Non-equivalence of the CD and EF sites of muscular parvalbumins. A 113Cd NMR study

Björn Lindman: fifty years in science and technology

Björn Lindman has for fifty years had an active role in science and technology. His main contributions are briefly described. In the science part particular emphasis is put on his studies of ion binding, of amphiliphilc self-association, of molecular diffusion in solution and of polymer-surfactant systems. Furthermore we describe his role in introducing scientific areas, his role in scientific collaborations and his contributions to scientific organizations. The text is concluded by some personal reflections by the author.

Use of (113)Cd NMR to probe the native metal binding sites in metalloproteins: an overview

Our laboratories have actively published in this area for several years and the objective of this chapter is to present as comprehensive an overview as possible. Following a brief review of the basic principles associated with (113)Cd NMR methods, we will present the results from a thorough literature search for (113)Cd chemical shifts from metalloproteins. The updated (113)Cd chemical shift figure in this chapter will further illustrate the excellent correlation of the (113)Cd chemical shift with the nature of the coordinating ligands (N, O, S) and coordination number/geometry, reaffirming how this method can be used not only to identify the nature of the protein ligands in uncharacterized cases but also the dynamics at the metal binding site. Specific examples will be drawn from studies on alkaline phosphatase, Ca(2+) binding proteins, and metallothioneins.In the case of Escherichia coli alkaline phosphatase, a dimeric zinc metalloenzyme where a total of six metal ions (three per monomer) are involved directly or indirectly in providing the enzyme with maximal catalytic activity and structural stability, (113)Cd NMR, in conjunction with (13)C and (31)P NMR methods, were instrumental in separating out the function of each class of metal binding sites. Perhaps most importantly, these studies revealed the chemical basis for negative cooperativity that had been reported for this enzyme under metal deficient conditions. Also noteworthy was the fact that these NMR studies preceded the availability of the X-ray crystal structure.In the case of the calcium binding proteins, we will focus on two proteins: calbindin D(9k) and calmodulin. For calbindin D(9k) and its mutants, (113)Cd NMR has been useful both to follow actual changes in the metal binding sites and the cooperativity in the metal binding. Ligand binding to calmodulin has been studied extensively with (113)Cd NMR showing that the metal binding sites are not directly involved in the ligand binding. The (113)Cd chemical shifts are, however, exquisitely sensitive to minute changes in the metal ion environment.In the case of metallothionein, we will reflect upon how (113)Cd substitution and the establishment of specific Cd to Cys residue connectivity by proton-detected heteronuclear (1)H-(113)Cd multiple-quantum coherence methods (HMQC) was essential for the initial establishment of the 3D structure of metallothioneins, a protein family deficient in the regular secondary structural elements of α-helix and β-sheet and the first native protein identified with bound Cd. The (113)Cd NMR studies also enabled the characterization of the affinity of the individual sites for (113)Cd and, in competition experiments, for other divalent metal ions: Zn, Cu, and Hg.

Cadmium-113 magnetic resonance spectroscopy

Cadmium-113 nuclear magnetic resonance spectroscopy has been used in studies of the structure and dynamics of inorganic and bioinorganic molecules. Chemical dynamics play an important role in the analysis of relaxation and chemical shift data. Naïve interpretations of relaxation data can be checked by performing these experiments at a variety of temperatures and magnetic field strengths. A combination of solid- and liquid-state nuclear magnetic resonance measurements can provide the user with unambiguous data on chemical shielding. These data can be used to characterize zinc and calcium ion binding sites in metalloproteins.

Ca2+/Mg2+ exchange in parvalbumin and other EF-hand proteins. A theoretical study

A remarkable conformational rearrangement occurs upon Ca2+/Mg2+ exchange in the C-terminal EF-hand site (labelled site EF or EF-4) of parvalbumin, as initially established by X-ray crystallography. Such a conformational rearrangement is characterised as follows: (i) the co-ordination number decreases from seven oxygen atoms in the Ca-loaded form to six oxygen atoms in the Mg-loaded form, the heptaco-ordination of Ca2+ corresponding with a skewed pentagonal bipyramid configuration of the seven oxygen atoms, whereas the hexaco-ordination of Mg2+ corresponds with a regular octahedral configuration of the six oxygen atoms; and (ii) Glu101, at the relative position 12 in the EF-hand loop sequence (labelled "Glu12"), acts as a bidentate ligand in the Ca-loaded form and as a monodentate ligand in the Mg-loaded form. As part of the conformational rearrangement, the chi1 dihedral angle undergoes a gauche(+) to gauche(-) transition upon substitution of Ca2+ by Mg2+, whereas the chi2 angle remains practically unchanged and the chi3 angles in both forms adopt a nearly mirror image relationship. In order to understand the molecular mechanisms underlying such a conformational rearrangement, we undertook a theoretical study using the free energy perturbation (FEP) method, starting from high-resolution crystal structures of the same parvalbumin (pike 4. 10 isoform) differing by the substitution of their two cationic sites EF-3 (or CD) and EF-4 (or EF), i.e. the 1pal structure with EF-3(Ca2+) and EF-4(Ca2+), the 4pal structure with EF-3(Ca2+) and EF-4(Mg2+). When Mg2+ is "alchemically" transformed into Ca2+ within the EF-4 site of 4pal, the conformational rearrangement of Glu12 is correctly predicted by the FEP calculation. When Ca2+ is transformed into Mg2+ within the EF-3 site of 4pal, the FEP calculation predicts the topology of the fully Mg-loaded form for which no crystallographic data is presently available. As expected, Glu62 (at the relative position 12 in EF-3 loop) is predicted to be a monodentate residue within a regular octahedral arrangement of six oxygen atoms around Mg2+. We also investigated the behaviour during Ca2+/Mg2+ exchange of two other typical EF-hand proteins, troponin C (TnC) and calmodulin (CaM), for which no three-dimensional structure of their Mg-loaded forms is available so far. It is also predicted that the EF-3 site of TnC and the EF-1 site of CaM have their invariant Glu12 residues switching from the bidentate to the monodentate configuration when Ca2+ is substituted by Mg2+, with six oxygen atoms being observed in the co-ordination sphere of the alchemically generated Mg2+ cation.

Europium(III) ion luminescence as a structural probe of parvalbumin isotypes

The 7F0----5D0 transition of Eu3+ is used to investigate the metal ion binding sites of five parvalbumin isotypes. Comparisons are based on the resolution of the Eu3+ excitation spectrum with a computer program using the Marquardt nonlinear regression algorithm. The Lorentzian-Gaussian product function provides the most effective approximation to the shape of the peaks, the positions of which were found to be related to differences in the amino acid residues at the binding sites. Below pH 6, spectra consist of two peaks near 579 nm, but as the pH is raised, the two peaks gradually diminish and two new, much broader peaks appear at 577 and 578 nm. The lower wavelength peak, at low pH, and the peak at 577 nm, at high pH, are assigned to the CD site. The two sites have nearly equal affinities for Eu3+ except in the northern pike III (pI 5.0) isotype. The excitation spectra are compared to that of the carp III (pI = 4.25) parvalbumin for which the complete crystal structure is available. This structure forms the basis for the molecular modeling studies of the altered binding sites. Preliminary results are presented regarding differences in solvent exposure of the CD and EF sites based on collision-induced energy transfer to [Co(NH3)6]3+.

Multinuclear magnetic resonance studies on the calcium (II) binding site in trypsin, chymotrypsin, and subtilisin

Two different nuclear magnetic resonance experiments were conducted to elucidate the properties of the Ca(II) binding locus on serine proteases in solution. Trypsin, alpha-chymotrypsin, and subtilisin were inactivated with diisopropyl fluorophosphate, and the distance of the phosphorus from Gd(III) in place of Ca(II) was determined from the lanthanide-induced relaxation on the 31P resonance. The distances found (between 20 and 21 A) were in excellent agreement with those reported in the X-ray crystallographic structures of trypsin and subtilisin, demonstrating that the method has wide applicability to systems for which no X-ray structure is available. Subsequently, the 113Cd spectra [in place of Ca(II)] were examined in the presence of the native enzymes. At ambient temperatures only a single 113Cd resonance could be observed, presumably representing the weighted average of the variously weakly bound ions and the free ion. At 280 K for trypsin and chymotrypsin, and at 268 K for subtilisin there was observed a resonance at ca. 65-70 ppm higher field than the previous averaged resonance that could be attributed to tightly bound Cd. The chemical shift of the resonance was consistent with its assignment to an octahedral environment around Cd with oxygen ligands.

Accumulation of cadmium in pancreatic beta cells is similar to that of calcium in being stimulated by both glucose and high potassium

The transport of Cd2+ and the effects of this ion on secretory activity and metabolism were investigated in beta cell-rich pancreatic islets isolated from obese-hyperglycemic mice. The endogenous cadmium content was 2.5 mumol/kg dry wt. After 60 min of incubation in a Ca2+-deficient medium containing 2.5 microM Cd2+ the islet cadmium content increased to 0.18 mmol/kg dry wt. This uptake was reduced by approx. 50% in the presence of 1.28 mM Ca2+. The incorporation of Cd2+ was stimulated either by raising the concentration of glucose to 20 mM or K+ to 30.9 mM. Whereas D-600 suppressed the stimulatory effect of glucose by 75%, it completely abolished that obtained with high K+. Only about 40% of the incorporated cadmium was mobilized during 60 min of incubation in a Cd2+-free medium containing 0.5 mM EGTA. It was possible to demonstrate a glucose-induced suppression of Cd2+ efflux into a Ca2+-deficient medium. Concentrations of Cd2+ up to 2.5 microM did not affect glucose oxidation, whereas, there was a progressive inhibition when the Cd2+ concentration was above 10 microM. Basal insulin release was stimulated by 5 microM Cd2+. At a concentration of 160 microM, Cd2+ did not affect basal insulin release but significantly inhibited the secretory response to glucose. It is concluded that the beta cell uptake of Cd2+ is facilitated by the activation of voltage-dependent Ca2+ channels. Apparently, the accumulation of Cd2+ mimics that of Ca2+ also involving a component of intracellular sequestration promoted by glucose.

Thermodynamic analysis of calcium binding to frog parvalbumin

The enthalpy of calcium binding to frog parvalbumin (Rana temporaria isoenzyme IVb, pI 4.75) has been measured by microcalorimetry. The reaction is exothermic; the heat of the reaction in 100 mM KCl, 50mM Tris, pH 8.0 at 12 degrees C is -19 kJ (mol site)-1 and -33 kJ (mol site)-1 in the presence of 1 mM magnesium. The shape of the titration curve indicates that the properties of the two calcium binding sites are different. The thermodynamic parameters measured for frog parvalbumin are compared with those of related parvalbumins from carp and whiting.

13C and 113Cd NMR studies of the chelation of metal ions by the calcium binding protein parvalbumin

13C NMR spectra are presented for the calcium binding protein parvalbumin (pI 4.25) from carp muscle in several different metal bound forms: with Ca2+ in both the CD and EF calcium binding sites, with Cd2+ in both sites, with 113Cd2+ in both sites, and with 113Cd2+ in the CD site and Lu3+ in the EF site. The different metals differentially shift the 13C NMR resonances of the protein ligands involved in chelation of the metal ion. In addition, direct 13C-113Cd spin-spin coupling is observed which allows the assignment of protein carbonyl and carboxyl 13C NMR resonances to ligands directly interacting with the metal ions in the CD and EF binding sites. The displacement of 113Cd2+ from the EF site by Lu3+ further allows these resonances to be assigned to the CD or EF site. The occupancy of the two sites in the two cadmium species and in the mixed Cd2+/Lu3+ species is verified by 113Cd NMR. The resolution in these 113Cd NMR spectra is sufficient to demonstrate direct interaction between the two metal binding sites.

Metal-ion binding to parvalbumin. A 113Cd-n.m.r. study of the binding of different lanthanide ions

113Cd-n.m.r. studies were used to investigate the binding of the lanthanide ions La3+, Gd3+, Tb3+, Yb3+ and Lu3+ to parvalbumins. It was shown that lanthanide ions with a smaller ionic radius bind sequentially to Cd2+-saturated parvalbumin, whereas those with a larger ionic radius bind with similar affinity to both the CD site and the EF site. The smallest ion, Lu3+, does in fact not compete significantly with Cd2+ for the CD site in carp parvalbumin, but appears to bind only to the EF site. This preference of the smaller lanthanide ions for the EF site was used to assign the n.m.r. signals for protein-bound 113Cd. By using Cd n.m.r. and Tb3+ fluorescence it was also shown for alpha-lineage parvalbumin from pike that these proteins possess a third site that can bind lanthanide ions. This site is, however, much weaker than in the beta-lineage parvalbumins. It was used to assign the 113Cd resonances from protein-bound Cd2+ ions in the spectrum of pike pI5.0 parvalbumin.

Zinc and cadmium in 5-aminolevulinic acid dehydratase. Equilibrium, kinetic, and 113Cd-nmr-studies

5-Aminolevulinic acid dehydratase (ALAD) from bovine liver contains zinc that is partially lost during the isolation of the enzyme. ALAD has its maximal activity at 10(-5) M ZnCl2. It binds 7.4 Zn per octameric protein with an association constant of 5.3 X 10(6)M-1. ALAD is inactivated by 1,10-phenanthroline or ethylenediaminetetraacetic acid (EDTA) but not by monodentate anions like cyanide or sulfide. After removal of zinc by chelating agents, the enzyme activity may be restored by Zn2+ or Cd2+. Removal of zinc by EDTA increases KM 60-fold and decreases Vmax to about 1/2 of its original value. The 113Cd nuclear magnetic resonance spectrum of the enzyme reconstituted with 113Cd-acetate exhibits a single sharp resonance signal at 79 ppm. It does not change by the addition of substrate but disappears when the inhibitor lead acetate is added. Therefore, an immediate interaction between the metal ion of the enzyme and the substrate is excluded, whereas lead changes the environment of cadmium and probably of zinc too.

Use of lanthanide-induced nuclear magnetic resonance shifts for determination of protein structure in solution: EF calcium binding site of carp parvalbumin

The binding of the paramagnetic lanthanide ion ytterbium to the calcium binding protein carp parvalbumin results in a series of 1H NMR resonances which are shifted far outside the envelope of the 1H NMR spectrum of the diamagnetic form of the protein; bound Yb3+ also induces shifts in the 13C NMR spectrum of parvalbumin and in the 113Cd NMR spectrum of cadmium-substituted parvalbumin. The interpretation of these lanthanide-shifted resonances in terms of the structure of the protein surrounding the metal binding site requires the determination of the orientation and principal elements of the magnetic susceptibility tensor of the protein-bound Yb3+ ion. A previous comparison [Lee, L., & Sykes, B. D. (1982) Biomolecular Structure Determination by NMR (Bothner-By, A. A., Glickson, J. D., & Sykes, B. D., Eds.) pp 169-188, Marcel Dekker, New York] of the observed Yb3+-shifted 1H NMR spectrum of parvalbumin with a calculated spectrum, based upon the X-ray structure and an initial determination of the magnetic susceptibility tensor, led to the conclusion that there were significant differences between the solution and X-ray structures. In this paper, the magnetic susceptibility tensor has been reevaluated with the aid of newly assigned 13C and 113Cd NMR resonances. The agreement between the calculated and observed spectra is now close overall.

Calcium and cadmium binding to troponin C. Evidence for cooperativity

Proton NMR is used to compare the structural changes induced in bovine cardiac troponin C on binding of cadmium and calcium ions. The same spectral changes are observed for both ion species. The rate of the conformational changes associated with cadmium binding to the two high-affinity sites is slow, that associated with cadmium ions binding to the low-affinity site is high. 113Cd-NMR spectra of cardiac troponin C feature two signals interpreted as due to cadmium ions bound to the strong sites. Strong arguments are given in favour of cooperativity in binding of the first two cadmium or calcium ions to cardiac and skeletal muscle troponin C.

A 113Cd and 1H NMR study of the interaction of calmodulin with D600, trifluoperazine and some other hydrophobic drugs

The interaction of calmodulin with D600 (a methoxy derivative of verapamil), trifluoperazine and some other drugs was studied by 113Cd and 1H NMR. All four cation binding sites of calmodulin were found to be affected by the binding of the drugs to calmodulin. The physiologically active and inactive forms of felodipine were found to give qualitatively the same changes in the 113Cd NMR spectra of calmodulin. The interpretation of this observation in terms of the physiological relevance of the binding to calmodulin is discussed. The binding constants for the two strongly bound trifluoperazine molecules were found to differ by one or two orders of magnitude. A competition study showed that trifluoperazine replaces D600 from at least one binding site on calmodulin. Moreover the binding of D600 was found to be calcium dependent. The data indicate that two calcium ions bound to calmodulin are sufficient to render the binding site(s) accessible for D600.

Cadmium-113 nuclear magnetic resonance studies of proteolytic fragments of calmodulin: assignment of strong and weak cation binding sites

Proteolytic fragments of bovine testis calmodulin were obtained by limited proteolysis with trypsin or thrombin. Cadmium-113 NMR studies showed that the tryptic fragment encompassing Ca2+ binding domains III and IV (TR2C) gave rise to a spectrum identical with that of the native protein. Two thrombic fragments containing either domains I, II, and III [TM1-(1-106)] or the single domain IV [TM2-(107-148)] both gave rise to one broad resonance only. These data indicate that domains III and IV comprise the two high-affinity Ca2+ binding sites in intact calmodulin and that disturbance of the structural relationship between domain III and domain IV markedly reduces the affinity of these two sites for Ca2+ ions. These observations are discussed with respect to other published accounts concerning the sequence in which the four calcium domains in calmodulin are filled.

Cadmium-113 nuclear magnetic resonance studies of bovine insulin: two-zinc insulin hexamer specifically binds calcium

By use of cadmium-113 nuclear magnetic resonance spectroscopy, a specific calcium ion binding site has been identified in the bovine two-zinc insulin hexamer. This site is composed of six glutamyl carboxylate groups clustered in the center of the hexamer, and is distinct from the normal zinc ion binding sites.

Cadmium-113 nuclear magnetic resonance investigation of metal binding sites in concanavalin A

Cadmium-113 nuclear magnetic resonance studies are presented on the 113Cd-substituted protein concanavalin A (Con A). This protein has two different conformations, locked and unlocked, as described previously by Brown et al. [Brown, R. D., III, Brewer, C. F., & Koenig, S. H. (1977) Biochemistry 16, 3883]. The unlocked form of Con A gives one 113Cd resonance, indicating rapid exchange of the metal ions between the solution and the binding sites. Solutions of the locked form show three resonances: a free cadmium resonance (68 ppm), a resonance assigned to 113 Cd occupying the manganese site (46 ppm), and a resonance assigned to 113Cd occupying the calcium site (--125 ppm). In addition, Pb(II) is shown to bind to the calcium site and Zn(II) is shown to have high affinity for both sites. Data have been presented in previous literature that support a model in which Con A binds monosaccharides in a different manner than it binds oligosaccharides. However, if this difference exists, it does not affect the metal binding sites. Also, some heterogeneity in Con A has been reported in the literature; however, we have shown that the presence of these heterogeneities does not affect the 113 Cd NMR parameters.

A thermodynamic analysis of the binding of calcium and magnesium ions to parvalbumin

Microcalorimetry and equilibrium dialysis were used to determine the thermodynamic functions delta H0, delta G0 and delta S0 guiding the interaction of Ca2+ and Mg2+ with purified carp muscle isoparvalbumin of pI 4.25. The equilibrium dialysis studies indicate equal affinities of the two metal sites of parvalbumin for either Ca2+ or Mg2+ with equilibrium constants of KCa = 2.7 X 10(9) M-1, and KMg = 9.5 X 10(4) M-1. Binding of the two metal ions is fully competitive with no indication for cooperative effects. The apparent Ca2+ affinity constant K'Ca in the presence of 1 mM Mg2+ is 2.8 X 10(7) M-1, and the Mg2+-Ca2+ exchange equilibrium constant equals 2.8 X 10(4) M-1. Microcalorimetry shows that parvalbumin exhibits negative reaction enthalpies of -37.2 kJ/mol metal site for Ca2+ binding and -25.1 kJ/mol site for Mg2+-Ca2+ exchange, yielding delta H0 = -12.1 kJ/mol site for Mg2+ complex formation. Enthalpy changes are linearly dependent upon the amount of metal bound to the protein, thus corroborating the equal affinities of the two sites. Reaction entropies delta S0 are +55.2 J x mol-1 x K-1 for Ca2+ complex formation and +54.8 x mol-1 x K-1 for Mg2+ complex formation. Thus the respective metal binding processes are driven by both enthalpy and entropy conbinations, and are reminiscent of Ca2+ binding to troponin C. The reaction entropy observed during Mg2+-Ca2+ exchange (0.4 J x mol-1 x k-1) is negligible in spite of the markedly different hydration entropies for Ca2+ and Mg2+. This indicates that the two metal complexes of parvalbumin do not have the same conformation entropy. Since no variation in the intrinsic protein fluorescence was observed upon metal exchange, the conformation differences must be restricted to the immediate environment of the metal binding sites.

Cadmium-113 nuclear magnetic resonance studies of cadmium-substituted derivatives of bovine superoxide dismutase

We have prepared the following cadmium-113-substituted derivatives of bovine superoxide dismutase and recorded the nuclear magnetic resonance (NMR) spectrum of the cadmium: 2Cd(II), in which Cd(II) is presumed to bind to the Zn(II) site and the copper site is unoccupied, and 2Cd(II)--2Cu(I), which is analogous to the reduced form of the native protein. NMR transitions were observed at 310 ppm downfield from Cd(ClO4)2 for 2Cd(II) and at 320 ppm for the 2Cd(II)--2Cu(I)-containing proteins. In each case the observed line width was 27 +/- 2 Hz. The following conclusions were drawn. (a) The very small chemical-shift difference between the two derivatives indicates that the Cd(II) binding site is very similar in both samples. It follows from this result and previous work that the imidazolato bridge is protonated on the Cu side upon reduction of the Cu ion from the II to I valence state. (b) The extremely narrow line width of the resonance in both forms suggests a virtual identity of Cd(II) bound to both subunits of the molecule. (c) The relaxation time, T1 = 1.2 s, is caused by approximately equal contributions from chemical-shift anisotropy and dipolar interactions with nearby protons.

The interaction of cadmium and certain other metal ions with proteins and nucleic acids

The toxic effects of cadmium and other selected divalent cations are presumed to be related to specific chemical and physical characteristics of the ion. The chemistry of cadmium and metal ions in general is reviewed from the viewpoint of such relevant properties as ion polarizability, electronic structure, and the hard-soft characteristics. The softness of metal ions is seen as a useful single parameter to correlate with the affinity for nucleic acids and proteins and with toxic effects. The effects of cadmium on nucleic acids and proteins are examined for a number of specific cases to illustrate the variety of interactions that are well recognized and to demonstrate the utility of soft metal ions as reagents and probes for examining the relationship of structure and function in these macromolecules.

NMR studies of primary and secondary sites of parvalbumins using the two paramagnetic probes Gd (III) and Mn (II)

The binding of cations by parvalbumins was studied by the proton relaxation enhancement (PRE) method using the paramagnetic probes Gd(III) and Mn(II). Gd(III) appears as a specific probe of the primary sites CD and EF with the following binding parameters: n = 2, KdGd = 0.5 x 10(-11) M and epsilon b = 2.3. The low value of epsilon b is the result of a nearly complete dehydration of the protein bound ions. Competition experiments between Gd(III) and various diamagnetic cations show the following order of affinity for the EF and CD sites: Mg2+ less than Zn2+ less than Sr2+ less than Ca2+ less than Cd2+ less than La3+ less than or equal to Gd3+. Mn 2+ is a specific probe of a secondary site with the following binding parameters: n = 1, KdMn = 0.6 x 10(-3) M and epsilon b = 17. The high value of epsilon b suggests that the protein bound Mn(II) has retained most of its hydration shell. Competition experiments between (Mn(II) and different cations show similar affinities for this site: Ca2+ less than or equal to Mg2+ less than or equal to Cd2+ less than or equal to Mn2+. This secondary site is located near the EF primary site.

Calcium, magnesium and the conformation of parvalbumin during muscular activity

The conformation of perch parvalbumin in the Ca-, Mg- and metal-free state was studied by intrinsic fluorescence, trypsin susceptibility, thiol titration and circular dichroism. The data reveal that Ca-parvalbumin has a more compact structure than the metal-free protein, with a high alpha-helical content and a buried thiol. No difference in conformation could be detected between Mg- and Ca-parvalvumin, indicating that the Ca-Mg exchange that may take place during muscular activity is accompanied by little or no structural changes. Furthermore, recently published kinetic parameters can now be interpreted as meaning that, during the contraction-relaxation cycle, parvalbumin often stays in the Mg-form instead of switching to the Ca-form which is predominant in vitro.