Subunit E is a component of the peripheral stalk(s) that couples membrane and peripheral subunits of the V-ATPase complex. In order to elucidate the function of subunit E, site-directed mutations were performed at the amino terminus and carboxyl terminus. Except for S78A and D233A/T202A, which exhibited V 1 V o assembly defects, the function of subunit E was resistant to mutations. Most mutations complemented the growth phenotype of vma4⌬ mutants, including T6A and D233A, which only had 25% of the wild-type ATPase activity. Residues Ser-78 and Thr-202 were essential for V 1 V o assembly and function. The mutation S78A destabilized subunit E and prevented assembly of V 1 subunits at the membranes. Mutant T202A membranes exhibited 2-fold increased V max and about 2-fold less of V 1 V o assembly; the mutation increased the specific activity of Vacuolar Hϩ -ATPase (V-ATPase) 1 proton pumps are present on vacuoles, lysosomes, endosomes, secretory vesicles, and Golgi of all eukaryotic cells where they maintain the acidic pH required for the multiple cellular processes achieved in these organelles (1-3). In kidneys, osteoclasts, neutrophils, and other specialized cells (3), V-ATPases are located also on the plasma membrane, where ATP-driven proton translocation to the extracellular space supports urine acidification, bone resorption, and cytosolic pH regulation among other processes.Amino acid sequence conservation and heterologous genetic complementation of V-ATPase subunits from mammals and plants in yeast (5-11) have shown that V-ATPases are structurally and functionally highly conserved pumps. The yeast V-ATPase complex consists of 14 different subunits organized into two domains, V 1 and V o (1-3). ATP hydrolysis is catalyzed in V 1 , which is peripherally bound to the cytosolic side of the membrane and consists of subunits A-H. Integral to the membrane is V o , which forms the proton transporting domain and consists of subunits a, c, cЈ, cЉ, d, and e (2, 3, 12). Connecting V 1 to V o are one central stalk made of subunits D and F and one to three peripheral stalks consisting of subunits C, E, G, H, and the amino terminus domain of the V o subunit a (13-17).V-ATPases operate by a rotary mechanism of proton transport (18, 19) similar to that of the F-ATPases (20, 21), and both molecular motors share functional homolog subunits involved in rotation and catalysis (22). Similar to subunits ␤ and ␣ of the mitochondrial F-ATPase enzyme, subunits A and B form a hexamer where ATP binds and is hydrolyzed by the V 1 domain. Subunit D is functionally equivalent to ␥ of F 1 and constitutes the rotating central stalk tightly associated with the proteolipid rotor in V o . Comparable with subunits a and c from F 0 , the ring of proteolipid subunits (c, cЈ, and cЉ) and the V o subunit a form the path for proton transport across the membrane. Despite an overall structural similarity, there are important differences that distinguish V-ATPases from F-ATPases. One difference is the possibility of two or three peripheral stalks per V...

A biochemistry laboratory was designed for an undergraduate course to help students better understand the link between molecular engineering and biochemistry. Students identified unknown yeast strains with high specificity using SDS-PAGE and Western blot analysis of whole cell lysates. This problem-solving exercise is a common application of biochemistry in biotechnology research. Three different strains were used: a wild-type and two mutants for the proton pump vacuolar ATPase (V-ATPase). V-ATPases are multisubunit enzymes and the mutants used were deletion mutants; each lacked one structural gene of the complex. After three, three-hour labs, mutant strains were easily identified by the students and distinguished from wild-type cells analyzing the pattern of SDS-PAGE distribution of proteins. Identifying different subunits of one multimeric protein allowed for discussion of the structure and function of this metabolic enzyme, which captured the interest of the students. The experiment can be adapted to other multimeric protein complexes and shows improvement of the described methodology over previous reports, perhaps because the problem and its solution are representative of the type of techniques currently used in research labs.

In this undergraduate biochemistry laboratory experiment, the vacuolar ATPase protein complex is purified from yeast cell extracts by doing immunoprecipitations under nondenaturing conditions. Immunoprecipitations are performed using monoclonal antibodies to facilitate data interpretation, and subunits are separated on the basis of their molecular size by SDS-PAGE. Both integral membrane and peripheral subunits are detected in Coomassie Blue-stained gels, and the identity of several subunits are confirmed by Western blots. Western blots serve to illustrate reproducibility and authenticity of the results and help students understand that they could use immunoblotting to detect subunits that are not visualized by Coomassie stain. The molecular mass of the subunits is estimated by their migration relative to molecular marker proteins in the same gel and used to estimate the size of the entire complex. Just like in biochemistry research, students learn to integrate several techniques to solve the subunit composition of a protein complex. These experiments are an alternative to classical protein purification techniques and can be adapted to study most protein complexes composed of membrane-bound and peripheral subunits from yeast. Instructors can use this approach to teaching proteomics and introduce students to systems biology. Because numerous yeast proteins are epitope tagged, instructors could use commercially available antibodies to study a protein complex of interest.Keywords: Immunoprecipitations, protein complexes, Western blots, protein purification, proteomics.Characterization of membrane-bound protein complexes is fundamental in biochemistry. Many cellular proteins are membrane-bound and possess multiple subunits that associate in a specific manner to enhance efficiency. However, isolation and characterization of membranebound proteins is a difficult task, which coupled with the complexity intrinsic with multiple subunits makes the study of most protein complexes a challenge.Immunoprecipitations offer an alternative to classical chromatographic techniques and can be used to purify proteins by one fractionation step. Nondenaturing immunoprecipitations, which are done under relatively mild conditions, can reveal components of steady-state assembled protein complexes [1, 2] as well as transient protein complexes [1]. Therefore, the protocol we describe can be further extended to introduce students to systems biology. The principle behind this powerful technique is simple. Antibodies are used to detect the protein under study as an antigen. Because antibodies have great affinity for their antigens, a highly specific antigen-antibody complex is formed. The antigen-antibody is complexed to the protein A-Sepharose (an antibody-binding protein linked to Sepharose beads) and harvested by centrifugation. Any protein(s) associated with the antigen is co-immunoprecipitated. SDS-PAGE is used to separate proteins on the basis of their molecular size, and standard protein markers in the same gel serve to generate calibra...

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