Passage of Fl-ATPase through a centrifuge column [Penefsky, H. S. (1979) Methods Enzymol. 56, 527-5301 caused formation of a product with a relative molecular mass of 72000 as determined by sodium dodecyl sulfate/ polyacrylamide gel electrophoresis. The product was identified as cross-linked a and 6 subunits by using Western blots and subunit-specific monoclonal antibodies. The cross-link was reversed by 50 mM dithiothreitol implying that it was a disulfide bridge. Formation of the cross-link was inhibited by 2 mM EDTA and was stimulated in some buffers by the addition of 10 pM CuC12. Time course experiments indicated that the majority of the cross-link formed while the enzyme was passing through the column. Thus the cross-link induced by column centrifugation arose from the rapid, heavy-metal-ion-catalysed oxidation of two sulfhydryl groups, one on the a subunit and one on the 6 subunit, to a disulfide. These results demonstrate that care must be exercised when running proteins through centrifuge columns as potentially deleterious disulfide formation can result.An anti-/3 monoclonal antibody was capable of immunoprecipitating the entire enzyme including the crosslinked subunits, implying that the cross-linked a and 6 subunits were still a part of F1. The formation of the crosslink affected neither the hydrolytic activity of the enzyme nor its susceptibility to inhibition by E subunit. The cross-linked enzyme was unable to bind to F1-depleted membranes in experiments in which soluble F1 and membranes were senarated bv centrifugation. Column centrifugation did not generate the cross-link on membrane- The proton-translocating ATPase of Escherichia coli couples the proton motive force generated by the respiratory chain enzymes to the synthesis of ATP [ l -51. The enzyme consists of two parts: a water-soluble portion named F1 which contains the catalytic activity of the enzyme, and an integral membrane portion named Fo which functions as a protonspecific pore. Fl consists of five types of subunits named a -E in order of decreasing molecular mass and has a subunit stoichiometry of ~3 / 3~y 6~.The catalytic site is thought to reside on the /3 subunits; the a subunits have tight nucleotide binding sites; and the y subunit is thought to organize the a and / 3 subunits into a catalytic active complex. Both the 6 and E subunits are implicated in the binding of the a3p3y complex It is believed that in F1 there are three catalytic sites that act in an alternating manner with strong site-site cooperativity [8]. Much interest is presently directed at the nature of conformational changes which occur within F1 during catalysis. One hypothesis mentioned by Gresser et al. [9] and developed more recently by Cox et al. [lo] that during catalysis there is a rotational movement of the CI -/3 hexamer with respect to the minor subunits. The proximity of each pair of a -p subunits to a particular minor subunit or a particular surface of a minor subunit would be directly reflected in the stage of catalysis the a -pair was undergoing. O...