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

Flexibility of Binding Site is Essential to the Ca2+ Selectivity in EF-Hand Calcium-Binding Proteins

High binding affinity and selectivity of metal ions are essential to the function of metalloproteins. Thus, understanding the factors that determine these binding characteristics is of major interest for both fundamental mechanistic investigations and guiding of the design of novel metalloproteins. In this work, we perform QM cluster model calculations and quantum mechanics/molecular mechanics (QM/MM) free energy simulations to understand the binding selectivity of Ca2+ and Mg2+ in the wild-type carp parvalbumin and its mutant. While a nonpolarizable MM model (CHARMM36) does not lead to the correct experimental trend, treatment of the metal binding site with the DFTB3 model in a QM/MM framework leads to relative binding free energies (ΔΔGbind) comparable with experimental data. For the wild-type (WT) protein, the calculated ΔΔGbind is ∼6.6 kcal/mol in comparison with the experimental value of 5.6 kcal/mol. The good agreement highlights the value of a QM description of the metal binding site and supports the role of electronic polarization and charge transfer to metal binding selectivity. For the D51A/E101D/F102W mutant, different binding site models lead to considerable variations in computed binding affinities. With a coordination number of seven for Ca2+, which is shown by QM/MM metadynamics simulations to be the dominant coordination number for the mutant, the calculated relative binding affinity is ∼4.8 kcal/mol, in fair agreement with the experimental value of 1.6 kcal/mol. The WT protein is observed to feature a flexible binding site that accommodates a range of coordination numbers for Ca2+, which is essential to the high binding selectivity for Ca2+ over Mg2+. In the mutant, the E101D mutation reduces the flexibility of the binding site and limits the dominant coordination number of Ca2+ to be seven, thereby leading to reduced binding selectivity against Mg2+. Our results highlight that the binding selectivity of metal ions depends on both the structural and dynamical properties of the protein binding site.

Historical Perspective: Heat production and chemical change in muscle. Roger C. Woledge

The objective of this article is to provide an historical perspective on a review of "Heat production and chemical change in muscle" written by Roger C. Woledge and published in Progress in Biophysics and Molecular Biology 50 years ago. We first provide a brief but broad summary of the history of muscle chemistry prior to 1971 and then address the central theme of the 1971 review - that of energy balance. Energy balance is a method to establish whether all the energetically significant biochemical reactions accompanying muscle contraction have been identified. Woledge adopted the method to compare the measured enthalpy output (i.e., the sum of the heat output and work output) to that expected from the extent of known biochemical reactions. Prior work had suggested that the observed and expected enthalpy outputs were similar but Woledge proposed that the expected heat had been overestimated and that, hence, there must be an unidentified reaction that accounted for as much as half the heat produced by a contracting muscle. We describe investigations carried out after the review that vindicated that view, ultimately characterising the processes producing the unexplained enthalpy which, in turn, led to identification of the hitherto unknown reaction. Those experiments and a more recent resurrection of the approach using fluorescent probes to monitor ATP turnover have now accounted for the processes that underlie the complex time courses of muscle heat production and ATP turnover during contraction, at least in the classical frog sartorius muscle preparation. However, the few studies performed on mammalian muscles since then have produced results that are difficult to reconcile with the ideas derived from energy balance studies of amphibian and fish muscles, thereby suggesting a new objective for energy balance studies.

Beyond Chelation: EDTA Tightly Binds Taq DNA Polymerase, MutT and dUTPase and Directly Inhibits dNTPase Activity

EDTA is commonly used as an efficient chelator of metal ion enzyme cofactors. It is highly soluble, optically inactive and does not interfere with most chemicals used in standard buffers making EDTA a common choice to generate metal-free conditions for biochemical and biophysical investigations. However, the controversy in the literature on metal-free enzyme activities achieved using EDTA or by other means called our attention to a putative effect of EDTA beyond chelation. Here, we show that EDTA competes for the nucleotide binding site of the nucleotide hydrolase dUTPase by developing an interaction network within the active site similar to that of the substrate. To achieve these findings, we applied kinetics and molecular docking techniques using two different dUTPases. Furthermore, we directly measured the binding of EDTA to dUTPases and to two other dNTPases, the Taq polymerase and MutT using isothermal titration calorimetry. EDTA binding proved to be exothermic and mainly enthalpy driven with a submicromolar dissociation constant considerably lower than that of the enzyme:substrate or the Mg:EDTA complexes. Control proteins, including an ATPase, did not interact with EDTA. Our findings indicate that EDTA may act as a selective inhibitor against dNTP hydrolyzing enzymes and urge the rethinking of the utilization of EDTA in enzymatic experiments.

Components of activation heat in skeletal muscle

Activation heat (q_A) production by muscle is the thermal accompaniment of the release of Ca²⁺ from the sarcoplasmic reticulum (SR) into the cytoplasm, its interactions with regulatory proteins and other cytoplasmic Ca²⁺ buffers and its return to the SR. The contribution of different Ca²⁺-related reactions to q_A is difficult to determine empirically and therefore, for this study, a mathematical model was developed to describe Ca²⁺ movements and accompanying thermal changes in muscle fibres in response to stimulation. The major sources of heat within a few milliseconds of the initiation of Ca²⁺ release are Ca²⁺ binding to Tn and Pv. Ca²⁺ binding to ATP produces a relatively small amount of heat. Ca²⁺ dissociation from ATP and Tn, with heat absorption, are of similar time course to the decline of force. In muscle lacking Pv (e.g. mouse soleus), Ca²⁺ is then rapidly pumped into the SR. In muscles with Pv, Ca²⁺ that dissociates from Tn and ATP binds to Pv and then dissociates slowly (over 10 s of seconds) and is then pumped into the SR; the net effect of these two processes is heat absorption. It is proposed that this underlies Hill's "negative delayed heat". After all the Ca²⁺ is returned to the SR, q_A is proportional to the amount of Ca²⁺ released into the cytoplasm. In muscles with Pv this is 20-60 s after Ca²⁺ release; in muscles without Pv, all Ca²⁺ is returned to the SR soon after the end of force relaxation.

How an electric field can modulate the metal ion selectivity of protein binding sites: insights from DFT/PCM calculations

An electric field (internal or external) is a potent force that can modulate the metal selectivity of a protein binding site.

Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity

The diversity of functions carried out by EF hand-containing calcium-binding proteins is due to various interactions made by these proteins as well as the range of affinity levels for Ca²⁺ displayed by them. However, accurate methods are not available for prediction of binding affinities. Here, amino acid patterns of canonical EF hand sequences obtained from available crystal structures were used to develop a classifier that distinguishes Ca²⁺-binding loops and non Ca²⁺-binding regions with 100% accuracy. To investigate further, we performed a proteome-wide prediction for E. histolytica, and classified known EF-hand proteins. We compared our results with published methods on the E. histolytica proteome scan, and demonstrated our method to be more specific and accurate for predicting potential canonical Ca²⁺-binding loops. Furthermore, we annotated canonical EF-hand motifs and classified them based on their Ca²⁺-binding affinities using support vector machines. Using a novel method generated from position-specific scoring metrics and then tested against three different experimentally derived EF-hand-motif datasets, predictions of Ca²⁺-binding affinities were between 87 and 90% accurate. Our results show that the tool described here is capable of predicting Ca²⁺-binding affinity constants of EF-hand proteins. The web server is freely available at http://202.41.10.46/calb/index.html.

Divers models of divalent cation interaction to calcium-binding proteins: techniques and anthology

Intracellular Ca(2+)-binding proteins (CaBPs) are sensors of the calcium signal and several of them even shape the signal. Most of them are equipped with at least two EF-hand motifs designed to bind Ca(2+). Their affinities are very variable, can display cooperative effects, and can be modulated by physiological Mg(2+) concentrations. These binding phenomena are monitored by four major techniques: equilibrium dialysis, fluorimetry with fluorescent Ca(2+) indicators, flow dialysis, and isothermal titration calorimetry. In the last quarter of the twentieth century reports on the ion-binding characteristics of several abundant wild-type CaBPs were published. With the advent of recombinant CaBPs it became possible to determine these properties on previously inaccessible proteins. Here I report on studies by our group carried out in the last decade on eight families of recombinant CaBPs, their mutants, or truncated domains. Moreover this chapter deals with the currently used methods for quantifying the binding of Ca(2+) and Mg(2+) to CaBPs.

Target binding to S100B reduces dynamic properties and increases Ca(2+)-binding affinity for wild type and EF-hand mutant proteins

Mutations in the second EF-hand (D61N, D63N, D65N, and E72A) of S100B were used to study its Ca(2+) binding and dynamic properties in the absence and presence of a bound target, TRTK-12. With (D63N)S100B as an exception ((D63N)K(D)=50±9 μM), Ca(2+) binding to EF2-hand mutants were reduced by more than 8-fold in the absence of TRTK-12 ((D61N)K(D)=412±67 μM, (D65N)K(D)=968±171 μM, and (E72A)K(D)=471±133 μM), when compared to wild-type protein ((WT)K(D)=56±9 μM). For the TRTK-12 complexes, the Ca(2+)-binding affinity to wild type ((WT+TRTK)K(D)=12±10 μM) and the EF2 mutants was increased by 5- to 14-fold versus in the absence of target ((D61N+TRTK)K(D)=29±1.2 μM, (D63N+TRTK)K(D)=10±2.2 μM, (D65N+TRTK)K(D)=73±4.4 μM, and (E72A+TRTK)K(D)=18±3.7 μM). In addition, R(ex), as measured using relaxation dispersion for side-chain (15)N resonances of Asn63 ((D63N)S100B), was reduced upon TRTK-12 binding when measured by NMR. Likewise, backbone motions on multiple timescales (picoseconds to milliseconds) throughout wild type, (D61N)S100B, (D63N)S100B, and (D65N)S100B were lowered upon binding TRTK-12. However, the X-ray structures of Ca(2+)-bound (2.0Å) and TRTK-bound (1.2Å) (D63N)S100B showed no change in Ca(2+) coordination; thus, these and analogous structural data for the wild-type protein could not be used to explain how target binding increased Ca(2+)-binding affinity in solution. Therefore, a model for how S100B-TRTK-12 complex formation increases Ca(2+) binding is discussed, which considers changes in protein dynamics upon binding the target TRTK-12.

Metal-specific structural changes in parvalbumin

Parvalbumin is a small protein of EF-hand family whose main role is considered to be metal buffering. Recent evidences indicate that parvalbumin also fulfills more complicated functions, which may be determined by the diversity in structural changes in response to the binding of different metal cations. In the present work the conformations of α and β isoforms of pike parvalbumin in the Ca(2+)- and Mg(2+)-loaded state were studied by intrinsic fluorescence, circular dichroism and bis-ANS extrinsic fluorescence. We have determined the structural region causing different spectral response on the binding of Mg(2+)- and Ca(2+) ions in pike β-parvalbumin. Our data reveal similarity of the metal-bound forms of α-parvalbumin. In contrast, those of β isoform differ significantly in the tyrosine spectral range. We also discuss the possible physiological consequences of the structural rearrangements accompanied Mg(2+)/Ca(2+) exchange in pike β-parvalbumin.

Regional variation in parvalbumin isoform expression correlates with muscle performance in common carp (Cyprinus carpio)

The mechanical properties of the axial muscles vary along the length of a fish's body. This variation in performance correlates with the expression of certain muscle proteins. Parvalbumin (PARV) is an important calcium binding protein that helps modulate intracellular calcium levels which set the size and shape of the muscle calcium transient. It therefore has a central role in determining the functional properties of the muscle. Transcript data revealed eight specific isoforms of PARV in common carp (Cyprinus carpio) skeletal muscle which we classified as alpha1 and beta1-7. This study is the first to show expression of all eight skeletal muscle PARV isoforms in carp at the protein level and relate regional differences in expression to performance. All of the PARV isoforms were characterised at the protein level using 2D-PAGE and tandem mass spectrometry. Comparison of carp muscle from different regions of the fish revealed a higher level of expression of PARV isoforms beta4 and beta5 in the anterior region, which was accompanied by an increase in the rate of relaxation. We postulate that changes in specific PARV isoform expression are an important part of the adaptive change in muscle mechanical properties in response to varying functional demands and environmental change.

Parvalbumin isoforms for enhancing cardiac diastolic function

Diastolic heart failure (DHF), characterized by depressed myocardial relaxation performance and poor ventricular filling, is a distinct form of heart failure accounting for nearly half of the heart failure patients with otherwise normal systolic performance. Defective intracellular calcium (Ca2+) cycling is an important mechanism underlying impaired relaxation in DHF. Recently, genetic manipulation of Ca2+ handling proteins in cardiac myocytes has been explored for its potential therapeutic application in DHF. Specifically, ectopic expression of the skeletal muscle Ca2+ binding protein parvalbumin (Parv) has been shown to accelerate myocardial relaxation in vitro and in vivo. Parv acts as a unique "delayed" Ca2+ buffer during diastole by promoting Ca2+ transient decay and sequestration and corrects diastolic dysfunction in an energy-independent manner. This brief review summarizes the rationale and development of Parv gene transfer approaches for DHF, and in particular, discusses the divergent effects of Parv isoforms on cardiac myocyte Ca2+ handling and contractile function with the long-range goal of alleviating diastolic dysfunction in DHF.

Temperature sensitivity of calcium binding for parvalbumins from Antarctic and temperate zone teleost fishes

Parvalbumin (PV) is a soluble calcium-binding protein that is especially abundant in fast-twitch muscles of fish and other lower vertebrates. Despite its prevalence in ectothermic taxa, few data address the effects of temperature on PV binding function. In this study, calcium dissociation constants (KD) were measured as a function of temperature (0-25 degrees C) for PV from two Antarctic (Gobionotothen gibberifrons and Chaenocephalus aceratus) and two temperate zone fish species (Cyprinus carpio and Micropterus salmoides). Measurements by fluorometric competitive binding assay show that KD values for PVs from the Antarctic species were significantly higher at all assay temperatures and were less sensitive to temperature relative to carp and bass. However, estimates of KD are fundamentally similar for PVs from the Antarctic and temperate zone species when examined at their native physiological temperature. Variation in pH and ionic strength within a physiologically relevant range had only modest effects on KD. Thermodynamics of calcium binding to PV from G. gibberifrons and C. carpio was measured by isothermal microcalorimetry. When measured at 15 degrees C, the Gibbs free energy change (deltaG) was significantly greater for calcium binding to PV from G. gibberifrons than from carp (-43.4+/-1.5 kJ mol(-1) and -46.6+/-3.0 kJ mol(-1), respectively), and the relative contribution of entropy to deltaG for calcium binding to PV from the Antarctic species was about twice that of carp (deltaS=16.0+/-0.8 J degrees C(-1) mol(-1) for G. gibberifrons; deltaS=7.5+/-0.8 J degrees C(-1) mol(-1) for C. carpio).

Structural basis for sequential displacement of Ca(2+) by Yb(3+) in a protozoan EF-hand calcium binding protein

We have studied the displacement of Ca(2+)by the trivalent lanthanide ions (Yb(3+)) in a protozoan (Entamoeba histolytica) Ca(2+)-binding protein (EhCaBP), by NMR and thermodynamics. We have demonstrated, for the first time, how one can use in a combined fashion the utility of NMR and thermodynamics to have an insight to the relative binding specificities/affinity between Ca(2+) and Yb(3+). As revealed by the titration experiments, Yb(3+) displaces Ca(2+) from the four metal binding sites present in EhCaBP in a sequential manner. The study provides a structural origin for such a sequential Ca(2+) displacement by Yb(3+) in EhCaBP.

Structure-fluorescence correlations in a single tryptophan mutant of carp parvalbumin: solution structure, backbone and side-chain dynamics

Heterogeneous fluorescence intensity decays of tryptophan in proteins are often rationalized using a model which proposes that different rotameric states of the indole alanyl side-chain are responsible for the observed fluorescence lifetime heterogeneity. We present here the study of a mutant of carp parvalbumin bearing a single tryptophan residue at position 102 (F102W) whose fluorescence intensity decay is heterogeneous and assess the applicability of a rotamer model to describe the fluorescence decay data. We have determined the solution structure of F102W in the calcium ligated state using multi-dimensional nuclear magnetic resonance (NMR) and have used the minimum perturbation mapping technique to explore the possible existence of multiple conformations of the indole moiety of Trp102 of F102W and, for comparison, Trp48 of holo-azurin. The maps for parvalbumin suggest two potential conformations of the indole side-chain. The high energy barrier for rotational isomerization between these conformers implies that interwell rotation would occur on time-scales of milliseconds or greater and suggests a rotamer basis for the heterogeneous fluorescence. However, the absence of alternate Trp102 conformers in the NMR data (to within 3 % of the dominant species) suggests that the heterogeneous fluorescence of Trp102 may arise from mechanisms independent of rotameric states of the Trp side-chain. The map for holo-azurin has only one conformation, and suggests a rotamer model may not be required to explain its heterogeneous fluorescence intensity decay. The backbone and Trp102 side-chain dynamics at 30 degrees C of F102W has been characterized based on an analysis of (15)N NMR relaxation data which we have interpreted using the Lipari-Szabo formalism. High order parameter (S(2)) values were obtained for both the helical and loop regions. Additionally, the S(2) values imply that the calcium binding CD and EF loops are not strictly equivalent. The S(2) value for the indole side-chain of Trp102 obtained from the fluorescence, NMR relaxation and minimum perturbation data are consistent with a Trp moiety whose motion is restricted.

Investigating site-specific effects of the -X glutamate in a parvalbumin CD site model peptide

The -X glutamate in a 33-residue model peptide comprising the CD site of carp parvalbumin 4.25 (ParvCD) was replaced with aspartate (ParvCD-XD) and the effect on calcium-dependent dimerization and calcium affinity assessed. The peptide ParvCD demonstrates a 10(5)-fold lower calcium affinity than the same site in the native protein. Both the ParvCD and ParvCD-XD model peptides fail to bind magnesium. The low calcium affinity and failure of the model ParvCD site to bind magnesium may be due to higher enthalpic costs of chelation by the -X glutamate. Replacement of the -X glutamate with an aspartate resulted in a twofold increase in the calcium affinity of both the monomer and dimer forms and a twofold increase in the calcium dependent dimerization of the peptide. A -X glutamate to aspartate replacement in 33-residue model peptides corresponding to bovine brain calmodulin site 3 (R. M. Procyshyn and R. E. Reid, Arch. Biochem. Biophys. 311, 425-429, 1994) and in Escherichia coli d-galactose-binding protein (S. K. Drake, K. L. Lee, and J. J. Falke, Biochemistry 35, 6697-6705, 1996) agree with results in the ParvCD site. However, in rat oncomodulin a -X glutamate to aspartate replacement increases calcium affinity (R. C. Hapak, P. J. Lammers, W. A. Palmisano, E. R. Birnbaum, and M. T. Henzl, J. Biol. Chem. 264, 18751-18760, 1989). The different effect of a -X glutamate to aspartate substitution in the different sites suggests site-specific factors dictating the thermodynamic contribution of the -X glutamate to calcium affinity.

Conformational stabilities of the rat alpha- and beta-parvalbumins

It is widely believed that beta-parvalbumin (PV) isoforms are intrinsically less stable than alpha-parvalbumins, due to greater electrostatic repulsion and an abbreviated C-terminal helix. However, when examined by differential scanning calorimetry, the apo-form of the rat beta-PV (i.e. oncomodulin) actually displays greater thermal stability than the alpha-PV. Whereas the melting temperature of the a isoform is 45.8 degrees C at physiological pH and ionic strength, the Tm for the beta isoform is more than 7 degrees higher (53.6 degrees C). This result suggests that factors besides net charge and C-terminal helix length strongly influence parvalbumin conformational stability. Extension of the F helix in the beta-PV, by insertion of Ser-109, has a modest stabilizing effect, raising the Tm, by 1.1 degrees. Truncation of the alpha-PV F helix, by removal of Glu-108, has a more profound impact, lowering the Tm by 4.0 degrees.

Oncomodulin is expressed exclusively by outer hair cells in the organ of Corti

Oncomodulin (OM) is a small, acidic calcium-binding protein first discovered in a rat hepatoma and later found in placental cytotrophoblasts, the pre-implantation embryo, and in a wide variety of neoplastic tissues. OM was considered to be exclusively an oncofetal protein until its recent detection in extracts of the adult guinea pig's organ of Corti. Here we report that light and electron microscopic immunostaining of gerbil, rat, and mouse inner ears with a monoclonal antibody against recombinant rat OM localizes the protein exclusively in cochlear outer hair cells (OHCs). At the ultrastructural level, high gold labeling density was seen overlying the nucleus, cytoplasm, and the cuticular plate of gerbil OHCs. Few, if any, gold particles were present over intracellular organelles and the stereocilia. Staining of a wide range of similarly processed gerbil organs failed to detect immunoreactive OM in any other adult tissues. The mammalian genome encodes one alpha- and one beta-isoform of parvalbumin (PV). The widely distributed alpha PV exhibits a very high affinity for Ca2+ and is believed to serve as a Ca2+ buffer. By contrast, OM, the mammalian beta PV, displays a highly attenuated affinity for Ca2+, consistent with a Ca2+-dependent regulatory function. The exclusive association of OM with cochlear OHCs in mature tissues is likely to have functional relevance. Teleological considerations favor its involvement in regulating some aspect of OHC electromotility. Although the fast electromotile response of OHCs does not require Ca2+, its gain and magnitude are modulated by efferent innervation. Therefore, OM may be involved in mediation of intracellular responses to cholinergic stimulation, which are known to be Ca2+ regulated. (J Histochem Cytochem 46:29-39, 1998)

Oncomodulin is abundant in the organ of Corti

A small, acidic Ca(2+)-binding protein (CBP-15) was recently detected in extracts of the mammalian auditory receptor organ, the organ of Corti [Senarita et al. (1995) Hear. Res. 90, 169-175]. N-terminal sequence data for CBP-15 [Thalmann et al. (1995) Biochem. Biophys. Res. Commun. 215, 142-147] implied membership in the parvalbumin family and possible identity with the mammalian beta-parvalbumin oncomodulin. As shown herein, the latter conclusion is supported by strong cross-reactivity between CBP-15 and isoform-specific antibodies to oncomodulin. Moreover, we have succeeded in amplifying the guinea pig CBP-15 coding sequence from organ of Corti cDNA using degenerate oligonucleotide primers based on the rat oncomodulin sequence. The deduced amino acid sequence of guinea pig CBP-15 displays 90%, 92%, and 98% identity with mouse, rat, and human oncomodulin isoforms. Demonstration of the presence of oncomodulin in the organ of Corti is the first documentation of this substance in a postnatal mammalian tissue.

Self-association of CPV3, an avian thymic parvalbumin

The avian parvalbumin called CPV3 readily forms disulfide-linked oligomers. Sedimentation data presented herein reveal that CPV3 also undergoes noncovalent self-association. Interestingly, the noncovalent interaction is promoted by either Ca2+ or Mg2+, whereas covalent complex formation displays an absolute requirement for the Ca(2+)-bound protein. Apo-CPV3 exhibits an apparent sedimentation coefficient of 2.08 S at 20 degrees C, in 0.15 M NaCl, 0.025 M HEPES-NaOH, pH 7.4. This value increases to 2.85 S or 3.16 S with addition of 1.0 mM Ca2+ or 5.0 mM Mg2+, respectively. Least-squares analysis of sedimentation equilibrium data suggests that 100 microM apo-CPV3 is primarily a mixture of monomeric and dimeric forms. With the addition of Ca2+, the equilibrium becomes exclusively monomer-trimer, with negligible amounts of dimer. A comparable distribution is observed in the presence of Mg2+.

Quantitative measurements of the cooperativity in an EF-hand protein with sequential calcium binding

Positive cooperativity, defined as an enhancement of the ligand affinity at one site as a consequence of binding the same type of ligand at another site, is a free energy coupling between binding sites. It can be present both in systems with sites having identical ligand affinities and in systems where the binding sites have different affinities. When the sites have widely different affinities such that they are filled with ligand in a sequential manner, it is often difficult to quantify or even detect the positive cooperativity, if it occurs. This study presents verification and quantitative measurements of the free energy coupling between the two calcium binding sites in a mutant form of calbindin D9k. Wild-type calbindin D9k binds two calcium ions with similar affinities and positive cooperativity--the free energy coupling, delta delta G, is around -8 kJ.mol-1 (Linse S, et al., 1991, Biochemistry 30: 154-162). The mutant, with the substitution Asn 56-->Ala, binds calcium in a sequential manner. In the present work we have taken advantage of the variations among different metal ions in terms of their preferences for the two binding sites in calbindin D9k. Combined studies of the binding of Ca2+, Cd2+, and La3+ have allowed us to conclude that in this mutant delta delta G < -6.4 kJ.mol-1, and that Cd2+ and La3+ also bind to this protein with positive cooperativity. The results justify the use of the (Ca2+)1 state of the Asn 56-->Ala mutant, as well as the (Cd2+)1 state of the wild type, as models for the half-saturated states along the two pathways of cooperative Ca2+ binding in calbindin D9k.

Molecular tuning of ion binding to calcium signaling proteins

Intracellular calcium plays an essential role in the transduction of most hormonal, neuronal, visual, and muscle stimuli. (Recent reviews include Putney, 1993; Berridge, 1993a,b; Tsunoda, 1993; Gnegy, 1993; Bachset al.1992; Hanson & Schulman, 1992; Villereal & Byron, 1992; Premack & Gardner, 1992; Meanset al.1991).

Calcium and magnesium binding to rat parvalbumin

Ca2+ and Mg2+ binding to rat parvalbumin was measured by means of the fluorescent Ca2+ indicator fluo-3 using a method developed earlier [Eberhard, M. & Erne, P. (1991) Eur. J. Biochem. 202, 1333-1338]. We demonstrate that rat parvalbumin contains two equivalent Ca2+/Mg2+ binding sites and that Ca2+ and Mg2+ compete for the same sites. Dissociation constants (Kd) for Ca2+ and Mg2+ in Hepes buffer containing 150 mM K+ at 35 degrees C and pH 7.2 are 11.0 +/- 1.8 nM and 41 +/- 8 microM, respectively. At an ionic strength below 0.2 M, Kd values of Ca2+ binding to rat parvalbumin are approximately proportional to the ion concentration. Kd values of Ca2+ binding were found to be about fourfold larger in the presence of Na+ as compared with K+, indicating that Na+ distinctly influences Ca2+ binding to rat parvalbumin. Both Ca2+ and Mg2+ binding to parvalbumin are exothermic whereas Ca2+ and Mg2+ binding to fluo-3 are endothermic entropy-driven processes.

Thermodynamics of cation binding to Nereis sarcoplasmic calcium-binding protein. Direct binding studies, microcalorimetry and conformational changes

Nereis sarcoplasmic calcium-binding protein contains three functional EF-hand sites which bind Ca2+ or Mg2+ competitively. Here it was confirmed over a large range of [Mg2+] that the positive cooperativity in binding of Ca2+ (nH = 2) is the result of allostery in Mg2+ dissociation. At pH 7.5, Ca2+ or Mg2+ binding provokes the release of 1.4 mol proton/mol protein, whereas no protons are released during Ca(2+)-Mg2+ exchange. The enthalpy change as a function of Ca2+ binding yields a two-step curve with an inflection point at 1 mol Ca2+/mol protein and a maximum of -66 kJ/mol at 3 mol Ca2+/mol protein. Binding of three Mg2+ ions is cooperative (nH = 1.8) with a maximal enthalpy change of -15.1 kJ/mol protein. Difference spectroscopy led to the conclusion that, in the metal-free protein, the structure around the aromatic residues is well organized, but that Tyr and Trp residues are still solvent-exposed. Upon Ca2+ binding Tyr and Trp spectra are blue-shifted, but some Trp residues are confined to a positively charged pocket. Examination of the Ca(2+)-saturated three-dimensional crystal structure confirmed that Trp4 and Trp57 are located in such pockets or clefts, close to the surface. During the allosteric T----R transition, promoted by binding of the first Mg2+, the Trp residues move to a hydrophobic environment. For both Ca2+ and Mg2+, the enthalpy change and the conformational change in the environment of the aromatic residues is much more pronounced in the first, than in the subsequent two binding steps. In this respect, the latter seem to be equivalent.

Tightly-bound divalent cation of actin

Actin is known to undergo reversible monomer-polymer transitions that coincide with various cell activities such as cell shape changes, locomotion, endocytosis and exocytosis. This dynamic state of actin filament self-assembly and disassembly is thought to be regulated by the properties of the monomeric actin molecule and in vivo by the influence of actin-associated proteins. Of major importance to the properties of the monomeric actin molecule are the presence of one tightly-bound ATP and one tightly-bound divalent cation per molecule. In vivo the divalent cation is thought to be Mg2+ (Mg-actin) but in vitro standard purification procedures result in the preparation of Ca-actin. The affinity of actin for a divalent cation at the tight binding site is in the nanomolar range, much higher than earlier thought. The binding kinetics of Mg2+ and Ca2+ at the high affinity site on actin are considered in terms of a simple competitive binding mechanism. This model adequately describes the published observations regarding divalent cation exchange on actin. The effects of the tightly-bound cation, Mg2+ or Ca2+, on nucleotide binding and exchange on actin, actin ATP hydrolysis activity and nucleation and polymerization of actin are discussed. From the characteristics that are reviewed, it is apparent that the nature of the bound divalent cation has a significant effect on the properties of actin.

Identification of a novel parvalbumin in avian thymic tissue

A novel calcium-binding protein has been isolated from chicken thymus tissue. Its molecular weight (approximately 11,500) and characteristic interactions with Tb3+ and Eu3+ identify the protein as a member of the parvalbumin family. Electrophoretically distinct from both chicken (muscle) parvalbumin and avian thymic hormone, it represents the third parvalbumin to be identified in avian tissues and the second to be identified in the avian thymus gland.

Molecular cloning of the thymus-specific parvalbumin known as avian thymic hormone: isolation of a full length cDNA and expression of the recombinant protein in Escherichia coli

The complete coding sequence of the thymus-specific parvalbumin called avian thymic hormone (ATH) has been cloned into Escherichia coli. The translated amino acid sequence was found to be identical to the sequence of map turtle parvalbumin at 90 of 108 positions. Northern blot analysis of thymic RNA indicated a transcript length of approximately 1050 bp. However, the ATH cDNA probe failed to hybridize to poly(A)+ RNA from chicken leg muscle, a further indication that avian thymic hormone is distinct from the muscle-associated parvalbumin previously isolated from chicken. Southern analysis of chicken genomic DNA suggests the presence of a single copy of the ATH gene, and the absence of hybridization between an ATH cDNA fragment and genomic DNA from rat and rabbit is confirmatory evidence that ATH expression is restricted to avian species. One of the full length ATH cDNA clones harbored an insert that lacked all 5' noncoding sequences. This cDNA was inserted without further alteration into the prokaryotic expression vector, pKK223-3. The resulting construction, which contains eleven base pairs between the Shine-Dalgarno sequence and the initiation codon, affords reasonably high levels of expression in E. coli. In most respects, recombinant ATH mimics the tissue-derived protein, retaining a similarly high affinity for Ca2+ ion (KCa = 14 +/- 5 nM). However, in contrast to ATH isolated from chicken thymus tissue, the N-terminal alanine of recombinant ATH is unacetylated. As a result, the isoelectric point is shifted upward from 4.3 to approximately 4.8.

Heat capacity and entropy changes of troponin C from bullfrog skeletal muscle induced by calcium binding

In order to elucidate the structural changes of bullfrog skeletal muscle troponin C (TnC) caused by Ca2+ binding, microcalorimetric titrations were performed in both the absence and presence of Mg2+, at pH 7.0, and at 5 degrees, 15 degrees, and 25 degrees C. The results indicate that, in the absence of Mg2+, Ca2+ binding to sites 1 and 2 gives rise to a large hydrophobic effect, a sequestering of nonpolar groups on the surface of molecule to the interior, and a tightening of the molecular structure as a whole. In contrast, hydrophobic groups were exposed from the interior to the surface of molecule and the molecular mobility was increased, upon Ca2+ binding to site 3. Ca2+ binding to site 4 induced much less change in the conformation of TnC molecule than that to the other sites. The presence of 5 mM Mg2+ dramatically reduced the magnitude of the conformational changes in TnC on Ca2+ binding to sites 1 and 2. On the other hand, the conformational changes by Ca2+ binding to sites 3 and 4 were not affected by Mg2+. Ca2+ binding to site 3 of TnC, thus, causes the conformational changes distinctly different from those upon Ca2+ binding to the other sites. The conformational changes upon Ca2+ binding to site 3 of TnC are also clearly distinct from the Ca2(+)-induced conformational changes of parvalbumins, but are similar to those of calmodulin. Site 3 of TnC may, therefore, be the regulatory site in muscle contraction, and the exposure or generation of hydrophobic groups on the surface of molecule as well as the increase in molecular mobility may be the common characteristics of the regulation by Ca2(+)-binding proteins.

Heat capacity and entropy changes of the major isotype of the toad (Bufo) parvalbumin induced by calcium binding

The possible structural changes in the major isotype of parvalbumin from the toad (Bufo bufo japonicus) skeletal muscle caused by Ca2+ and Mg2+ binding have been analyzed by microcalorimetric titrations. Parvalbumin was titrated with Ca2+ in both the absence and presence of Mg2+ and with Mg2+ in the absence of Ca2+, at pH 7.0, and at 5 degrees, 15 degrees, and 25 degrees C. The two sites in a molecule were equivalent on Mg2(+)-Ca2+ exchange, but distinguishable on Ca2+ and Mg2+ binding. The reactions of parvalbumin with Ca2+ are exothermic at every temperature in both the absence and presence of Mg2+, but those with Mg2+ are always endothermic except for the binding to site 1 at 25 degrees C. The magnitudes of the hydrophobic and internal vibrational contributions to the heat capacity and entropy changes of parvalbumin on Ca2+ and Mg2+ binding and Mg2(+)-Ca2+ exchange have been estimated by the empirical method of Sturtevant [Sturtevant, J. M. (1977) Proc. Natl Acad. Sci. USA 74, 2236-2240]. Although no major conformational changes were noted between Ca2(+)- and Mg2(+)-bound forms of toad parvalbumin, the conformational difference was larger in Ca2+ (or Mg2+) binding to site 1 than site 2. This may indicate that the metal-free form is much less stable than any form with Ca2+ (or Mg2+) bound at one site at least. On Mg2(+)-Ca2+ exchange, the vibrational as well as hydrophobic entropy is only slightly increased in a parallel manner. In contrast, on Ca2+ (or Mg2+) binding, the hydrophobic entropy increases but the vibrational entropy decreases; the former indicates the sequestering of nonpolar groups from the surface to the interior of a molecule, and the latter suggests that the overall structures are tightened on Ca2+ (or Mg2+) binding but loosened on Mg2(+)-Ca2+ exchange. Despite the clear distinctions in the thermodynamic features, the conformational changes of toad parvalbumin are essentially the same as those of the two isotypes of bullfrog parvalbumins on Ca2+ binding and Mg2(+)-Ca2+ exchange.

Calbindin D-28k and parvalbumin in the rat nervous system

This paper describes the distribution of structures stained with mono- and polyclonal antibodies to the calcium-binding proteins calbindin D-28k and parvalbumin in the nervous system of adult rats. As a general characterization it can be stated that calbindin antibodies mainly label cells with thin, unmyelinated axons projecting in a diffuse manner. On the other hand, parvalbumin mostly occurs in cells with thick, myelinated axons and restricted, focused projection fields. The distinctive staining with antibodies against these two proteins can be observed throughout the nervous system. Calbindin D-28k is primarily associated with long-axon neurons (Golgi type I cells) exemplified by thalamic projection neurons, strionigral neurons, nucleus basalis Meynert neurons, cerebellar Purkinje cells, large spinal-, retinal-, cochlear- and vestibular ganglion cells. Calbindin D-28k occurs in all major pathways of the limbic system with the exception of the fornix. Calbindin D-28k is, however, also found in some short-axon cells (Golgi type II), represented by spinal cord interneurons in layer II and interneurons of the cerebral cortex. It is also detectable in some ependymal cells and abundantly occurs in vegetative centres of the hypothalamus. The "paracrine core" of the nervous system and its adjunct (1985, Nieuwenhuys, Chemoarchitecture of the Brain. Springer, Berlin) is very rich in calbindin D-28k. The distribution of calbindin D-28k-positive neurons is very similar to that of the dihydroperydine subtype of calcium channels. Most of the cells containing calbindin D-28k are vulnerable to neurodegenerative processes. Parvalbumin-immunoreactive neurons have a different, and mostly complementary distribution compared with those which react with calbindin D-28k antisera, but in a few cases (Purkinje cells of the cerebellum, spinal ganglion neurons), both calcium-binding proteins co-exist in the same neuron. Many parvalbumin-immunoreactive cells in the central nervous system are interneurons (Golgi type II) and, to a lesser extent, long-axon cells (Golgi type I), whereas conditions are vice versa in the peripheral nervous system. Intrinsic parvalbuminic neurons are prominent in the cerebral cortex, hippocampus, cerebellar cortex and spinal cord. Long-axon parvalbumin-immunoreactive neurons are, for example, the Purkinje cells, neurons of the thalamic reticular nucleus, globus pallidus, substantia nigra (pars reticulata) and a subpopulation among large spinal-, retinal-, cochlear- and vestibular ganglion cells. Parvalbumin is rich in cranial nerve nuclei related to eye movements. In addition to nervous elements, parvalbumin immunoreactivity occurs in a few ependymal cells and in some pillar cells of the organ of Corti.(ABSTRACT TRUNCATED AT 400 WORDS)

Theoretical estimation of the calcium-binding constants for proteins from the troponin C superfamily based on a secondary structure prediction method. I. Estimation procedure

Proteins belonging to the TNC superfamily are known to be built of two, three, four, or six domains of closely similar amino acid sequences. Each domain binds no more than one calcium ion and shows a characteristic helix-loop-helix structure when in the calcium-bound state. Conformational properties of all the domains known so far have been analysed by us using a secondary structure prediction method (Garnier, J., Osguthorpe, D.J. & Robson, B. (1978). J. molec. Biol. 120, 97). Significant differences in distribution of residues predicted as being in the helical, beta-turn, and coil conformations have been found between the strongly, weakly, and non-binding domains. We could determine the ideal prediction pattern characteristic for the domains with the highest affinity for calcium. On the basis of our analysis and observations made by other authors we worked out a few simple rules which made it possible to compare conformational properties of a given domain with the ideal reference pattern and estimate, in this way, the Ca2+-binding constant of the domain. In native proteins the domains are known to be organized in pairs. The Ca2+-binding constant for a two-domain region could be evaluated from the sum of the estimation points attributed to each of its components. Using our method it is possible to predict the binding constants of typical domains and two-domain regins with a precision of one order of magnitude. Data on amino acid sequences and calcium-binding constants of all known proteins, believed to be the members of the TNC superfamily, have been reviewed. References to virtually all papers published on this subject before the end of 1987 are given.

Effect of carbon dioxide on heat production of frog skeletal muscles

1. Maintenance heat produced in tetani of frogs' sartorius muscles (Rana japonica) was measured under various values of intracellular pH (pHi) brought about by increasing the CO2 concentration in Ringer solution. The pHi values were measured using 31P nuclear magnetic resonance from the chemical shifts of the inorganic phosphate resonance. The pHi was 7.10 +/- 0.009 (mean +/- S.E. of the mean, n = 10) in the gas mixture of 5% CO2/95% O2 at 4 degrees C and it was reduced to 6.44 +/- 0.001 (n = 23) in 45% CO2. 2. As CO2 was increased, the maximum force was decreased and relaxation was prolonged. This is in accordance with the results of Edman & Mattiazzi (1981) and Curtin (1986). 3. An increase in CO2 induced a reduction of the maintenance heat production, which can be divided into stable and labile heats (Aubert, 1956). The stable heat, which is produced with a steady rate during contraction, was decreased as CO2 was increased. The labile heat, which is produced with an exponentially declining rate, was not significantly altered by increasing CO2 within the range studied. 4. The effect of previous contractile activity on the labile heat production, i.e. the time course of repriming of the labile heat, could be described by an equation with two exponential terms in 5% CO2 in accordance with the result of Peckham & Woledge (1986). The time course of repriming of the labile heat was not affected by increasing CO2 to 20%.

Determination of magnesium binding to macromolecules

An equilibrium dialysis technique for examining magnesium binding to macromolecules is described. The technique is used to determine the binding constants of magnesium to human prothrombin. This procedure should be of great utility for many biochemical systems which exhibit magnesium affinity.