Fusion of influenza virus with target membranes is induced by acid and involves complex changes in the viral fusion protein hemagglutinin. At 0 degree C, in a first kinetically resolvable step, the hemagglutinin polypeptide 2 (HA2) N-terminal segment (fusion peptide) is exposed and inserts into the target membrane (Tsurudome, M., Glück, R., Graf, R., Falchetto, R., Schaller, U., and Brunner, J. (1992) J. Biol. Chem. 267, 20225-20232). We now report studies of the changes taking place at pH 5.0 and 37 degrees C, conditions that result in fusion or, in the absence of a target membrane, in inactivation of the virus' fusion capacity. To this end, we synthesized the new photosensitive phospholipid, 1-palmitoyl-2-[decanedioyl mono-[2-(125I)iodo-4-(3-trifluoromethyl-3H-diazirin-3-yl)-benzyl]e ster]- sn-glycero-3-phosphocholine (specific radioactivity, > 2000 Ci/mmol), and worked out a protocol to incorporate this lipid into the viral membrane. Subsequent photoactivation of the reagent resulted in selective labeling of the C-terminal portion of the HA2 polypeptide chain, in agreement with the membrane topology of hemagglutinin. When, however, prior to reagent activation, the viruses were exposed at pH 5.0, 37 degrees C, both the HA2 C-terminal and the N-terminal regions were labeled, suggesting that the HA2 N-terminal segment (fusion peptide) inserted into the viral membrane. Possible implications for fusion and virus inactivation are discussed.