Abstract M13 major coat protein was derivatized with BODIPY ( n-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza- s-indacene-3-yl)methyl iodoacetamide), and its aggregation was studied in 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC) and DOPC/1,2-dioleoyl- sn-glycero-3-[phospho-rac-(1-glycerol)] (DOPG) or 1,2-dioleoyl- sn-glycero-3-phosphoethanolamine (DOPE)/DOPG (model systems of membranes with hydrophobic thickness matching that of the protein) using photophysical methodologies (time-resolved and steady-state self-quenching, absorption, and emission spectra). It was concluded that the protein is essentially monomeric, even in the absence of anionic phospholipids. The protein was also incorporated in pure bilayers of lipids with a strong mismatch with the protein transmembrane length, 1,2-dierucoyl- sn-glycero-3-phosphocholine (DEuPC, longer lipid) and 1,2-dimyristoleoyl- sn-glycero-3-phosphocholine (DMoPC, shorter lipid), and in lipidic mixtures containing DOPC and one of these lipids. The protein was aggregated in the pure vesicles of mismatching lipid but remained essentially monomeric in the mixtures as detected from BODIPY fluorescence emission self-quenching. From fluorescence resonance energy transfer (FRET) measurements (donor- n-(iodoacetyl)aminoethyl-1-sulfonaphthylamine (IAEDANS)-labeled protein; acceptor-BODIPY labeled protein), it was concluded that in the DEuPC/DOPC and DMoPC/DOPC lipid mixtures, domains enriched in the protein and the matching lipid (DOPC) are formed.