Ligand-induced conformational changes in the Escherichia coli F1 adenosine triphosphatase probed by trypsin digestion

Sulfite and membrane energization induce two different active states of the Paracoccus denitrificans F0F1-ATPase

Activation of the latent ATPase activity of inside-out vesicles from plasma membranes of Paracoccus denitrificans was studied. Several factors were found to induce activation: heat, membrane energization by succinate oxidation, methanol, oxyanions (sulfite, phosphate, arsenate, bicarbonate) and limited proteolysis with trypsin. Among the oxyanions, sulfite induced the higher increase in ATPase activity. Sulfite functioned as a nonessential activator that slightly modified the affinity for ATP and increased notoriously the Vmax. There was a competitive effect between sulfite, bicarbonate and phosphate for ATPase activation; their similar chemical geometry suggests that these oxyanions have a common binding site on the enzyme. Dithiothreitol did not affect the ATPase activity. ATPase activation by sulfite was decreased by uncoupler, enhanced by trypsin and inhibited by ADP, oligomycin and venturicidin. In contrast, activation induced by succinate was less sensitive to ADP, oligomycin, venturicidin and trypsin. It is proposed that the active states induced by sulfite and succinate reflect two conformations of the enzyme, in which the inhibitory subunit epsilon is differently exposed to trypsin.

The absence of the mitochondrial ATP synthase delta subunit promotes a slow growth phenotype of rho- yeast cells by a lack of assembly of the catalytic sector F1

In the yeast Saccharomyces cerevisiae, inactivation of the gene encoding the delta subunit of the ATP synthase led to a lack of assembly of the catalytic sector. In addition a slow-growth phenotype was observed on fermentable medium. This alteration appears in strains lacking intact mitochondrial DNA and showing a defect in the assembly of the catalytic sector, such as the yeast strain inactivated in the gene encoding the epsilon subunit. In rho mitochondria having an intact F1, the ion movement resulting from the exchange of ADP formed in the organelle and ATP entering the mitochondrial compartment led to a mitochondrial transmembranous potential delta psi that was sensitive to carboxyactractyloside. This ion movement was dramatically decreased in rho mitochondria lacking the delta subunit and thus the F1 sector, whereas a cell devoid of delta subunit and complemented with a plasmid harboring the ATPdelta gene displayed an assembled F1, a normal generation time and a fully restored mitochondrial potential. This result could be linked to the involvement of the membrane potential delta psi which is indispensible for mitochondrial biogenesis.

Conformational changes of the mitochondrial F1-ATPase epsilon-subunit induced by nucleotide binding as observed by phosphorescence spectroscopy

Changes in conformation of the epsilon-subunit of the bovine heart mitochondrial F1-ATPase complex as a result of nucleotide binding have been demonstrated from the phosphorescence emission of tryptophan. The triplet state lifetime shows that whereas nucleoside triphosphate binding to the enzyme in the presence of Mg2+ increases the flexibility of the protein structure surrounding the chromophore, nucleoside diphosphate acts in an opposite manner, enhancing the rigidity of this region of the macromolecule. Such changes in dynamic structure of the epsilon-subunit are evident at high ligand concentration added to both the nucleotide-depleted F1 (Nd-F1) and the F1 preparation containing the three tightly bound nucleotides (F1(2,1)). Since the effects observed are similar in both the F1 forms, the binding to the low affinity sites must be responsible for the conformational changes induced in the epsilon-subunit. This is partially supported by the observation that the Trp lifetime is not significantly affected by adding an equimolar concentration of adenine nucleotide to Nd-F1. The effects on protein structure of nucleotide binding to either catalytic or noncatalytic sites have been distinguished by studying the phosphorescence emission of the F1 complex prepared with the three noncatalytic sites filled and the three catalytic sites vacant (F1(3,0)). Phosphorescence lifetime measurements on this F1 form demonstrate that the binding of Mg-NTP to catalytic sites induces a slight enhancement of the rigidity of the epsilon-subunit. This implies that the binding to the vacant noncatalytic site of F1(2,1) must exert the opposite and larger effect of enhancing the flexibility of the protein structure observed in both Nd-F1 and F1(2,1). The observation that enhanced flexibility of the protein occurs upon addition of adenine nucleotides to F1(2,1) in the absence of Mg2+ provides direct support for this suggestion. The connection between changes in structure and the possible functional role of the epsilon-subunit is discussed.

ATP synthase of yeast mitochondria. Isolation of the F1 delta subunit, sequence and disruption of the structural gene

The delta-subunit was isolated from the purified yeast F1. Partial protein sequences were determined by direct methods. From this information, degenerated primers were constructed. A part of the ATP delta gene was amplified by polymerase chain reaction from yeast genomic DNA. From the amplified DNA sequence, a nondegenerated oligonucleotide probe was constructed to isolate a 2.6-kbp BamHI-EcoRI DNA fragment bearing the whole gene. A 1036-bp DraI fragment was sequenced. A 480-bp open reading frame encoding a 160-amino-acid polypeptide is described. The deduced amino acid sequence is 22 amino acids longer than the mature protein, which is 138 amino acids long with a mass of 14,555 Da. The delta-subunit of Saccharomyces cerevisiae is 21%, 35%, 52% identical and 66%, 61% and 92% similar to the epsilon-subunit of Escherichia coli and the delta-subunits of beef heart and Neurospora crassa, respectively. A null mutant was constructed. The mutation was recessive and dramatically affected mitochondrial DNA stability since the transformed cells were 100% cytoplasmic petite. The double mutant (rho-, ATP delta::URA3) displayed low or no ATPase activity with an unstable catalytic sector, since a polyclonal antibody directed against the beta subunit did not coprecipitate the alpha subunit.

Product-activation of Escherichia coli membrane-bound H(+)-ATPase (F1F0-ATPase) connected with epsilon-subunit at alkaline pH

Mutant strain AN1518 or AN2387 (Gly48-->Asp in epsilon-subunit) and partial revertant strain AN2540 (Gly48-->Asp, Pro47-->Ser in epsilon-subunit) of E. coli were used in a kinetic study of membrane-bound H(+)-ATPase. It was found that at pH 9.0 mutant strain AN1518 or AN2387 and partial revertant strain AN2540 gave a low initial rate, which increased with time until linearity was reached after 1-2 min. This phenomenon was prominent in mutant strains, but was not so obvious in wild-type AN346 of E. coli; this property is similar to F1-ATPase reported by Cox [1]. The mechanism of the slow activation of membrane-bound H(+)-ATPase was further investigated in this paper. The experimental results indicated that the hydrolytic rate of E. coli F1F0-ATPase that increased with time was membrane protein concentration- and pH-dependent, and that the product ADP produced during ATP hydrolysis is the factor causing the slow activation. Preincubation of the hydrolytic product ADP with a concentration comparable to that produced in the assay (20 microM) caused initial activation of ATP hydrolysis and abolished the slow activation. On the other hand, with the removal of ADP during the progress of the hydrolytic reaction it could be seen that the slow activation was abolished as well. In order to test the relationship between the epsilon-subunit and ADP involved in the slow activation, trypsin treatment was carried out on the membrane-bound H(+)-ATPase of various strains. The activation observed after trypsin treatment was on the order of AN1518 > AN2540 > AN346. The activation effects of ADP and trypsin were not found to be additive. This implies that ADP acted in a similar way to trypsin, i.e., to cause removal of the epsilon-subunit. A tentative mechanism of the slow activation was proposed that ADP, a product of ATP hydrolysis, could induce conformational changes of F1F0 at alkaline pH 9.0, thus weakening the binding strength between the epsilon-subunit and other subunits of F1F0, and resulting in removal or partial removal of the epsilon-subunit. This further impaired the coupling of F1 and F0 in the mutant strains; as a consequence the rate of ATP hydrolysis was increased.

Electron microscopy of the F1F0 ATP synthase: from structure to function

The F1F0 ATP synthase is the large multisubunit complex which uses the proton gradient of energetically active membranes to synthesize ATP. While biochemical and genetic approaches have characterized the composition of the enzyme and elucidated many details of its mechanism and assembly, electron microscopy has been the tool of primary importance in determining the arrangement of the many subunits which comprise the F1F0. The highly cooperative catalytic mechanism is tightly coupled to transmembrane proton translocation in a separate and rather distant sector of the complex. An understanding of this intricate process and its control requires an appreciation of subunit interactions, starting with their locations relative to one another. Electron microscopy has provided most of the available structural information on the F1F0, and recent applications of cryo-electron microscopy have captured different functionally relevant configurations which may finally address longstanding questions about subunit rearrangements during the catalytic cycle.

Interaction of beef-heart mitochondrial F1-ATPase with immobilized ATP in the presence of dimethylsulfoxide

Dimethylsulfoxide [Me2SO, 30% (v/v)] promotes the formation of ATP from ADP and phosphate catalyzed by soluble mitochondrial F1-ATPase. The effects of this solvent on the interaction of beef-heart mitochondrial F1 with the immobilized ATP of Agarose-hexane-ATP were studied. In the presence of Me2SO, F1 bound less readily to the immobilized ATP, but once bound was more difficult to elute with exogenous ATP. This suggests that not only was the binding affinity for adenine nucleotide at the first binding site affected but that adenine nucleotide binding affinity at the second and/or third sites, which interact cooperatively with the first site to release bound nucleotide, was also affected. A reduction in the binding of [3H]ADP to these sites was shown. A change in the conformation of F1 in 30% (v/v) Me2SO was demonstrated by crosslinking and by the increased resistance of the enzyme to cold denaturation.

Structure of the Escherichia coli ATP synthase and role of the gamma and epsilon subunits in coupling catalytic site and proton channeling functions

The structure of the Escherichia coli ATP synthase has been studied by electron microscopy and a model developed in which the alpha and beta subunits of the F1 part are arranged hexagonally (in top view) alternating with one another and surrounding a central cavity of around 35 A at its widest point. The alpha and beta subunits are interdigitated in side view for around 60 A of the 90 A length of the molecule. The F1 narrows and has three-fold symmetry at the end furthest from the F0 part. The F1 is linked to F0 by a stalk approximately 45 A long and 25-30 A in diameter. The F0 part is mostly buried in the lipid bilayer. The gamma subunit provides a domain that extends into the central cavity of the F1 part. The gamma and epsilon subunits are in a different conformation when ATP + Mg2+ are present in catalytic sites than when ATP + EDTA are present. This is consistent with these two small subunits switching conformations as a function of whether or not phosphate is bound to the enzyme at the position of the gamma phosphate of ATP. We suggest that this switching is the key to the coupling of catalytic site events with proton translocation in the F0 part of the complex.

Structure-function relationships of domains of the delta subunit in Escherichia coli adenosine triphosphatase

The topology of the and subunit of the Escherichia coli adenosinetriphosphatase (ECF1) has been explored by proteinase digestion and chemical labeling methods. The delta subunit of ECF1 could be cleaved selectively by reaction of the enzyme complex with very low amounts of trypsin (1:5000, w/w). Cleavage of the delta subunit occurred serially from the C-terminus. The N-terminal fragments of the delta subunit remained bound to the core ECF1 complex through sucrose gradient centrifugation, indicating that part of the binding of this subunit involves the N-terminal segment. ECF1, in which around 20 amino acids had been removed from the C-terminus of delta, still bound to ECF0 but DCCD sensitivity of the ATPase activity was lost. When ECF1 was reacted with N-ethyl[14C]maleimide ([14C]NEM) in the native state, only one of the two Cys residues on the delta subunit was modified. This residue, Cys-140, was also labeled in ECF1F0. Cys-140 was shown to be involved in the disulfide bridge between alpha and delta subunits that is generated when ECF1 is treated with CuCl2. Thus, the C-terminal part of the delta subunit around Cys-140 can interact with the core ECF1 complex. These results suggest a model for the delta subunit in which the central part of polypeptide is a part of the stalk, with both N- and C-termini associated with ECF1.

Catalytic site nucleotide and inorganic phosphate dependence of the conformation of the epsilon subunit in Escherichia coli adenosinetriphosphatase

The rate of trypsin cleavage of the epsilon subunit of Escherichia coli F1 (ECF1) has been found to be ligand-dependent, as measured indirectly by the activation of the enzyme that occurs on protease digestion, or when followed directly by monitoring the cleavage of this subunit using monoclonal antibodies. The cleavage of the epsilon subunit was fast in the presence of ADP alone, ADP + MG2+, ATP + EDTA, or AMP-PNP, but slow when Pi was added along with ADP + Mg2+ or when ATP + Mg2+ was added to generate ADP + Pi (+Mg2+) in the catalytic site(s). The half-maximal concentration of Pi required in the presence of ADP + Mg2+ to protect the epsilon subunit from cleavage by trypsin was 50 microM, which is in the range measured for the high-affinity binding of Pi to F1. The ligand-dependent conformational changes in the epsilon subunit were also examined in cross-linking experiments using the water-soluble carbodiimide 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide (EDC). In the presence of ATP + Mg2+ or ADP + Mg2+ + Pi, the epsilon subunit cross-linked to beta in high yield. With ATP + EDTA or ADP + Mg2+ (no Pi), the yield of the beta-epsilon cross-linked product was much reduced. We conclude that the epsilon subunit undergoes a conformational change dependent on the presence of Pi. It has been found previously that binding of the epsilon subunit to ECF1 inhibits ATPase activity by decreasing the off rate of Pi [Dunn, S. D., Zadorozny, V. D., Tozer, R. G., & Orr, L. E. (1987) Biochemistry 26, 4488-4493]. This reciprocal relationship between Pi binding and epsilon-subunit conformation has important implications for energy transduction by the E. coli ATP synthase.

Role of minor subunits in the structural asymmetry of the Escherichia coli F1-ATPase

The beta subunits of the Escherichia coli F1-ATPase react independently with chemical reagents (Stan-Lotter, H. and Bragg, P.D. (1986) Arch. Biochem. Biophys. 248, 116-120). Thus, one beta subunit is readily crosslinked to the epsilon subunit, another reacts with N-N'-dicyclohexylcarbodiimide (DCCD), and a third one is modified by 4-chloro-7-nitrobenzofurazan (NbfCl). This asymmetric behaviour is not due to the association of the delta and epsilon subunits of the ATPase molecule with specific beta subunits since it is maintained in a delta, epsilon-deficient form of the enzyme.

Molecular architecture of Escherichia coli F1 adenosinetriphosphatase

The structure of the E. coli F1 ATPase (ECF1) has been studied by a novel combination of two specimen preparation and image analysis techniques. The molecular outline of the ECF1 was determined by three-dimensional reconstruction of images of negatively stained two-dimensional crystals of ECF1. Internal features were revealed by analysis of single particles of ECF1, preserved in their native state in a thin layer of amorphous ice, and examined by cryoelectron microscopy. Various projections of the unstained ECF1 were interpreted consistently with the three-dimensional structure in negative stain, yielding a more informative description of the enzyme than otherwise possible. Results show that the ECF1 is a roughly spherical complex approximately 90-100 A in diameter. Six elongated protein densities (the alpha and beta subunits, each approximately 90 A X approximately 30 A in size) comprise its hexagonally modulated periphery. At the center of the ECF1 is an aqueous cavity which extends nearly or entirely through the length of the complex. A compact protein density, located at one end of the hexagonal barrel and closely associated with one of the peripheral subunits, partially obstructs the central cavity.

Binding of dicyclohexylcarbodiimide to a native F1-ATPase-inhibitor protein complex isolated from bovine heart mitochondria

The effect and the binding of dicyclohexylcarbodiimide (DCCD) to a soluble native F1-ATPase-inhibitor protein complex (F1-IP) isolated from heart mitochondria was studied. About one mol DCCD bound per mol F1-IP complex; this inhibited its ATPase activity by more than 95%, ever under conditions that led to maximal hydrolysis. Bound DCCD localized to beta-subunits of the F1-IP complex. Cross-linking of the DCCD labeled complex with N-(ethoxy-carbonyl)-2-ethoxydihydroquinoline yielded a protein with a Mr 65,000-67,000 that contained IP as evidenced by its reaction with IP antibodies. No alpha-subunits were detected in this cross-linked product. The Mr 65,000-67,000 protein corresponds to beta-subunits cross-linked with IP (Klein et al, Biochemistry 1980; 19, 2919-2925). However, no DCCD was found in the cross-linked beta-subunit-IP product of labeled native F1-IP. Thus the beta-subunit in contact with IP is distinct from the other two beta-subunits of the enzyme.