). These changes have not been shown to be directly related to qE, but they complicate the interpretation of the role of PsbS. As another example, the altered qE dynamics of the lut2 mutant, which lacks lutein, may be due to the misfolding of light-harvesting proteins rather than a change in see more the qE mechanism (Dall’Osto et al. 2006). Nonetheless, the A. thaliana qE mutants buy Vorinostat have provided a powerful tool for studying the components and mechanism of qE. Triggering of qE We now turn to a description of tools to study qE triggering. A complete understanding of the triggering of qE by \(\Updelta\hboxpH\) requires

characterizing the value of the lumen pH at which the components of qE are turned on. It is important to know the pH level at which any pH-sensitive qE components are activated and whether these pH levels are absolute or modulated by other environmental factors. It is also important to characterize the “steepness” of the pH dependence of qE. A steep pH dependence would correlate to a “switch” from fully on to fully off in a short pH range. By contrast, a shallow pH Resminostat dependence would correspond to a “dial,” where the activation level gradually changes from off to on. In addition to quantifying the response of the proteins involved in qE to protonation, a complete understanding of qE triggering requires knowing the response of PSII to the protonation

of these key proteins. This response could involve conformational changes within or between proteins and is discussed in the “Formation of qE in the grana membrane” section. Although work with chemical inhibitors has convincingly shown that qE is triggered by acidification of the lumen, quantifying the qE response to lumen pH is challenging. This challenge arises from the fact that the complexes involved in qE are embedded in the thylakoid membrane and that the pH-sensitive components of these complexes are located in the lumen space. To characterize the response of qE to \(\Updelta\hboxpH,\) researchers have sought to measure the lumen pH and determine the pK as of key proteins and enzymes. These downstream responses to the pH trigger have been investigated by a combination of measuring the lumen pH and correlating it to the amount of qE. The effect of \(\Updelta\hboxpH\) on qE has been quantified by fitting the relationship between observed qE quenching and measured lumen pH to various equations, as in Takizawa et al.