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

113 Cd as a Probe in NMR Studies of Allosteric Host‐Guest‐Ligand Complexes of Porphyrin Cage Compounds

Cadmium porphyrin cage compounds Cd1 and ¹¹³Cd1 have been synthesized from the free base porphyrin cage derivative H₂1 and Cd(OAc)₂ ⋅ 2 H₂O or ¹¹³Cd(OAc)₂ ⋅ 2 H₂O, respectively. The compounds form allosteric complexes with the positively charged guests N,N′‐dimethylimidazolium hexafluorophosphate (DMI) and N,N′‐dimethylviologen dihexafluorophosphate (Me₂V), which bind in the cavity of the cage, and tbupy, which coordinates as an axial ligand to the outside of the cage. In the presence of tbupy, the binding of DMI in Cd1 is enhanced by a factor of ∼31, while the presence of DMI or Me₂V in the cavity of Cd1 enhances the binding of tbupy by factors of 55 and 85, respectively. The X‐ray structures of the coordination complexes of Cd1 with acetone, acetonitrile, and pyridine, the host‐guest complex of Cd1 with a bound viologen guest, and the ternary allosteric complex of Cd1 with a bound DMI guest and a coordinated tbupy ligand, were solved. These structures revealed relocations of the cadmium center in and out of the porphyrin plane, depending on whether a guest or a ligand is present. ¹¹³Cd NMR could be employed as a tool to quantify the binding of guests and ligands to ¹¹³Cd1. 1D EXSY experiments on the ternary allosteric system Cd1‐tbupy‐Me₂V revealed that the coordination of tbupy significantly slowed down the dissociation of the Me₂V guest. Eyring plots of the dissociation process revealed that this kinetic allosteric effect is entropic in nature.

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.

Crystal structure of native and Cd/Cd-substituted Dioclea guianensis seed lectin. A novel manganese-binding site and structural basis of dimer-tetramer association

Diocleinae legume lectins are a group of oligomeric proteins whose subunits display a high degree of primary structure and tertiary fold conservation but exhibit considerable diversity in their oligomerisation modes. To elucidate the structural determinants underlaying Diocleinae lectin oligomerisation, we have determined the crystal structures of native and cadmium-substituted Dioclea guianensis (Dguia) seed lectin. These structures have been solved by molecular replacement using concanavalin (ConA) coordinates as the starting model, and refined against data to 2.0 A resolution. In the native (Mn/Ca-Dguia) crystal form (P4(3)2(1)2), the asymmetric unit contains two monomers arranged into a canonical legume lectin dimer, and the tetramer is formed with a symmetry-related dimer. In the Cd/Cd-substituted form (I4(1)22), the asymmetric unit is occupied by a monomer. In both crystal forms, the tetrameric association is achieved by the corresponding symmetry operators. Like other legume lectins, native D. guianensis lectin contains manganese and calcium ions bound in the vicinity of the saccharide-combining site. The architecture of these metal-binding sites (S1 and S2) changed only slightly in the cadmium/cadmium-substituted form. A highly ordered calcium (native lectin) or cadmium (Cd/Cd-substituted lectin) ion is coordinated at the interface between dimers that are not tetrameric partners in a similar manner as the previously identified Cd(2+) in site S3 of a Cd/Ca-ConA. An additional Mn(2+) coordination site (called S5), whose presence has not been reported in crystal structures of any other homologous lectin, is present in both, the Mn/Ca and the Cd/Cd-substituted D. guianensis lectin forms. On the other hand, comparison of the primary and quaternary crystal structures of seed lectins from D. guianensis and Dioclea grandiflora (1DGL) indicates that the loop comprising residues 117-123 is ordered to make interdimer contacts in the D. grandiflora lectin structure, while this loop is disordered in the D. guianensis lectin structure. A single amino acid difference at position 131 (histidine in D. grandiflora and asparagine in D. guianensis) drastically reduces interdimer contacts, accounting for the disordered loop. Further, this amino acid change yields a conformation that may explain why a pH-dependent dimer-tetramer equilibrium exists for the D. guianensis lectin but not for the D. grandiflora lectin.

Sequential structural changes upon zinc and calcium binding to metal-free concanavalin A

The lectin concanavalin A (ConA) sequentially binds a transition metal ion in the metal-binding site S1 and a calcium ion in the metal-binding site S2 to form its saccharide-binding site. Metal-free ConA crystals soaked with either Zn2+ (apoZn-ConA) or Co2+ (apoCo-ConA) display partial binding of these ions in the proto-transition metal-binding site, but no further conformational changes are observed. These structures can represent the very first step in going from metal-free ConA toward the holoprotein. In the co-crystals of metal-free ConA with Zn2+ (Zn-ConA), the zinc ion can fully occupy the S1 site. The positions of the carboxylate ligands Asp10 and Asp19 that bridge the S1 and S2 sites are affected. The ligation to Zn2+ orients Asp10 optimally for calcium ligation and stabilizes Asp19 by a hydrogen bond to one of its water ligands. The neutralizing and stabilizing effect of the binding of Zn2+ in S1 is necessary to allow for subsequent Ca2+ binding in the S2 site. However, the S2 site of monometallized ConA is still disrupted. The co-crystals of metal-free ConA with both Zn2+ and Ca2+ contain the active holoprotein (ConA ZnCa). Ca2+ has induced large conformational changes to stabilize its hepta-coordination in the S2 site, which comprise the trans to cis isomerization of the Ala207-Asp208 peptide bond accompanied by the formation of the saccharide-binding site. The Zn2+ ligation in ConA ZnCa is similar to Mn2+, Cd2+, Co2+, or Ni2+ ligation in the S1 site, in disagreement with earlier extended x-ray absorption fine structure results that suggested a lower coordination number for Zn2+.

Crystallographic structure of metal-free concanavalin A at 2.5 A resolution

The three-dimensional structure of demetallized concanavalin A has been determined at 2.5 A resolution and refined to a crystallographic R-factor of 18%. The lectin activity of concanavalin A requires the binding of both a transition metal ion, generally Mn2+, and a Ca2+ ion in two neighboring sites in close proximity to the carbohydrate binding site. Large structural differences between the native and the metal-free lectin are observed in the metal-binding region and consequently for the residues involved in the specific binding of saccharides. The demetallization invokes a series of conformational changes in the protein backbone, apparently initiated mainly by the loss of the calcium ion. Most of the Mn2+ ligands retain their position, but the Ca2+ binding site is destroyed. The Ala207-Asp208 peptide bond, in the beta-strand neighboring the metal-binding sites, undergoes a cis to trans isomerization. The cis conformation for this bond is a highly conserved feature among the leguminous lectins and is critically maintained by the Ca2+ ion in metal-bound concanavalin A. A further and major change adjacent to the isomerized bond is an expansion of the loop containing the monosaccharide ligand residues Leu99 and Tyr100. The dispersion of the ligand residues for the monosaccharide binding site (Asn14, Agr228, Asp208, Leu99, and Tyr100) in metal-free concanavalin A abolishes the lectin's ability to bind saccharides. Since the quaternary structure of legume lectins is essential to their biological role, the tetramer formation was analyzed. In the crystal (pH 5), the metal-free concanavalin A dimers associate into a tetramer that is similar to the native one, but with a drastically reduced number of inter-dimer interactions. This explains the tetramer dissociation into dimers below pH values of 6.5.

Binding of lanthanum and gadolinium ions to concanavalin A studied calorimetrically at 25 degrees C

The interaction between Concanavalin A (ConA) and the lanthanide ions La3+ and Gd3+ has been studied calorimetrically at 25 degrees C. The measurements were carried out at a pH of 4.5, where the protein exists prevailingly as a dimer. Calorimetry allows the direct determination of the binding enthalpy and the evaluation of both the apparent association constant, and the apparent free energy and entropy. Three groups of data were collected. The first concerns the interaction of the 'native' protein, i.e., fully metallized with Mn2+ and Ca2+, with the lanthanides. The second concerns the interaction of the completely demetallized protein with La3+ and Gd3+. Finally, the affinity of each complex was tested for the specific sugar alpha-methylmannopyranoside. The analysis of the thermodynamic parameters obtained, led to the following conclusions: 1) a specific site, named S3, exists on the protein for the lanthanides, distinct from the S1 site of the transition metal and from the S2 site, specific for calcium. There is only one S3 site per protomer when the protein has Mn2+ in S1 and Ca2+ in S2. Moreover, there is no appreciable competition for S1 and S2 from the lanthanides. The 'native' protein, metallized with La3+ or Gd3+, is a fully functional protein. 2) The demetallized protein (ApoCon A) has at least two sites per protomer for the lanthanides. The hypothesis is that, besides the S3 site, the lanthanides, in the absence of Mn2+, can also occupy the S1, but not the S2, site. The protein metallized only with gadolinium ion is completely inactive toward the interaction with the mannoside. The same happens when, along with gadolinium, only calcium or manganese is present. Hence, in the absence of the transition metal in S1 or of calcium in S2, the protein is not in the conformation suitable to interact with its specific substrate.

Divalent cation binding to the high- and low-affinity sites on G-actin

Metal binding to skeletal muscle G-actin has been assessed by equilibrium dialysis using 45Ca2+ and by kinetic measurements of the increase in the fluorescence of N-acetyl-N'-(5-sulfo-1-naphthyl)-ethylenediamine-labeled actin. Two classes of cation binding sites were found on G-actin which could be separated on the basis of their Ca2+ affinity: a single high-affinity site with a Kd considerably less than 1 microM and three identical moderate-affinity binding sites with a Kd of 18 microM. The data for the Mg2+-induced fluorescence enhancement of actin labeled with N-acetyl-N'-(5-sulfo-1-naphthyl)ethylenediamine support a previously suggested mechanism [Frieden, C. (1982) J. Biol. Chem. 257, 2882-2886] in which Ca2+ is replaced by Mg2+ at the moderate affinity site(s), followed by a slow actin isomerization. This isomerization occurs independently of Ca2+ release from the high-affinity site. The fluorescence data do not support a mechanism in which this isomerization is directly related to Ca2+ release from the high-affinity site. Fluorescence changes of labeled actin associated with adding metal chelators are complex and do not reflect the same change induced by Mg2+ addition. Fluorescence changes in the labeled actin have also been observed for the addition of Cd2+ or Mn2+ instead of Mg2+. It is proposed actin may undergo a host of subtle conformational changes dependent on the divalent cation bound. We have also developed a method by which progress curves of a given reaction can be analyzed by nonlinear regression fitting of kinetic simulations to experimental reaction time courses.(ABSTRACT TRUNCATED AT 250 WORDS)

NMR studies of ion binding in biological systems

Biological systems must have evolved in an interplay between a great many organic and inorganic compounds. As a result a considerable number of elements - estimates range between 25 and 30 - are essential for higher life forms such as animals and man (Underwood, 1977; Williams, 1983, 1984).

Yeast inorganic pyrophosphatase. A model for active-site structure based on 113Cd2+ and 31P NMR studies

Equilibrium dialysis and 113Cd2+ NMR studies in the presence of inorganic phosphate (Pi) provide clear evidence for the existence of four well-defined Cd2+ sites per yeast inorganic pyrophosphatase subunit. Parallel 31P NMR studies demonstrate the existence of two binding sites per subunit for Pi and provide strong confirmatory evidence for a small amount of enzyme-bound inorganic pyrophosphate in equilibrium with enzyme-bound Pi. Such inorganic pyrophosphate formation was demonstrated by chemical analysis earlier [Welsh, K.M., Armitage, I.M., & Cooperman, B.S. (1983) Biochemistry 22, 1046-1054]. In this same earlier paper, we provided evidence for inner-sphere contact between enzyme-bound Cd2+ and Pi bound in the higher affinity of the two Pi sites. We now present heteronuclear decoupling evidence that one to three different Cd2+ ions make such contact. The divalent metal ion cofactor conferring the highest activity on inorganic pyrophosphatase is Mg2+, and we present evidence from competition experiments that such inner-sphere contact is also likely for the Mg2+-enzyme. On the other hand, these experiments also show that some metal ion binding sites on the enzyme bind Mg2+ and not Cd2+, and some bind Cd2+ and not Mg2+. These results are considered along with others obtained recently in proposing an active-site structure for inorganic pyrophosphatase.

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.

Metal ion binding and conformational transitions in concanavalin A: a structure-function study

The affinity of the lectin Concanavalin A (Con A) for saccharides, and its requirement for metal ions such as Mn2+ and Ca2+, have been known for about 50 years. However the relationship between metal ion binding and the saccharide binding activity of Con A has only recently been examined in detail. Brown et al. (Biochemistry 16, 3883 (1977)) showed that Con A exists as a mixture of two conformational states: a "locked" form and an "unlocked" form. The unlocked form of the protein weakly binds metal ions and saccharide, and is the predominate conformation of demetallized Con A (apo-Con A) at equilibrium. The locked form binds two metal ions per monomer with the resulting complex(es) possessing full saccharide binding activity. Brown and coworkers measured the kinetics of the transition of the unlocked form to the fully metallized locked conformation containing Mn2+ and Ca2+. They also demonstrated that Mn2+ alone could form a locked ternary complex with Con A, and that rapid removal of the ions resulted in a metastable form of apo-Con A in the locked conformation which slowly (hours at 25 degrees C) reverted back to (predominantly) the unlocked conformation. The ability to form either conformation in the absence or presence of metal ions has thus allowed us to explore the relationship between metal ion binding and conformational transitions in Con A as determinants of the saccharide binding activity of the lectin. Based on the kinetics of the transition of unlocked apo-Con A to fully metallized locked Con A, and X-ray crystallographic data, it appears that the transition between the two conformations of Con A involves a cis-trans isomerization of an Ala-Asp peptide bond in the backbone of the protein, near one of the two metal ion binding sites. The relatively large activation energy for the transition (approximately 22 kcal M-1) results in relatively slow interconversions between the conformations (from minutes to days), whereas the equilibria with metal ions and saccharide are rapid. Thus, many metastable complexes can be formed and a variety of transition pathways between the two conformations studied. We have identified and characterized binary, ternary, and quaternary complexes of both conformations of Con A containing Mn2+ and saccharide, and have determined both metal ion and saccharide dissociation constants for all of them, as well as equilibrium and kinetic values for the conformational transitions between them.(ABSTRACT TRUNCATED AT 400 WORDS)

Kinetics of conformational transitions of demetalized Concanavalin A

Demetalized Concanavalin A exists in two conformational states, known as locked (PL) and unlocked (P) [Brown et al., Biochemistry 16, 3883 (1977)]. The equilibrium ratio [PL]/[P] is 0.14 +/- 0.01 at 25 degrees C, pH 6.4 [Brown et al., Biochemistry 21, 465 (1982)]. We now report values of the rate constants for the P in equilibrium; k1 = (33 +/- 4 h)-1 and k-1 = (4.6 +/- 0.6 h)-1 for the P leads to PL and PL leads to P transitions, respectively, at 25 degrees C, pH 6.4. The experiments utilize the fact that saccharide binds to PL [Koenig et al., Biochemistry 17, 4251 (1978)], producing a time-dependent increase in the total concentration of locked forms at equilibrium, and use a new technique for measuring this concentration.

Kinetic studies of the demetallization and inactivation of concanavalin A

The demetallization of various metallo derivatives of Concanavalin A (i.e., MnMnPL, CoMnPL, CaCaPL, CoCaPL and MnCaPL, where PL represents protein in a locked conformation) has been examined by three separate procedures. These include the treatment of the protein with the metal ion chelators, EDTA and terpyridine, and subjecting the protein to low pH (i.e., pH 1.2). In all three procedure and for all five species examined, the immediate product of protein demetallization was the PL conformation previously described by Brown, R.D., III, Brewer, C.F. and Koenig, S.H. (Biochemistry (1977) 16, 3883-3896). The rates of dissociation of the metals from the different protein species, as measured spectrophotometrically using terpyridine, were found to be identical to the rates (k1) of loss of protein sugar binding affinity in the presence of EDTA as measured by assays with the fluorescent sugar, 4-methylumbelliferyl alpha-D-mannoside. The kinetic and thermodynamic data associated with the inactivation of the protein species have allowed the different metallo derivatives to be classed into two general categories. Class I forms include MnMnPL, CoMnPL and CaCaPL and possess an average k1 (25 degrees C) value of 3.88 X 10(-2) s-1 and an average Ea of 14.2 kcal X mol-1. Class II forms CoCaPL and MnCaPL have average values for k1 (25 degrees C) and Ea of 3.67 X 10(-5) s-1 and 21.6 kcal X mol-1, respectively.

Conformational equilibrium of demetalized concanavalin A

Concanavalin A (Con A) is known to exist in two conformations [Brown, R. D., III, Brewer, C. F., & Koenig, S. H. (1977) Biochemistry 16, 3883-3896] that differ in their metal ion and saccharide binding properties. The conformation that binds metal ions tightly, and which is associated with saccharide binding, has been designated as "locked" and that which binds metal ions only weakly as "unlocked". In the presence of excess metal ions, such as Mn2+ and Ca2+, essentially 100% of the protein is in the locked conformation. The scheme proposed to explain these effects [Koenig, S. H., Brewer, C. F., & Brown, R. D., III (1978) Biochemistry 17, 4251-4260] predicts an equilibrium between these conformations for the apoprotein. By monitoring the solvent proton relaxation dispersion as equimolar concentrations of Mn2+ and Ca2+ are titrated, at 5 degrees C, into an apo-Con A solution that had been equilibrated at 25 degrees C, we find that 12.5% of the apoprotein is in the locked conformation, corresponding to an energy separation of 1.2 kcal mol-1. We also show that these conformations can be separated by column chromatography at 5 degrees C and that the 100% unlocked form prepared in this way returns to the expected equilibrium mixture when kept at 25 degrees C.