Evidence of a calcium-induced structural change in the ATP-binding site of the sarcoplasmic-reticulum Ca2+-ATPase using terbium formycin triphosphate as an analogue of Mg-ATP

8-Azapurines as isosteric purine fluorescent probes for nucleic acid and enzymatic research

The 8-azapurines, and their 7-deaza and 9-deaza congeners, represent a unique class of isosteric (isomorphic) analogues of the natural purines, frequently capable of substituting for the latter in many biochemical processes. Particularly interesting is their propensity to exhibit pH-dependent room-temperature fluorescence in aqueous medium, and in non-polar media. We herein review the physico-chemical properties of this class of compounds, with particular emphasis on the fluorescence emission properties of their neutral and/or ionic species, which has led to their widespread use as fluorescent probes in enzymology, including enzymes involved in purine metabolism, agonists/antagonists of adenosine receptors, mechanisms of catalytic RNAs, RNA editing, etc. They are also exceptionally useful fluorescent probes for analytical and clinical applications in crude cell homogenates.

The structure and interactions of Ca(2+)-ATPase

Electron crystallographic studies on membrane crystals of Ca(2+)-ATPase reveal different patterns of ATPase-ATPase interactions depending on enzyme conformation. Physiologically relevant changes in Ca2+ concentration and membrane potential affect these interactions. Ca2+ induced difference FTIR spectra of Ca(2+)-ATPase triggered by photolysis of caged Ca2+ are consistent with changes in secondary structure and carboxylate groups upon Ca2+ binding; the changes are reversed during ATP hydrolysis suggesting that a phosphorylated enzyme form of low Ca2+ affinity is the dominant intermediate during Ca2+ transport. A two-channel model of Ca2+ translocation is proposed involving the membrane-spanning helices M2-M5 and M4, M5, M6 and M8 respectively, with separate but interacting Ca2+ binding sites.

Effects of polycations on Ca2+ binding to the Ca(2+)-ATPase

Spermine and polyarginine have been shown to increase the rate of dissociation of Ca2+ from the Ca(2+)-ATPase of skeletal-muscle sarcoplasmic reticulum. They also decrease the affinity of the ATPase for Mg2+ as detected by changes in the fluorescence intensity of the ATPase labelled with 4-(bromomethyl)-6,7-dimethoxycoumarin (DMC). Polyarginine itself also decreases the fluorescence intensity of DMC-labelled ATPase. These results are consistent with binding of spermine and polyarginine to a gating site controlling the rate of access of Ca2+ to its binding sites on the ATPase. A basic peptide PLN-(1-25) corresponding to residues 1-25 of phospholamban had no effect on the rate of dissociation of Ca2+ or on the fluorescence of DMC-labelled ATPase. Spermine, polyarginine and PLN-(1-25) all increased the equilibrium constant E1/E2, and spermine and polyarginine increased the rate of Ca2+ binding to the ATPase, consistent with an increase in the rate of the E2-->E1 transition. Spermine displaced Tb3+ and Ruthenium Red from the ATPase, consistent with binding in the stalk region of the ATPase. Polyarginine and PLN-(1-25), however, had no effect on Tb3+ or Ruthenium Red binding, suggesting a greater specificity in binding basic peptides to the ATPase than spermine.

Changes in the profile structure of the sarcoplasmic reticulum membrane induced by phosphorylation of the Ca2+ ATPase enzyme in the presence of terbium: a time-resolved x-ray diffraction study

The design of the time-resolved x-ray diffraction experiments reported in this and an accompanying paper was based on direct measurements of enzyme phosphorylation using [gamma-32P]ATP that were employed to determine the extent to which the lanthanides La3+ and Tb3+ activate phosphorylation of the Ca2+ATPase and their effect on the kinetics of phosphoenzyme formation and decay. We found that, under the conditions of our experiments, the two lanthanides are capable of activating phosphorylation of the ATPase, resulting in substantial levels of phosphoenzyme formation and they slow the formation and dramatically extend the lifetime of the phosphorylated enzyme conformation, as compared with calcium activation. The results from the time-resolved, nonresonance x-ray diffraction work reported in this paper are consistent with the enzyme phosphorylation experiments; they indicate that the changes in the profile structure of the SR membrane induced by terbium-activated phosphorylation of the ATPase enzyme are persistent over the much longer lifetime of the phosphorylated enzyme and are qualitatively similar to the changes induced by calcium-activated phosphorylation, but smaller in magnitude. These results made possible the time-resolved, resonance x-ray diffraction studies reported in an accompanying paper utilizing the resonance x-ray scattering from terbium, replacing calcium, to determine not only the location of high-affinity metal-binding sites in the SR membrane profile, but also the redistribution of metal density among those sites upon phosphorylation of the Ca2+ATPase protein, as facilitated by the greatly extended lifetime of the phosphoenzyme.

Two states of the nucleotide-binding site of sarcoplasmic reticulum adenosine triphosphatase detected by the calcium-dependent reaction with adenosine 5'-[gamma-imidazolidate]triphosphate and adenosine 5'-[beta-imidazolidate]diphosphate

The Ca(2+)-ATPase from sarcoplasmic reticulum can be inhibited by adenosine 5'-[gamma-imidazolidate]triphosphate through the formation of an intramolecular cross-link at the active site which is dependent on the presence of Ca2+ [Bill, E., Gutowski, Z. & Bämert, H.G. (1988). Calcium-dependent inactivation of the Ca(2+)-ATPase from sarcoplasmic reticulum by chemically reactive adenosine triphosphate, Eur. J. Biochem. 176, 119-124] In the present study we show that adenosine 5'-[beta-imidazolidate]diphosphate is likewise an inhibitor of the Ca(2+)-ATPase effecting a similar inhibition pattern on phosphate release and Ca2+ transport. The overall reaction is Ca2+ dependent and produces a protein band that in SDS/PAGE is indistinguishable from that seen with ATP[imidazolidate]. This shows that the side chain of Asp351 which is claimed to be involved in the cross-linking reaction must be in reach of both the beta and the gamma phosphate moiety of the respective nucleotides. The cross-linked product is formed by a two-step reaction. The first step is the fast reaction of nucleotide imidazolidate presumably at the phosphorylation site (Asp351) under-formation of a mixed anhydride that covalently links nucleotide and protein. Subsequently, the nucleotide is released by a substitution reaction with a second amino acid side chain. This cross-linking reaction is strictly Ca2+ dependent and, remarkably, requires Ca2+ to be added before addition of the inhibitor. It proceeds at two rates and suggests that there are two states of the nucleotide-bindings site. This is also supported by the fact that in the absence of CA2+, ATP[imidazolidate] reacts only in approximately 50% of the calculated ATP-binding sites (based on 80-90% ATPase of total sarcoplasmic reticulum protein) with no subsequent cross-linking reaction.

Localization of a putative magnesium-binding site within the cytoplasmic domain of the sarcoplasmic reticulum Ca(2+)-ATPase

The amino acid sequences of several P-type ATPases share regions of high similarity. The functions of some of these regions, although several proposals have been made, have not yet been absolutely identified. In particular, one of these domains, located within the cytoplasmic loop in the area known as the 'hinge' domain, exhibits the highest degree of conservation. In the sarcoplasmic reticulum Ca(2+)-ATPase (SERCA-1), this region is located at residues 700-712. Comparison of the sequence in this domain with calcium-binding proteins reveals similarities with the center of the helix-loop-helix EF-hand structure that is known to form divalent-cation-binding sites. A 38-residue polypeptide, corresponding to the domain 682-719 of the Ca(2+)-ATPase was synthesized and tested for its ability to bind divalent cations. Circular-dichroism, intrinsic-fluorescence and fluorescence-energy-transfer studies performed on this polypeptide in solution support the hypothesis that this domain has, in the protein, the ability to bind a divalent cation, presumably Mg2+, with an affinity of 10-15 mM. This property is observed for the isolated polypeptide in aqueous solvent and in the presence of low concentrations of the alpha-helix promoter 2,2,2-trifluoroethanol. Substitution of either one or two critical amino acids in the sequence induces a significant reduction of the binding properties. It is proposed that this sequence is involved in the co-ordination of a Mg2+ in the nucleotide-binding site and/or in the phosphorylation site of P-type ATPases.

Ruthenium red affects the intrinsic fluorescence of the calcium-ATPase of skeletal sarcoplasmic reticulum

We have studied the effect of Ruthenium red on the sarcoplasmic reticulum Ca(2+)-ATPase. Ruthenium red does not modify the Ca2+ pumping activity of the enzyme, despite its interaction with cationic binding sites on sarcoplasmic reticulum vesicles. Two pools of binding sites were distinguished. One pool (10 nmol/mg) is dependent upon the presence of micromolar Ca2+ and may therefore represent the high-affinity Ca2+ transport sites of the Ca(2+)-ATPase. However, Ruthenium red only slightly competes with Ca2+ on these sites. The other pool (15-17 nmol/mg) is characterized as low-affinity cation binding sites of sarcoplasmic reticulum, distinct from the Mg2+ site involved in the ATP binding to the Ca(2+)-ATPase. The interaction of Ruthenium red with these low-affinity cation binding sites, which may be located either on the Ca(2+)-ATPase or on surrounding lipids, decreases tryptophan fluorescence level of the protein. As much as 25% of the tryptophan fluorescence of the Ca(2+)-ATPase is quenched by Ruthenium red (with a dissociation constant of 100 nM), tryptophan residues located near the bilayer being preferentially affected.

Functional characterization of lanthanide binding sites in the sarcoplasmic reticulum Ca(2+)-ATPase: do lanthanide ions bind to the calcium transport site?

Gd3+ binding sites on the purified Ca(2+)-ATPase of sarcoplasmic reticulum were characterized at 2 and 6 degrees C and pH 7.0 under conditions in which 45Ca2+ and 54Mn2+ specifically labeled the calcium transport site and the catalytic site of the enzyme, respectively. We detected several classes of Gd3+ binding sites that affected enzyme function: (a) Gd3+ exchanged with 54Mn2+ of the 54MnATP complex bound at the catalytic site. This permitted slow phosphorylation of the enzyme when two Ca2+ ions were bound at the transport site. The Gd3+ ion bound at the catalytic site inhibited decomposition of the ADP-sensitive phosphoenzyme. (b) High-affinity binding of Gd3+ to site(s) distinct from both the transport site and the catalytic site inhibited the decomposition of the ADP-sensitive phosphoenzyme. (c) Gd3+ enhanced 4-nitro-2,1,3-benzoxadiazole (NBD) fluorescence in NBD-modified enzyme by probably binding to the Mg2+ site that is distinct from both the transport site and the catalytic site. (d) Gd3+ inhibited high-affinity binding of 45Ca2+ to the transport site not by directly competing with Ca2+ for the transport site but by occupying site(s) other than the transport site. This conclusion was based mainly on the result of kinetic analysis of displacement of the enzyme-bound 45Ca2+ ions by Gd3+ and vice versa, and the inability of Gd3+ to phosphorylate the enzyme under conditions in which GdATP served as a substrate. These results strongly suggest that Ln3+ ions cannot be used as probes to structurally and functionally characterize the calcium transport site on the Ca(2+)-ATPase.

Emerging views on the structure and dynamics of the Ca2(+)-ATPase in sarcoplasmic reticulum

The ATP-dependent Ca2+ transport in sarcoplasmic reticulum involves transitions between several structural states of the Ca2(+)-ATPase, that occur without major changes in the secondary structure. The rates of these transitions are modulated by the lipid environment and by interactions between ATPase molecules. Although the Ca2(+)-ATPase restricts the rotational mobility of a population of lipids, there is no evidence for specific interaction of the Ca2(+)-ATPase with phospholipids. Fluorescence polarization and energy transfer (FET) studies, using site specific fluorescent indicators, combined with crystallographic, immunological and chemical modification data, yielded a structural model of Ca2(+)-ATPase in which the binding sites of Ca2+ and ATP are tentatively identified. The temperature dependence of FET between fluorophores attached to different regions of the ATPase indicates the existence of 'rigid' and 'flexible' regions within the molecule characterized, by different degrees of thermally induced structural fluctuations.