, and ؉18 daltons. The masses of the modifications suggest that the tryptophan is modified to kynurenine (؉4), a keto-͞ amino-͞hydroxy-(؉16) derivative, and a dihydro-hydroxy-(؉18) derivative of the indole side chain. Peptide synthesis and MS͞MS confirmed the kynurenine assignment. The ؉16 and ؉18 tryptophan modifications may be intermediates formed during the oxidative cleavage of the indole ring to give kynurenine. The sitedirected mutations, W352C, W352L, and W352A, exhibit an increased rate of photoinhibition relative to wild type. We hypothesize that Trp-352 oxidative modifications are a byproduct of PSII water-splitting or electron transfer reactions and that these modifications target PSII for turnover. As a step toward understanding the tertiary structure of this CP43 peptide, structural modeling was performed by using molecular dynamics.mass spectrometry ͉ collision-induced dissociation ͉ tryptophan ͉ kynurenine ͉ photoinhibition P hotosystem II (PSII) is a protein-pigment complex located in thylakoid membranes of plants, eukaryotic algae, and cyanobacteria. PSII catalyzes the light-driven oxidation of water to O 2 , and the reduction of plastoquinone. PSII contains both intrinsic and extrinsic polypeptides. The intrinsic polypeptides include chlorophyll-binding proteins, CP47, CP43, and the D1 and D2 polypeptides (reviewed in ref. 1). The D2͞D1 heterodimer binds P 680 , pheophytin, and the quinone receptors, Q A and Q B (2). Three extrinsic subunits, the manganese stabilizing, 24-kDa, and 18-kDa proteins, are required for maximum oxygen evolution in plants (3, 4). Recently, a 3.8-Å structure of the cyanobacterial PSII reaction center has been reported (5, 6).The intrinsic PSII subunits, CP43 and CP47, function as light-harvesting proteins and play a role in PSII assembly and activity (7-11). CP47 and CP43 have similar tertiary and secondary structures (5). Each polypeptide has six membranespanning regions and a large luminal, hydrophilic loop (E) between helix V and VI (5, 7). In Synechocystis sp. PCC 6803, loop E of the CP43 subunit extends from residue Asn-280 to . Mutations or deletions in this loop inactivate or impair PSII activity in Synechocystis (9, 11-13).Posttranslational modifications can play important roles in the assembly, degradation, structure, and function of proteins. However, little is known about the roles of such modifications in membrane proteins. For example, in cytochrome c oxidase, a crosslinked tyrosine-histidine cofactor has been identified at the binuclear metal site (14); the function of this cofactor has not yet been definitively established. Recently, it has been suggested that posttranslationally modified amino acids, containing carbonyl groups, covalently bind hydrazines and amines at the catalytic site of PSII (10, 15). Because amines and hydrazines are inhibitors of photosynthetic water oxidation, it was suggested that these carbonyl-containing amino acids play roles in the structure, function, or assembly of PSII.To obtain more information about posttranslational mod...