Protein 3-nitrotyrosine (3-NY) immunoreactivity of rat brain homogenate was localized to a ca. 50 kDa protein band by western blot (WB) analysis. The nitrated proteins were localized to the raft fraction obtained by centrifugation of the homogenate in a sucrose density gradient, which contained specific raft markers such as flotillin-1 and caveolin-1. Purification of the nitrated raft proteins either by a combination of reversed-phase high-performance liquid chromatography (HPLC) and sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) or by immunoprecipitation (IP) with protein- and modification-specific antibodies coupled to WB and HPLC-electrospray ionization-tandem mass spectrometry (ESI--MS/MS) analysis allowed us to identify two proteins modified by 3-NY: flotillin-1 and alpha-tubulin. Both alpha- and beta-tubulin were detected in the rat brain raft fraction as abundant proteins, which co-immunoprecipitate with flotillin-1 and caveolin-1. Importantly, some protein-protein interactions in rafts were disrupted in 3-NY-containing proteins, e.g. caveolin-1 was dissociated from a complex with flotillin-1 and alpha-tubulin. The analysis of age dependencies did not show any significant change in protein nitration and expression of flotillin-1 and alpha-tubulin, but a decrease in the brain caveolin-1 level for old (34 months) versus young (6 months) rats. The putative mechanism of nitric oxide synthase (NOS) activity regulation by the level of caveolin expression and raft protein-protein interactions is discussed.