NanoESI Mass Spectrometry of Rubisco and Rubisco Activase Structures and Their Interactions with Nucleotides and Sugar Phosphates

Ribulose bisphosphate carboxylase/oxygenase (Rubisco) is the protein that is responsible for the fixation of carbon dioxide in photosynthesis. Inhibitory sugar phosphate molecules, which can include its substrate ribulose-1,5-bisphosphate (RuBP), can bind to Rubisco catalytic sites and inhibit catalysis. These are removed by interaction with Rubisco activase (RA) via an ATP hydrolytic reaction. Here we show the first nanoESI mass spectra of the hexadecameric Rubisco and of RA from a higher plant (tobacco). The spectra of recombinant, purified RA revealed polydispersity in its oligomeric forms (up to hexamer) and that ADP was bound. ADP was removed by dialysis against a high ionic strength solution and nucleotide binding experiments showed that ADP bound more tightly to RA than AMP-PNP (a non-hydrolysable ATP analog). There was evidence that there may be two nucleotide binding sites per RA monomer. The oligomerization capacity of mutant and wild-type tobacco RA up to hexamers is analogous to the subunit stoichiometry for other AAA+ enzymes. This suggests assembly of RA into hexamers is likely the most active conformation for removing inhibitory sugar phosphate molecules from Rubisco to enable its catalytic competency. Stoichiometric binding of RuBP or carboxyarabinitol bisphosphate (CABP) to each of the eight catalytic sites of Rubisco was observed.     

Exploring sites on mitochondrial ATPase for catalysis, regulation, and inhibition.

Evidence is presented that mitochondrial ATPase has two types of sites that bind adenine nucleotides. The catalytic site, C, binds the substrates ATP, GTP, or ITP and the inhibitor guanylyl imidodiphosphate (GMP-PNP). A second type of site, R, binds ATP, ADP, adenylyl imidodiphosphate (AMP-PNP), and the chromium complexes of ATP or ADP. All of these substances binding to the R site inhibit the hydrolysis of ATP in a competitive manner; their inhibition of hydrolysis of ITP and GTP is noncompetitive. GMP-PNP inhibits oxidative phosphorylation in submitochondrial particles but AMP-PNP does not. The localization on mitochondrial membranes of sites for the binding of various antibiotics that inhibit oxidative phosphorylation is discussed.     

Physical and enzymatic properties of nucleotide-depleted beef heart mitochondrial adenosine triphosphatase.

Tightly bound adenine nucleotides are removed from multiple binding sites on beef heart mitochondrial ATPase (F1) by chromatography on columns of Sephadex equilibrated with 50% glycerol. Release of nucleotides from the enzyme is associated with large decreases in sedimentation velocity (from 11.9 S to 8.4 S) which may be observed in concentrated solutions of polyols. Polyol-induced conformational changes are reversed when the enzyme is returned to dilute buffers. The nucleotide-depleted enzyme restores oxidative phosphorylation in F1-deficient submitochondrial particles. Reconstitution of nucleotide-depleted F1 with the ATP analog (adenylyl-imidodiphosphate (AMP-PNP), almost 5 moles of AMP-PNP per mole of enzyme, results in preparations with substantially inhibited ATPase activity which nevertheless restores oxidative phosphorylation and the 32Pi-ATP exchange reaction in F1-deficient submitochondrial particles. Incubation of the analog-labeled enzyme with ATP and Mg++ results in partial displacement of the analog and a time-dependent recovery of ATPase activity.     

Purification and properties of membrane-bound coupling factor-latent ATPase from Mycobacterium phlei.

The membrane bound coupling factor-latent ATPase was solubilized from the membrane vesicles of Mycobacterium phlei by using 0.25 M sucrose or low ionic strength buffer. Purification of the solubilized enzyme by use of Sepharose-ADP conjugate gel yielded a homogenous preparation of latent ATPase which was purified about 216-fold in a single step with an 84% yield. The enzyme exhibits a specific activity of 39 mumoles of ATP hydrolyzed per min per mg protein. The purified enzyme exhibits coupling factor activity. Electrophoresis in two dissociating solvent systems indicates that the enzyme contains at least three major polypeptides of molecular weights 56,000, 51,000, and 46,000 daltons, and two minor polypeptides of 30,000 and 17,000 daltons. Equilibrium binding studies of ADP with purified coupling factor-latent ATPase reveal the presence of two nucleotide binding sites per molecule with an apparent Ka of 8.1 X 10(-5) M. By use of affinity chromatography, another latent ATPase has been isolated from the solubilized enzyme, which does not exhibit coupling factor activity.     

Binding of single nucleotides to H+-ATP synthases observed by fluorescence resonance energy transfer

F(0)F(1)-ATP synthases couple proton translocation with the synthesis of ATP from ADP and phosphate. The enzyme has three catalytic nucleotide binding sites, one on each beta-subunit; three non-catalytic binding sites are located mainly on each alpha-subunit. In order to observe substrate binding to the enzyme, the H(+)-ATP synthase from Escherichia coli was labelled selectively with the fluorescence donor tetramethylrhodamine (TMR) at position T106C of the gamma-subunit. The labelled enzymes were incorporated into liposomes and catalysed proton-driven ATP synthesis. The substrate ATP-Alexa Fluor 647 was used as the fluorescence acceptor to perform intermolecular fluorescence resonance energy transfer (FRET). Single molecules are detected with a confocal set-up. When one ATP-Alexa Fluor 647 binds to the enzyme, FRET can be observed. Five stable states with different intermolecular FRET efficiencies were distinguished for enzyme-bound ATP-Alexa Fluor 647 indicating binding to different binding sites. Consecutive hydrolysis of excess ATP resulted in stepwise changes of the FRET efficiency. Thereby, gamma-subunit movement during catalysis was directly monitored with respect to the binding site with bound ATP-Alexa Fluor 647.     

ENERGY-REGULATED FUNCTIONAL TRANSITIONS OF CHLOROPLAST ATPASE

The functional transitions of the membrane-bound chloroplast ATPase (CF₁) as influenced by low ADP and uncoupler concentrations are investigated by measurements of initial and steady-state ATP hyrolysis and concomitant membrane energization. Following activation of latent ATP hydrolysis by light in the presence of dithioerythritol, the resulting steady-state ATP hydrolysis depends on the dark-period ( t _d) bteween light activation and ATP addition. ADP, added during t _d, inhibits this activity ( K _i about 2 μ M ) and induces a lag in the onset of ATP hydrolysis. The extent of membrane energization as monitored by an aminoacridine fluorescent probe is proportional to the ATPase activity.
An uncoupler amplifies the inhibitory effect of ADP if added during f _d, whereas it induces the normal stimulation of ATP hydrolysis in the absence of ADP. The ADP effect, which is different from product inhibition, is interpreted as a conformational interaction with CF₁ causing an increase of the energy threshold required for the inactive → active transition of the CF₁ molecules. These results are in harmony with currently proposed models of CF₁ regulation by adenine nucleotides based on binding studies.
The inactive → active transition of CF₁ conformation is investigated by analysis of the lag in the onset of ATP hydrolysis at different ADP concentrations and by means of varied light pulses and single-turnover flashes, using the electric potential indicating absorption change at 515 nm as a probe for the onset of ATP hydrolysis. The half-time of the process leading to fully (re)activated ATP hydrolysis is about 0.25 s. The ATP-dependent flash-induced inactive → active transition occurs within a few turnovers of electron flow.     

Probing conformational variations at the ATPase site of the RNA helicase DbpA by high-field electron-nuclear double resonance spectroscopy

The RNA helicase DbpA promotes RNA remodeling coupled to ATP hydrolysis. It is unique because of its specificity to hairpin 92 of 23S rRNA (HP92). Although DbpA kinetic pathways leading to ATP hydrolysis and RNA unwinding have been recently elucidated, the molecular (atomic) basis for the coupling of ATP hydrolysis to RNA remodeling remains unclear. This is, in part, due to the lack of detailed structural information on the ATPase site in the presence and absence of RNA in solution. We used high-field pulse ENDOR (electron-nuclear double resonance) spectroscopy to detect and analyze fine conformational changes in the protein's ATPase site in solution. Specifically, we substituted the essential Mg(2+) cofactor in the ATPase active site for paramagnetic Mn(2+) and determined its close environment with different nucleotides (ADP, ATP, and the ATP analogues ATPγS and AMPPnP) in complex with single- and double-stranded RNA. We monitored the Mn(2+) interactions with the nucleotide phosphates through the (31)P hyperfine couplings and the coordination by protein residues through (13)C hyperfine coupling from (13)C-enriched DbpA. We observed that the nucleotide binding site of DbpA adopts different conformational states upon binding of different nucleotides. The ENDOR spectra revealed a clear distinction between hydrolyzable and nonhydrolyzable nucleotides prior to RNA binding. Furthermore, both the (13)C and the (31)P ENDOR spectra were found to be highly sensitive to changes in the local environment of the Mn(2+) ion induced by the hydrolysis. More specifically, ATPγS was efficiently hydrolyzed upon binding of RNA, similar to ATP. Importantly, the Mn(2+) cofactor remains bound to a single protein side chain and to one or two nucleotide phosphates in all complexes, whereas the remaining metal coordination positions are occupied by water. The conformational changes in the protein's ATPase active site associated with the different DbpA states occur in remote coordination shells of the Mn(2+) ion. Finally, a competitive Mn(2+) binding site was found for single-stranded RNA construct.     

The binding of Mn2+ and ADP to myosin.

The metal ion requirement of myosin-ADP binding was investigated by use of Mn2+. Mn2+ binds to two sets of noninteracting sites on myosin which are characterized by affinity constants of 10(6) and 10(3), M(-1) at 0.016 M KCl concentration. The maximum number of sites is 2 for the high affinity and 20-25 for the low affinity set. Binding of Mn2+ to the high affinity sites increases the affinity of ADP binding to myosin. F-actin inhibits ADP binding (Kiely, B., and Martonosi, A., Biochim. Biophys. Acta 172: 158-170 [1969]), but even at F-actin concentrations much higher than that required to saturate the actin binding sites of myosin or its proteolytic fragments, significant ADP binding remained. The actin insensitive portion of ADP binding was inhibited by 10(-4) M inorganic pyrophosphate or ATP. The results are discussed on the basis of a model in which actin and ADP bind to myosin at distinct but interacting sites.     

Testing for violations of microscopic reversibility in ATP-sensitive potassium channel gating

In pancreatic beta cells, insulin secretion is tightly controlled by the cells' metabolic state via the ATP-sensitive potassium (KATP) channel. ATP is a key mediator in this signaling process, where its role as an inhibitor of KATP channels has been extensively studied. Since the channel contains an ATPase as an accessory subunit, the possibility that ATP hydrolysis mediates KATP channel opening has also been proposed. However, a rigorous test of coupling between ATP hydrolysis and channel gating has not previously been performed. In the present work, we examine whether KATP channel gating obeys detailed balance in order to determine whether ATP hydrolysis is strongly coupled to the gating of the KATP channel. Single-channel records were obtained from inside-out patches of transiently transfected HEK-293 cells. Channel activity in membrane patches with exactly one channel shows no violations of microscopic reversibility. Although KATP channel gating shows long closed times on the time scale where ATP hydrolysis takes place, the time symmetry of channel gating indicates that it is not tightly coupled to ATP hydrolysis. This lack of coupling suggests that channel gating operates close to equilibrium; although detailed balance is not expected to hold for ATP hydrolysis, it still does so in channel gating. On the basis of these results, the function of the ATPase active site in channel gating may be to sense nucleotides by differential binding of ATP and ADP, rather than to drive a thermodynamically unfavorable conformational change.     

Study of the Simultaneous Binding of ADP and ATP on Coupling Factor CF-1 by a Modification of the Hummel and Dreyer Method

Abstract

A modification of the Hummel and Dreyer method⁽¹⁾, based on anion exchange separation is used here for the study of the simultaneous binding of ADP and ATP on spinach coupling factor CF₁.

This method gives the same results as gel filtration (dissociation constant and number of sites) when ADP alone is present.

The extent of binding of ADP and ATP is approximately the same when mixed in equimolecular ratio, but since endogenous ADP is irreversible bound, this nucleotide is predominant on CF₁.

The binding of one nucleotide is partly prevented by prealable mixing of CF₁ with the other nucleotide. This phenomenon occurs likely at the level of high affinity sites, where binding would not be entirely reversible, contrarily to low affinity sites.

This method is of potential application for other ligands separable by anion exchange chromatography and for other types of chromatography (reversed phase).     

Studies of substructure and tightly bound nucleotide in bacterial membrane ATPase.

Highly purified preparations of Streptococcus faecalis ATPase contain a similar but inactive protein detected by prolonged polyacrylamide gel electrophoresis. The inactive protein appears to arise by proteolytic cleavage of the major subunits in the enzyme. By use of a new technique, subunit analysis in SDS gels was performed on the enzyme band and the inactive protein band excised from a polyacrylamide gel after electrophoresis. The results indicated that the ATPase has the composition alpha3beta3gamma in which alpha = 60,000, beta = 55,000, and gamma = 37,000 daltons. The inactive protein appears to have the composition (f)6 in which f = 49,000 daltons. There is also evidence that the enzyme band contains some slightly modified forms of the ATPase, such as alpha3beta2 (f)gamma. The inactive protein lacks the capacity for tight nucleotide binding. Our experiments show that the tight ATPase-nucleotide complex formed in S. faecalis cells (the endogenous complex) behaves differently from the tight complex formed in vitro (the exogenous complex). We prepared a doubly labeled complex containing endogenous 32P-labeled ADP and ATP and exogenous 3H-labeled ADP. We observed that the addition of free nucelotide to the doubly labeled ATPase displaced the exogenous bound ligand from the enzyme but not the endogenous bound nucleotide. We suggest that the displaceable and nondisplaceable forms of the tight ATPase-nucleotide complex correspond to two different conformational states of the enzyme.     

Active transport of Na + and K + through animal cell membranes

The transport of Na⁺ out of the cell and K⁺ into the cell against a concentration gradient is catalyzed by a (Na⁺ + K⁺)-activated ATPase. The way in which the cations pass through the cell membrane has not yet been elucidated. Studies on the ATP hydrolysis revealed a Na⁺-dependent phosphorylation of the enzyme protein; the conformation of the enzyme also appears to change. The energy required for transport of the cations against their concentration gradients is probably provided by K⁺-dependent hydrolysis of the enzyme-bound phosphate. The enzyme can synthesize ATP from inorganic phosphate and ADP on reversal of the cation concentration gradient. By keeping the enzyme in a particular conformation, the cardiac glycoside ouabain specifically inhibits the Na⁺ pump.     

Human Rad51 mediated DNA unwinding is facilitated by conditions that favour Rad51-dsDNA aggregation

Background  

Human Rad51 (RAD51), analogous to its bacterial homolog, RecA, binds and unwinds double stranded DNA (dsDNA) in the presence of certain nucleotide cofactors. ATP hydrolysis is not required for this process, because even ATP non hydrolysable analogs like AMP-PNP and ATPγS, support DNA unwinding. Even ADP, the product of ATP hydrolysis, feebly supports DNA unwinding.     

Anion recognition in water with use of a neutral uranyl-salophen receptor

A new water-soluble uranyl-salophen complex incorporating two glucose units has been synthesized. This neutral derivative shows noteworthy binding affinity for fluoride in water thanks to the Lewis acid-base interaction occurring between the metal and the anion. Such interaction is strong enough to overcome the high hydration enthalpy of fluoride. Moreover this complex effectively binds hydrogen phosphate and exhibits remarkably strong association for nucleotide polyanions ADP(3-) and ATP(4-).     

Transient kinetic and isotopic tracer studies of the myosin adenosine triphosphatase reaction.

From transient kinetic studies of the Mg2+-dependent adenosine triphosphatase of myosin subfragment 1, prepared from rabbit skeletal muscle, a seven-step mechanism has been proposed. Features of this mechanism include two-step processes for ATP and ADP binding in which the binary complex isomerizes in addition to a rapid nucleotide association step. In the case of ATP a large negative standard free energy change is associated with the isomerization. An overall rate-limiting isomerization of the myosin-product complex prior to product release has been identified. Studies on the mechanism of cleavage of ATP bound to the active site indicate the process is readily reversible and can account for the observation that more than one oxygen of the product phosphate arises from water. This proposal has been substantiated by the finding that the oxygen atoms of the gamma-phosphoryl group of bound ATP also undergo extensive exchange with water.     

The possible role of tightly bound adenine nucleotides in oxidative and photosynthetic phosphorylation.

The tightly bound nucleotides of the beff-heart mitochondrial ATPase are released during cold inactivation followed by ammonium sulfate precipitation. During incubation at 0 degrees C the sedimentation coefficient (S20W) of the ATPase first declines from 12.1S to 9S. Prolonged incubation or precipitation with ammonium sulfate leads to dissociation of the 9S component into subunits with S20W of 3.5S. The 9S component still bears bound nucleotides which exchange more extensively and rapidly with added nucleotides than those bound to the active 12.1S component. The bound nucleotides are lost when the 9S form dissociates into the smaller subunits. Thus, firm binding of nucleotides is a property of the quarternary structure of the enzyme. The exchangeability of the nucleotides bound to the ATPase of chloroplast membranes is greatly increased in membranes illuminated in the presence of pyocyanine. Pi can exchange into both the beta and gamma positions of the bound nucleotides when the membranes are energized in the presence of Mg2+. The exchange of the nucleotides and the incorporation of Pi are insensitive to the inhibitor Dio-9 but are inhibited by the uncoupler S13. This inhibition by S13 parallels that of the inhibition of photosynthetic phosphorylation. These findings are discussed with regard to our hypothesis that electron transfer causes release of preformed tightly bound ATP from the ATPase by inducing a conformational change.     

布朗动力学理论模拟动态肌动蛋白纤维的增长

肌动蛋白的聚合耦合三磷酸腺酐(ATP)分子水解成二磷酸腺苷(ADP)分子和磷酸(Pi)的释放两个过程. 因此, 肌动蛋白纤维上的原聚体存在三种不同状态, 即分别结合ATP, ADP/Pi和ADP分子. 原聚体的不同状态导致纤维具有不同的空间图谱, 这些状态的空间分布将影响纤维的各种行为. 为此,建立了相应的分子模型,在布朗动力学模拟中实现了遵循时间演化的连续马尔可夫随机过程的解聚和水解反应; 重点阐述了如何实现纤维两端的聚合和解聚达到化学平衡的方法, 并系统研究了纤维在结合ATP分子的肌动蛋白单体溶液中的增长行为.     

Treadmilling of actin filaments via Brownian dynamics simulations

Actin polymerization is coupled to the hydrolysis of adenosine triphosphate (ATP) into adenosine diphosphate (ADP) and inorganic phosphate (P(i)). Therefore, each protomer within an actin filament can attain three different nucleotide states corresponding to bound ATP, ADP/P(i), and ADP. These protomer states form spatial patterns on the growing (or shrinking) filaments. Using Brownian dynamics simulations, the growth behavior of long filaments is studied, together with the associated protomer patterns, as a function of ATP-actin monomer concentration, C(T), within the surrounding solution. For concentrations close to the critical concentration C(T)=C(T,cr), the filaments undergo treadmilling, i.e., they grow at the barbed and shrink at the pointed end, which leads to directed translational motion of the whole filament. The corresponding nonequilibrium states are characterized by several global fluxes and by spatial density and flux profiles along the filaments. We focus on a certain set of transition rates as deduced from in vitro experiments and find that the associated treadmilling (or turnover) rate is about 0.08 monomers per second.     

多种精氨酸衍生物与ＡＴＰ作用及其催化ＡＴＰ水解的影响研究

分别使用荧光光谱法、 ~1H和~(31)P核磁方法对腺苷-5′-三磷酸(ATP)和多种L-精氨酸衍生物(L)的相互作用做了系统的研究, 得到了一些有意义的结果.在荧光滴定实验中, L对ATP有很强的荧光猝灭作用, 说明两者有较强的相互作用. ~1H和~(31)P核磁结果进一步证实了L与ATP的识别位点在ATP的嘌呤环和磷酸链上, 结合力为氢键和静电作用. 另外, 用~(31)P 核磁滴定的方法考察了L对ATP水解的影响, 发现不同的精氨酸衍生物对ATP水解的催化影响有很大的差异, 说明L对ATP的识别和催化其水解作用有较强的选择性. 此识别及催化作用的研究对深入理解精氨酸残基在ATP合酶中起到"触点"作用有一定的参考价值.