Proteins segregate into discrete subcellular compartments via a variety of mechanisms, including motor protein transport, local binding, and diffusion barriers. This physical separation of cell functions serves, in part, as a mechanism for controlling compartment activity by allowing regulation of local protein concentrations. In this study we explored how soluble protein size impacts access to the confined space within the retinal photoreceptor outer segment signaling compartment and discovered a strikingly steep relationship. We find that GFP monomers, dimers, and trimers expressed transgenically in frog rods are present in the outer segment at 1.8-, 2.9-, and 6.8-fold lower abundances, relative to the cell body, than the small soluble fluorescent marker, calcein. Theoretical analysis, based on statistical-mechanical models of molecular access to polymer meshes, shows that these observations can be explained by the steric hindrance of molecules occupying the highly constrained spaces between outer segment disc membranes. This mechanism may answer a long-standing question of how the soluble regulatory protein, arrestin, is effectively excluded from the outer segments of dark-adapted rods and cones. Generally, our results suggest an alternate mode for the control of protein access to cell domains based on dynamic, sizedependent compartmental partitioning that does not require diffusion barriers, active transport, or large numbers of immobile binding sites.any cellular functions take place in highly spatially constrained compartments such as primary cilia, microvilli, endoplasmic reticulum (ER)/Golgi, filopodia, or dendritic spines. Delivery and retention of membrane-associated proteins to these areas are mediated by several complementary mechanisms, including intraflagellar transport (1), local binding to relatively immobile structures (2), and barriers to diffusion between the specialized compartment and the rest of the cell (3-4). Although it is generally recognized that the activities of these compartments are regulated by soluble proteins, especially in the case of cell signaling (5), specific rules governing soluble protein access to the compartments are not well defined. We addressed this problem in rod photoreceptors of Xenopus laevis where visual signal transduction occurs within the narrow confines of a sensory cilium.Photoreceptor outer segments are ciliary organelles containing a stack of up to ∼2,000 flattened membrane vesicles called lamellar discs (5). The main protein component of these membranes is the visual pigment rhodopsin. Most other signaling proteins acting downstream of rhodopsin are tethered to the discs by posttranslational lipidation or single-pass transmembrane anchorage (6). An exception is arrestin, a soluble protein involved in the termination of the rhodopsin-mediated light response (7). An important feature of photoresponse regulation by arrestin is that arrestin levels in the outer segment are modulated in a light-dependent manner. Arrestin is nearly undetectable in the outer se...