Molecular interactions of archazolid with the V-ATPase

Archazolid is a novel and highly efficient inhibitor of the V-ATPase, a ubiquitous membrane energizing protein complex consisting of a cytosolic ATP-hydrolyzing V1 domain and a VO domain which mediates proton translocation via a membrane embedded ring of c subunits. The intention of the present thesis was to characterize the archazolid binding site within the V-ATPase on the molecular level. Initial labeling experiments with 14C-derivatives of archazolid and the Manduca sexta V-ATPase clearly identified the c subunit as binding partner for the inhibitor. Concurrently performed site-directed mutagenesis studies in Saccharomyces cerevisiae as well as continuous wave electron paramagnetic resonance spectroscopy, revealed that the amino acids tyrosine 142 and leucine 144, located within the fourth transmembrane helix of subunit c, contribute to archazolid binding. Strikingly, mutation of these amino acids to either asparagine or isoleucine resulted in a V-ATPase approximately 10-fold more sensitive to the inhibitor, indicating increased inhibitor-target interaction in both cases. In addition, inhibition assays with different derivatives of archazolid suggested close proximity of the C-15 of archazolid and tyrosine 142 of subunit c. Competition assays with NCD-4, a covalently binding inhibitor which specifically targets a highly conserved glutamate within subunit c that is essential for proton translocation, revealed that the archazolid binding site also comprises this amino acid. Since the three amino acids tyrosine 142, leucine 144 and glutamate 137 (positions according to the S. cerevisiae c subunit) form a triangle within the central part of subunit c, the archazolid binding site most likely resides within a single c subunit and the inhibitor probably directly prevents proton translocation by the c ring. A spin labeled derivative of archazolid was used to enlighten the stoichiometry of c subunits within the VO ring. The measurements, performed via double electron electron resonance spectroscopy on spin labeled archazolid bound to the M. sexta V-ATPase, revealed a clear distance distribution that suggested, based on the supposed binding site of archazolid, a number between 9 and 11 subunits in the ring. This number is in line with a previously suggested decameric arrangement of the M. sexta ring and excludes a hexameric structure which is frequently assumed to be valid for V-ATPases