fluorescence correlation spectroscopy ͉ fluorescence cross-correlation spectroscopy ͉ photon-counting histograms ͉ scaffold ͉ fluorescence resonance energy transfer A quantitative understanding of cellular systems requires temporally and spatially resolved characterization of dynamic molecular movement and interactions in live cell settings. Fluorescence correlation spectroscopy (FCS), f luorescence crosscorrelation spectroscopy (FCCS), and photon-counting histograms (PCH) are techniques that examine fluctuations of fluorescent molecules in and out of a low-intensity laser beam focused to a volume of Ͻ1 fl (1-6). In FCS, the fluctuations of a single species can be analyzed using statistical means to determine the average number of particles in the focal volume and the relative mobility of the fluorescent particles. An extension of FCS, fluorescence crosscorrelation spectroscopy (FCCS), is potentially useful for quantitative examination of interactions between specific pairs of proteins in live cells. In FCCS, fluctuations of two different fluorescent signals are recorded simultaneously and are analyzed using a cross-correlation function (6, 7). The amplitude of the crosscorrelation reflects the extent of codiffusion of the fluorescent molecules and hence their presence in the same mobile complex (Fig. 1A) (6, 8-10). PCH, however, is suited for examining the oligomeric status of the proteins of interest (5, 11). Although to date the in vivo application of these techniques is limited, recent progress in commercially available microscopes and the development of red fluorescent proteins (12) to pair with GFP have opened the door to biologists for live cell examination of mobility, association, and oligomeric status of proteins under native expression.Successful FCS requires low molecular concentration and high enough mobility to minimize photobleaching during data acquisition. This requirement makes FCS uniquely suitable for analyzing cytosolic biochemistry where the endogenous concentrations of protein molecules are low, and most molecules are sufficiently mobile. To date, the majority of live-cell FCS studies used exogenously introduced fluorescent molecules, and these analysis were somewhat hampered by the difficulty to control molecular concentrations. We reasoned that yeast may be a good model system for live-cell FCS because of the ease of introducing genetically encoded fluorescent tags to proteins expressed under the endogenous promoter at the native chromosomal loci. Native expression levels may be ideal for fluctuation measurements and allow for a meaningful and relevant account of particle numbers in the mobile pool.We applied FCS and FCCS to the study of protein complex formation in the MAPK cascade, a widely studied signaling pathway whose main components are shared across eukaryotic organisms. Members of the yeast MAPK cascade are involved in distinct morphogenetic and stress response pathways, such as mating in response to pheromones, filamentous growth in response to nutrient conditions, and stress r...