The transverse heterogeneity of the polypeptides associated with the Photosystem I (PSI) complex in spinach thylakoid membranes and in a highly resolved PSI preparation has been studied using the impermeant chemical modifier, 2,4,6-trinitrobenzenesulfonate (TNBS) and the proteolytic enzyme, Pronase E. The present study has shown that the PSI reaction center polypeptide of -62 kilodaltons and the 22 and 20 kilodalton polypeptides of the PSI light-harvesting chlorophyll protein (LHCPI) complex are not labeled by I'4CFTNBS in unfractionated thylakoids. On the other hand, the 23 kilodalton polypeptide of the PSI LHCP and the 19 and 14 kilodalton polypeptides associated with the PSI primary electron acceptor complex are readily labeled by I"4CITNBS and are exposed to the stromal side of the thylakoid. Differences and similarities in the labeling of polypeptides associated with the PSI complex in thylakoids and in the isolated PSI complex are also noted. Treatment of thylakoids with pronase had no effect on the organization of the polypeptides in the LHCPI or the reaction center core complex, as manifested by the separation of these two subcomplexes from pronasetreated membranes. The 62, 19, and 14 kilodalton polypeptides associated with the reaction center core complex and the 23 and 22 kilodalton polypeptides associated with LHCPI are sensitive to pronase treatment while the 20 kilodalton polypeptide of LHCPI was inaccessible to the protease. The proteolysis of the 62 kilodalton polypeptide generated first a single immunodetectable fragment at about 48 kilodaltons, and further proteolytic digestion generated two other fragments at 30 and 17 kilodaltons respectively. These results are discussed in relation to the organization of the PSI complex in spinach thylakoids. A model for the transmembrane topography of the polypeptide constituents of PSI has been developed. complexes to the overall structure of the chloroplast membrane is less well understood.It has recently been possible to isolate all the chloroplast membrane electron transfer complexes in highly resolved functional form (7,16,25), and subsequently it has been demonstrated that these complexes are reconstitutively active in catalyzing noncyclic electron transport from water to NADP when supplemented with soluble protein cofactors (19). The availability of these resolved complexes allows for detailed examination of structure-function relationships in the individual complexes and examination of the nature of the interactions between complexes. In the present study, we have considered the topographical orientation of the chloroplast PSI complex. The impermeant chemical probe, TNBS,3 labeled with "1C, has been used to modify stroma-exposed amino acid side chains on proteins in unfractionated thylakoid membranes and reactive groups in the resolved PSI complex of Mullet et al. (25). The labeling pattern of PSI polypeptides in the membranes has been compared with that of the isolated PSI complex and subfractions isolated from this complex. Since any one sp...