The atomic force microscope is a useful tool for imaging native biolog
ical structures at high resolution. In analogy to conventional immunol
abeling techniques, we have used antibodies directed against the C-ter
minus of bacteriorhodopsin to distinguish the cytoplasmic and extracel
lular surface of purple membrane while imaging in buffer solution. At
forces greater than or equal to 0.8 nN the antibodies were removed by
the scanning stylus and the molecular topography of the cytoplasmic pu
rple membrane surface was revealed. When the stylus was retracted, the
scanned membrane area was relabeled with antibodies within 10 min, Th
e extracellular surface of purple membrane was imaged at 0.7 nm resolu
tion, exhibiting a major and a minor protrusion per bacteriorhodopsin
monomer. As confirmed by immune-dot blot analysis and sodium dodecyl s
ulfate-gel electrophoresis, labeling of the purple membrane was not ob
served if the C-terminus of bacteriorhodopsin was cleaved off by papai
n.