Luminescence spectroscopy

Probing Lanmodulin's Lanthanide Recognition via Sensitized Luminescence Yields a Platform for Quantification of Terbium in Acid Mine Drainage

Lanmodulin is the first natural, selective macrochelator for f elements-a protein that binds lanthanides with picomolar affinity at 3 EF hands, motifs that instead bind calcium in most other proteins. Here, we use sensitized terbium luminescence to probe the mechanism of lanthanide recognition by this protein as well as to develop a terbium-specific biosensor that can be applied directly in environmental samples. By incorporating tryptophan residues into specific EF hands, we infer the order of metal binding of these three sites. Despite lanmodulin's remarkable lanthanide binding properties, its coordination of approximately two solvent molecules per site (by luminescence lifetime) and metal dissociation kinetics (k_off = 0.02-0.05 s^-1, by stopped-flow fluorescence) are revealed to be rather ordinary among EF hands; what sets lanmodulin apart is that metal association is nearly diffusion limited (k_on ≈ 10⁹ M^-1 s^-1). Finally, we show that Trp-substituted lanmodulin can quantify 3 ppb (18 nM) terbium directly in acid mine drainage at pH 3.2 in the presence of a 100-fold excess of other rare earths and a 100 000-fold excess of other metals using a plate reader. These studies not only yield insight into lanmodulin's mechanism of lanthanide recognition and the structures of its metal binding sites but also show that this protein's unique combination of affinity and selectivity outperforms synthetic luminescence-based sensors, opening the door to rapid and inexpensive methods for selective sensing of individual lanthanides in the environment and in-line monitoring in industrial operations.

Determination of affinities of lanthanide-binding proteins using chelator-buffered titrations

The recent discoveries of the first proteins that bind lanthanides as part of their biological function not only are relevant to the emerging field of lanthanide-dependent biology, but also hold promise to revolutionize the technologically critical rare earths industry. Although protocols to assess the thermodynamics of metal-protein interactions are well established for "traditional" metal ions in biology, the characterization of lanthanide-binding proteins presents a challenge to biochemists due to the lanthanides' Lewis acidity, propensity for hydrolysis, and high-affinity complexes with biological ligands. These properties necessitate the preparation of metal stock solutions with very low buffered "free" metal concentrations (e.g., femtomolar to nanomolar) for such determinations. Herein we describe several protocols to overcome these challenges. First, we present standardization methods for the preparation of chelator-buffered solutions of lanthanide ions with easily calculated free metal concentrations. We also describe how these solutions can be used in concert with analytical methods including UV-visible spectrophotometry, circular dichroism spectroscopy, Förster resonance energy transfer (FRET), and sensitized terbium luminescence, in order to accurately determine dissociation constants (K_ds) of lanthanide-protein complexes. Finally, we highlight how application of these methods to lanthanide-binding proteins, such as lanmodulin, has yielded insights into selective recognition of lanthanides in biology. We anticipate that these protocols will facilitate discovery and characterization of additional native lanthanide-binding proteins, will motivate the understanding of their biological context, and will prompt their applications in biotechnology.

Aqueous synthesis of a small-molecule lanthanide chelator amenable to copper-free click chemistry

The lanthanides (Ln3+), or rare earth elements, have proven to be useful tools for biomolecular NMR, X-ray crystallographic, and fluorescence analyses due to their unique 4f orbitals. However, their utility in biological applications has been limited because site-specific incorporation of a chelating element is required to ensure efficient binding of the free Ln3+ ion. Additionally, current Ln3+ chelator syntheses complicate efforts to directly incorporate Ln3+ chelators into proteins as the multi-step processes and a reliance on organic solvents promote protein denaturation and aggregation which are generally incompatible with direct incorporation into the protein of interest. To overcome these limitations, herein we describe a two-step aqueous synthesis of a small molecule lanthanide chelating agent amenable to site-specific incorporation into a protein using copper-free click chemistry with unnatural amino acids. The bioconjugate combines a diethylenetriaminepentaacetic acid (DTPA) chelating moiety with a clickable dibenzylcyclooctyne-amine (DBCO-amine) to facilitate the reaction with an azide containing unnatural amino acid. Incorporating the DBCO-amine avoids the use of the cytotoxic Cu2+ ion as a catalyst. The clickable lanthanide chelator (CLC) reagent reacted readily with p-azidophenylalanine (paF) without the need of a copper catalyst, thereby demonstrating proof-of-concept. Implementation of the orthogonal click chemistry reaction has the added advantage that the chelator can be used directly in a protein labeling reaction, without the need of extensive purification. Given the inherent advantages of Cu2+-free click chemistry, aqueous synthesis, and facile labeling, we believe that the CLC will find abundant use in both structural and biophysical studies of proteins and their complexes.

Calcium-induced human centrin 1 self-assembly and double-regulating the binding with peptide R18-Sfi1p

Centrin is a member of the EF-hand super-family that plays pivotal role in the centrosome duplication and separation. In the present paper, we characterized the properties of metal ions as well as peptide R18-Sfi1p binding to human centrin 1 (HsCen1) by fluorescence spectra and isothermal titration calorimetry (ITC). Four metal ions binding sites on HsCen1 were identified through ITC experiments. The conditional binding constants of the EF-hand domain on HsCen1 with Ca²⁺ were quantitatively calculated. In reversible manner, Ca²⁺ can induce HsCen1 self-assembly. In addition, HsCen1 bound with peptide R18-Sfi1p in calcium-dependent with middle-affinity. Phosphorylation at Ser170 weakened interaction HsCen1 with the substrate and removal calcium ions further weakened interactions of the two molecules. Hence, we inferred that centrin initiating downstream peptides may be a double-regulated process by calcium and phosphorylation. These results are of significance for understanding the relationship between PTM and metal regulation.

Copper binding affinity of the C2B domain of synaptotagmin-1 and its potential role in the nonclassical secretion of acidic fibroblast growth factor

Fibroblast growth factor 1 (FGF1) is a heparin-binding proangiogenic protein. FGF1 lacks the conventional N-terminal signal peptide required for secretion through the endoplasmic reticulum (ER)-Golgi secretory pathway. FGF1 is released through a Cu(2+)-mediated nonclassical secretion pathway. The secretion of FGF1 involves the formation of a Cu(2+)-mediated multiprotein release complex (MRC) including FGF1, S100A13 (a calcium-binding protein) and p40 synaptotagmin (Syt1). It is believed that the binding of Cu(2+) to the C2B domain is important for the release of FGF1 into the extracellular medium. In this study, using a variety of biophysical studies, Cu(2+) and lipid interactions of the C2B domain of Syt1 were characterized. Isothermal titration calorimetry (ITC) experiments reveal that the C2B domain binds to Cu(2+) in a biphasic manner involving an initial endothermic and a subsequent exothermic phase. Fluorescence energy transfer experiments using Tb(3+) show that there are two Cu(2+)-binding pockets on the C2B domain, and one of these is also a Ca(2+)-binding site. Lipid-binding studies using ITC demonstrate that the C2B domain preferentially binds to small unilamellar vesicles of phosphatidyl serine (PS). Results of the differential scanning calorimetry and limited trypsin digestion experiments suggest that the C2B domain is marginally destabilized upon binding to PS vesicles. These results, for the first time, suggest that the main role of the C2B domain of Syt1 is to serve as an anchor for the FGF1 MRC on the membrane bilayer. In addition, the binding of the C2B domain to the lipid bilayer is shown to significantly decrease the binding affinity of the protein to Cu(2+). The study provides valuable insights on the sequence of structural events that occur in the nonclassical secretion of FGF1.

Myoplasmic resting Ca2+ regulation by ryanodine receptors is under the control of a novel Ca2+-binding region of the receptor

Passive SR (sarcoplasmic reticulum) Ca²⁺ leak through the RyR (ryanodine receptor) plays a critical role in the mechanisms that regulate [Ca²⁺]_rest (intracellular resting myoplasmic free Ca²⁺ concentration) in muscle. This process appears to be isoform-specific as expression of either RyR1 or RyR3 confers on myotubes different [Ca²⁺]_rest. Using chimaeric RyR3–RyR1 receptors expressed in dyspedic myotubes, we show that isoform-dependent regulation of [Ca²⁺]_rest is primarily defined by a small region of the receptor encompassing amino acids 3770–4007 of RyR1 (amino acids 3620–3859 of RyR3) named as the CLR (Ca²⁺ leak regulatory) region. [Ca²⁺]_rest regulation by the CLR region was associated with alteration of RyRs’ Ca²⁺-activation profile and changes in SR Ca²⁺-leak rates. Biochemical analysis using Tb³⁺-binding assays and intrinsic tryptophan fluorescence spectroscopy of purified CLR domains revealed that this determinant of RyRs holds a novel Ca²⁺-binding domain with conformational properties that are distinctive to each isoform. Our data suggest that the CLR region provides channels with unique functional properties that modulate the rate of passive SR Ca²⁺ leak and confer on RyR1 and RyR3 distinctive [Ca²⁺]_rest regulatory properties. The identification of a new Ca²⁺-binding domain of RyRs with a key modulatory role in [Ca²⁺]_rest regulation provides new insights into Ca²⁺-mediated regulation of RyRs.

This paper reports the finding of a new class of Ca²⁺-binding domain of intracellular Ca²⁺ channels from muscle cells. This domain provides channels with distinctive properties that result in channel-specific modulation of the intracellular resting Ca²⁺ concentration.

Calciomics: integrative studies of Ca2+-binding proteins and their interactomes in biological systems

Calcium ion (Ca(2+)), the fifth most common chemical element in the earth's crust, represents the most abundant mineral in the human body. By binding to a myriad of proteins distributed in different cellular organelles, Ca(2+) impacts nearly every aspect of cellular life. In prokaryotes, Ca(2+) plays an important role in bacterial movement, chemotaxis, survival reactions and sporulation. In eukaryotes, Ca(2+) has been chosen through evolution to function as a universal and versatile intracellular signal. Viruses, as obligate intracellular parasites, also develop smart strategies to manipulate the host Ca(2+) signaling machinery to benefit their own life cycles. This review focuses on recent advances in applying both bioinformatic and experimental approaches to predict and validate Ca(2+)-binding proteins and their interactomes in biological systems on a genome-wide scale (termed "calciomics"). Calmodulin is used as an example of Ca(2+)-binding protein (CaBP) to demonstrate the role of CaBPs on the regulation of biological functions. This review is anticipated to rekindle interest in investigating Ca(2+)-binding proteins and Ca(2+)-modulated functions at the systems level in the post-genomic era.

Probing Ca2+-binding capability of viral proteins with the EF-hand motif by grafting approach

Ca(2+) is implicated in almost every step of the life cycle of viruses, including virus entry into host cells, virus replication, virion assembly, maturation, and release. However, due to the lack of prediction algorithms and rigorous validation methods, only limited cases of viral Ca(2+)-binding sites are reported. Here, we introduce a method to predict continuous EF-hand or EF-hand-like motifs in the viral genomes based on their primary sequences. We then introduce a grafting approach, and the use of luminescence resonance energy transfer and Ca(2+) competition assay for experimental verification of predicted Ca(2+)-binding sites. This protocol will be valuable for the prediction and identification of unknown Ca(2+)-binding sites in virus.

1-Aminocyclopropane-1-carboxylic acid oxidase: insight into cofactor binding from experimental and theoretical studies

1-Aminocyclopropane-1-carboxylic acid oxidase (ACCO) is a nonheme Fe(II)-containing enzyme that is related to the 2-oxoglutarate-dependent dioxygenase family. The binding of substrates/cofactors to tomato ACCO was investigated through kinetics, tryptophan fluorescence quenching, and modeling studies. α-Aminophosphonate analogs of the substrate (1-aminocyclopropane-1-carboxylic acid, ACC), 1-aminocyclopropane-1-phosphonic acid (ACP) and (1-amino-1-methyl)ethylphosphonic acid (AMEP), were found to be competitive inhibitors versus both ACC and bicarbonate (HCO(3)(-)) ions. The measured dissociation constants for Fe(II) and ACC clearly indicate that bicarbonate ions improve both Fe(II) and ACC binding, strongly suggesting a stabilization role for this cofactor. A structural model of tomato ACCO was constructed and used for docking experiments, providing a model of possible interactions of ACC, HCO(3)(-), and ascorbate at the active site. In this model, the ACC and bicarbonate binding sites are located close together in the active pocket. HCO(3)(-) is found at hydrogen-bond distance from ACC and interacts (hydrogen bonds or electrostatic interactions) with residues K158, R244, Y162, S246, and R300 of the enzyme. The position of ascorbate is also predicted away from ACC. Individually docked at the active site, the inhibitors ACP and AMEP were found coordinating the metal ion in place of ACC with the phosphonate groups interacting with K158 and R300, thus interlocking with both ACC and bicarbonate binding sites. In conclusion, HCO(3)(-) and ACC together occupy positions similar to the position of 2-oxoglutarate in related enzymes, and through a hydrogen bond HCO(3)(-) likely plays a major role in the stabilization of the substrate in the active pocket.

Luminescent chiral lanthanide(III) complexes as potential molecular probes

This perspective gives an introduction into the design of luminescent lanthanide(iii)-containing complexes possessing chiral properties and used to probe biological materials. The first part briefly describes general principles, focusing on the optical aspect (i.e. lanthanide luminescence, sensitization processes) of the most emissive trivalent lanthanide ions, europium and terbium, incorporated into molecular luminescent edifices. This is followed by a short discussion on the importance of chirality in the biological and pharmaceutical fields. The second part is devoted to the assessment of the chiroptical spectroscopic tools available (typically circular dichroism and circularly polarized luminescence) and the strategies used to introduce a chiral feature into luminescent lanthanide(iii) complexes (chiral structure resulting from a chiral arrangement of the ligand molecules surrounding the luminescent center or presence of chiral centers in the ligand molecules). Finally, the last part illustrates these fundamental principles with recent selected examples of such chiral luminescent lanthanide-based compounds used as potential probes of biomolecular substrates.

OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold

One of the many challenging tasks of protein design is the introduction of a completely new function into an existing protein scaffold. In this study, we introduce a new computational procedure OptGraft for placing a novel binding pocket onto a protein structure so as its geometry is minimally perturbed. This is accomplished by introducing a two-level procedure where we first identify where are the most appropriate locations to graft the new binding pocket into the protein fold by minimizing the departure from a set of geometric restraints using mixed-integer linear optimization. On identifying the suitable locations that can accommodate the new binding pocket, CHARMM energy calculations are employed to identify what mutations in the neighboring residues, if any, are needed to ensure that the minimum energy conformation of the binding pocket conserves the desired geometry. This computational framework is benchmarked against the results available in the literature for engineering a copper binding site into thioredoxin protein. Subsequently, OptGraft is used to guide the transfer of a calcium-binding pocket from thermitase protein (PDB: 1thm) into the first domain of CD2 protein (PDB:1hng). Experimental characterization of three de novo redesigned proteins with grafted calcium-binding centers demonstrated that they all exhibit high affinities for terbium (Kd) approximately 22, 38, and 55 microM) and can selectively bind calcium over magnesium.

The characterization for the binding of calcium and terbium to Euplotes octocarinatus centrin

Centrin is a member of the EF-hand superfamily that plays critical role in the centrosome duplication and separation. In the present paper, we characterized properties of metal ions binding to Euplotes octocarinatus centrin (EoCen) by fluorescence spectra and circular dichroism (CD) spectra. Changes of fluorescence spectra and alpha-helix contents of EoCen proved that Tb(3+) and Ca(2+) induced great conformational changes of EoCen resulting in exposing hydrophobic surfaces. At pH 7.4, Ca(2+) (and Tb(3+)) bond with EoCen at the ratio of 4:1. Equilibrium experiment indicated that Ca(2+) and Tb(3+) exhibited different binding capabilities for C- and N-terminal domains of protein. C-terminal domain bond with Ca(2+) or Tb(3+) approximately 100-fold more strongly than N-terminal. Aromatic residue-sensitized Tb(3+) energy transfer suggested that site IV bond to Tb(3+) or Ca(2+) more strongly than site III. Based on fluorescence titration curves, we reckoned the conditional binding constants of EoCen site IV quantitatively to be K(IV)=(1.23+/-0.51)x10(8)M(-1) and K(IV)=(6.82+/-0.33)x10(5)M(-1) with Tb(3+) and Ca(2+), respectively. Metal ions bond to EoCen in the order of IV>III>II, I.

Specificity of Mg2+ binding at the Group II intron branch site

Metal ions play a crucial role in the conformation and splicing activity of Group II introns. Results from 2-aminopurine fluorescence and solution NMR studies suggest that metal ion binding within the branch site region of native D6 of the Group II intron is specific for alkaline earth metal ions and involves inner sphere coordination. Although Mg(2+) and Ca(2+) still bind to a mutant stem loop sequence from which the internal loop had been deleted, ion binding to the mutant RNA results in decreased, rather than increased, exposure of the branch site residue to solvent. These data further support the role of the internal loop in defining branch site conformation of the Group II intron. The specific bound Mg(2+) may play a bivalent role: facilitates the extrahelical conformation of the branch site and has the potential to act as a Lewis acid during splicing.

pH-Induced changes in adsorbed cytochrome c. voltammetric and surface-enhanced resonance Raman characterization performed simultaneously at chemically modified silver electrodes

The influence of pH on the redox properties of cytochrome c (cyt c) adsorbed on roughened silver electrodes chemically modified with a self-assembled monolayer (SAM) of 11-mercapto-1-undecanoic acid (MUA) was studied with voltammetric techniques in combination with surface-enhanced resonance Raman scattering (SERRS). The experiments were performed simultaneously on the same electrode sample in a homemade spectroelectrochemical cell suitable for such applications. At pH 7.0 cyt c was found in its native state; at higher pH values (ranging from 8.0 to 9.0) the redox properties of the adsorbed protein varied considerably, featuring a redox behavior which does not resemble the one reported for the alkaline transition. Our results instead indicate the presence of an electrochemically inactive 6cLS species immobilized on MUA at pH 9.0. The pH-induced conformational changes observed for cyt c immobilized on the SAM of MUA were found to be repeatable and chemically reversible, meaning that the recovery of the electrochemical signal due to the native protein occurred instantaneously (on the second time scale) when the electrode was switched back to pH 7.0. The pH-induced changes observed were attributed to a conformational change involving a heme reorientation with respect to the electrode surface.

Calcium-binding to lens βB2- and βA3-crystallins suggests that all β-crystallins are calcium-binding proteins

Crystallins are the major proteins of a mammalian eye lens. The topologically similar eye lens proteins, beta- and gamma-crystallins, are the prototype and founding members of the betagamma-crystallin superfamily. Betagamma-crystallins have until recently been regarded as structural proteins. However, the calcium-binding properties of a few members and the potential role of betagamma-crystallins in fertility are being investigated. Because the calcium-binding elements of other member proteins, such as spherulin 3a, are not present in betaB2-crystallin and other betagamma-crystallins from fish and mammalian genomes, it was argued that lens betagamma-crystallins should not bind calcium. In order to probe whether beta-crystallins can bind calcium, we selected one basic (betaB2) and one acidic (betaA3) beta-crystallin for calcium-binding studies. Using calcium-binding assays such as 45Ca overlay, terbium binding, Stains-All and isothermal titration calorimetry, we established that both betaB2- and betaA3-crystallin bind calcium with moderate affinity. There was no significant change in their conformation upon binding calcium as monitored by fluorescence and circular dichroism spectroscopy. However, 15N-1H heteronuclear single quantum correlation NMR spectroscopy revealed that amide environment of several residues underwent changes indicating calcium ligation. With the corroboration of calcium-binding to betaB2- and betaA3-crystallins, we suggest that all beta-crystallins bind calcium. Our results have important implications for understanding the calcium-related cataractogenesis and maintenance of ionic homeostasis in the lens.

Voltammetric and surface-enhanced resonance Raman spectroscopic characterization of cytochrome C adsorbed on a 4-mercaptopyridine monolayer on silver electrodes

To combine voltammetric techniques with surface-enhanced resonance Raman scattering (SERRS), cytochrome c (cyt c) was immobilized on a roughened silver electrode chemically modified with a self-assembled monolayer (SAM) of 4-mercaptopyridine (PySH). All measurements were performed on the same electrode in a homemade spectroelectrochemical cell suitable for such applications. Cyt c on a PySH-SAM shows a quasi-reversible, monoelectronic, adsorption-controlled CV response with a formal reduction potential of -0.061 V (vs SCE), which is comparable to the values found for native cyt c adsorbed on different SAMs. SERRS spectra proved that cyt c adsorbed on a PySH monolayer is present in the native conformer (the B1 state). Voltammetric and SERRS experiments at high ionic strength revealed that the interaction between the SAM and the protein is electrostatic in nature. In conclusion, PySH was found to be suitable for adsorption of cyt c at SERRS-active silver surfaces. In comparison with other SAMs, PySH requires less time (10 min vs 12-18 h) to form a long-time durable and reproducible coating on the roughened electrode surface.

Surface-enhanced resonance Raman scattering of cytochrome P450-2D6 on coated silver hydrosols

Surface-enhanced resonance Raman scattering (SERRS) from dilute solutions (down to nanomolar concentrations) of human mono-oxygenase CYP2D6 is observed using aqueous dispersions of Ag nanoparticles (hydrosol) coated with self-assembled monolayers (SAMs) of mercaptoalkanoic acids of two different lengths. From a direct comparison with its resonance Raman spectrum in solution, CYP2D6 appears to fully retain its native structure upon adsorption on coated hydrosol through electrostatic interaction, while a structural change in the active site is observed when uncoated citrate-reduced hydrosol is used. Using SERRS on these biocompatible coated hydrosols, the effects of dextromethorphan on the enzyme's active site can be observed, demonstrating that CYP2D6 ability of binding substrates is preserved. Moreover, by tuning the wavelength of the exciting laser away from the main absorption band of the heme, the vibrational bands of the SAM coating are observed and analyzed to see how the presence of the protein affects the SAM structure.

Kinetic analysis of the metal binding mechanism of Escherichia coli manganese superoxide dismutase

The acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (MnSOD). In this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of Escherichia coli MnSOD in vitro, permitting a detailed kinetic characterization of the uptake mechanism. Apo-MnSOD metallation kinetics are "gated", zero order in metal ion for both the native Mn2+ and a nonnative metal ion (Co2+) used as a spectroscopic probe to provide greater sensitivity to metal binding. Cobalt-binding time courses measured over a range of temperatures (35-50 degrees C) reveal two exponential kinetic processes (fast and slow phases) associated with metal binding. The amplitude of the fast phase increases rapidly as the temperature is raised, reflecting the fraction of Apo-MnSOD in an "open" conformation, and its temperature dependence allows thermodynamic parameters to be estimated for the "closed" to "open" conformational transition. The sensitivity of the metallated protein to exogenously added chelator decreases progressively with time, consistent with annealing of an initially formed metalloprotein complex (k anneal = 0.4 min(-1)). A domain-separation mechanism is proposed for metal uptake by apo-MnSOD.

Citrate-reduced silver hydrosol modified with omega-mercaptoalkanoic acids self-assembled monolayers as a substrate for surface-enhanced resonance Raman scattering. A study with cytochrome c

A new citrate-reduced silver hydrosol coated with omega-mercaptoalkanoic acids (mercaptopropionic and mercaptoundecanoic acids) self-assembled monolayers was prepared and characterized with surface-enhanced Raman spectroscopy. The structure and the quality of the coating monolayers are discussed and compared to similar coated and uncoated silver hydrosols previously developed. As an application, the new hydrosol was used as a biocompatible and efficient metal substrate for a surface-enhanced resonance Raman scattering (SERRS) study of cytochrome c. The high-quality SERRS spectra reported of cytochrome c (obtained using only 1 microL of a micromolar cytochrome solution) are discussed and compared with data available from literature studies.

Linearly Moving Low-Volume Spectroelectrochemical Cell for Microliter-Scale Surface-Enhanced Resonance Raman Spectroscopy of Heme Proteins

Surface-enhanced resonance Raman spectra of cytochrome c on silver electrodes coated with self-assembled monolayers of mercaptopropionic acid were recorded at different potentials using 50 microL of a micromolar solution. For this purpose, a linearly moving, low-volume, small spectroelectrochemical cell was designed and used together with a Raman microprobe. The quality of the spectra obtained is good, and the spectra show essentially the same features reported by other authors using much larger volumes. The cell described in this paper is shown to be useful for studying the spectroelectrochemistry of photosensitive compounds such as heme proteins, which are available only in very small amounts (nanomoles to picomoles).

Cys32 and His105 Are the Critical Residues for the Calcium-dependent Cysteine Proteolytic Activity of CvaB, an ATP-binding Cassette Transporter

CvaB, a member of the ATP-binding cassette transporter superfamily, is the central membrane transporter of the colicin V secretion system in Escherichia coli. Cys32 and His105 in the N-terminal domain of CvaB were identified as critical residues for both colicin V secretion and cysteine proteolytic activity. By inhibiting degradation with N-ethylmaleimide and a mixture of protease inhibitors, a stable wild-type N-terminal domain (which showed cysteine protease activity when activated) was purified. Such protease activity was Ca2+- and concentration-dependent and could be inhibited by antipain, N-ethylmaleimide, EDTA, and EGTA. At low concentrations, the Ca2+ analogs Tb3+ and La3+ (but not Fe3+) significantly enhanced proteolytic activity, suggesting that the size of the cations is important for activity. Together with comparisons of the sequences of members of the cysteine protease family, these results indicate that Cys32 and His105 are the critical residues in the CvaB N-terminal domain for the calcium-dependent cysteine protease activity and secretion of colicin V.

Binding of europium(III) ions to RNA stem loops: role of the primary hydration sphere in complex formation

Understanding the process by which RNA molecules fold into stable structures includes study of the role of site-bound metal ions. Because the alkaline earth metal ions typically associated with RNA structure [most often Mg(II)] do not provide convenient spectroscopic signals, replacement with metal ions having spectroscopically useful properties has been a valuable approach. The luminescence properties of the lanthanide(III) series, in particular europium(III), have made them useful in the study of complexation with biomolecules. We review the physical, chemical, and spectroscopic characteristics of Eu(III) that contribute to its value as a probe of RNA-metal ion interactions, and examples of information obtained from studies of Eu(III) bound to small RNA stem loops. Although Eu(III) has similar site preference to Mg(II), luminescence and isothermal titration calorimetry measurements indicate that Ln(III) loses water molecules from the inner hydration sphere more readily than does Mg(II), resulting in more direct coordination between RNA and the metal ion and very different energetics of binding. In some cases, e.g., a GAAA tetraloop, binding appears to occur by a lock and key process; in the same base sequence containing certain deoxynucleoside substitutions that alter loop structure, binding appears to occur by an induced fit process.

Steady-state luminescence investigation of the binding of Eu(III) and Tb(III) ions with synthetic peptides derived from plant thionins

This work reports Eu(III) and Tb(III) luminescence titrations in which the lanthanide ions were used as spectroscopic probes for Ca(II) ions to determine the metal binding ability of Ac-NESVKEEGGW-NH(2) and Ac-NESVKEDGGW-NH(2). These decapeptides correspond to the putative calcium binding region of the plant antifungal proteins SI-alpha1 from Sorghum bicolor and of Zeathionin from Zea mays, respectively. The luminescence spectra for the Eu(III)-decapeptide system (red emission) with the excitation at the Trp band at 280 nm showed an enhancement of the intensities of the 5D(0)-->7F(J) transitions (where J=0-4) with increments of Eu(III) ion concentration. The photoluminescence titration data of the terbium ion (green emission) in the decapeptide solutions showed intensification of the 5D(4)-->7F(J) transitions (J=0-6), similar to that observed for the Eu(III) ion. Thus, energy transfer from Ac-NESVKEEGGW-NH(2) and Ac-NESVKEDGGW-NH(2) to the trivalent lanthanide ions revealed that these peptides are capable of binding to these metal ions with association constants of the order of 10(5) M(-1). The amino acid derivative Ac-Trp-OEt also transferred energy to Tb(III) and Eu(III) ions as judged from the quenching of tryptophan luminescence. However, the energy transfers were significantly lower. Taken together the luminescence titration data indicated that Ac-NESVKEEGGW-NH(2) and Ac-NESVKEDGGW-NH(2) bind efficiently to both trivalent lanthanide ions and that these ions may be used as probes to distinguish an anionic peptide from a neutral amino acid derivative.

Metal-binding studies for a de novo designed calcium-binding protein

To understand the key determinants in calcium-binding affinity, a calcium-binding site with pentagonal bipyramid geometry was designed into a non-calcium-binding protein, domain 1 of CD2. This metal-binding protein has five mutations with a net charge in the coordination sphere of -5 and is termed DEEEE. Fluorescence resonance energy transfer was used to determine the metal-binding affinity of DEEEE to the calcium analog terbium. The addition of protein concentration to Tb(III) solution results in a large enhancement of Tb(III) fluorescence due to energy transfer between terbium ions and aromatic residues in CD2-D1. In addition, both calcium and lanthanum compete with terbium for the same desired metal binding pocket. Our designed protein exhibits a stronger affinity for Tb(III), with a K(d) of 21 microM, than natural calcium-binding proteins with a similar Greek key scaffold.

Calcium binding properties of gamma-crystallin: calcium ion binds at the Greek key beta gamma-crystallin fold

The beta- and gamma-crystallins are closely related lens proteins that are members of the betagamma-crystallin superfamily, which also include many non-lens members. Although beta-crystallin is known to be a calcium-binding protein, this property has not been reported in gamma-crystallin. We have studied the calcium binding properties of gamma-crystallin, and we show that it binds 4 mol eq of calcium with a dissociation constant of 90 microm. It also binds the calcium-mimic spectral probes, terbium and Stains-all. Calcium binding does not significantly influence protein secondary and tertiary structures. We present evidence that the Greek key crystallin fold is the site for calcium ion binding in gamma-crystallin. Peptides corresponding to Greek key motif of gamma-crystallin (42 residues) and their mutants were synthesized and studied for calcium binding. These peptides adopt beta-sheet conformation and form aggregates producing beta-sandwich. Our results with peptides show that, in Greek key motif, the amino acid adjacent to the conserved aromatic corner in the "a" strand and three amino acids of the "d" strand participate in calcium binding. We suggest that the betagamma superfamily represents a novel class of calcium-binding proteins with the Greek key betagamma-crystallin fold as potential calcium-binding sites. These results are of significance in understanding the mechanism of calcium homeostasis in the lens.

Structural characteristics of protein binding sites for calcium and lanthanide ions

Surveys of X-ray structures of Ca2+-containing and lanthanide ion-containing proteins and coordination complexes have been performed and structural features of the metal binding sites compared. A total of 515 structures of Ca2+-containing proteins were considered, although the final data set contained only 44 structures and 60 Ca2+ binding sites with a total of 323 ligands. Eighteen protein structures containing lanthanide ions were considered with a final data set containing eight structures and 11 metal binding sites. Structural features analysed include coordination numbers of the metal ions, the identity of their ligands, the denticity of carboxylate ligands, and the type of secondary structure from which the ligands are derived. Three general types of calcium binding site were identified in the final data set: class I sites supply the Ca2+ ligands from a continuous short sequence of amino acids; class II sites have one ligand supplied by a part of the amino acid sequence far removed from the main binding sequence; and class III sites are created by amino acids remote from one another in the sequence. The abundant EF-hand type of Ca2+ binding site was under-represented in the data set of structures analysed as far as its biological distribution is concerned, but was adequately represented for the chemical survey undertaken. A turn or loop structure was found to provide the bulk of the ligands to Ca2+, but helix and sheet secondary structures are slightly better providers of bidentate carboxylate ligation than turn or loop structures. The average coordination number for Ca2+ was 6.0, though for EF-hand sites it is 7. The average coordination number of a lanthanide ion in an intrinsic protein Ca2+ site was 7.2, but for the adventitious sites was only 4.4. A survey of the Cambridge Structural Database showed there are small-molecule lanthanide complexes with low coordination numbers but it is likely that water molecules, which do not appear in the electron density maps, are present for some lanthanide sites in proteins. A detailed comparison of the well-defined Ca2+ and lanthanide ion binding sites suggests that a reduction of hydrogen bonding associated with the ligating residues of the binding sites containing lanthanide ions may be a response to the additional positive charge of the lanthanide ion. Major structural differences between Ca2+ binding sites with weak and strong binding affinities were not obvious, a consequence of long-range electrostatic interactions and metal ion-induced protein conformational changes modulating affinities.

Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA

BACKGROUND

Bacterial signal recognition particle (SRP), consisting of 4.5S RNA and Ffh protein, plays an essential role in targeting signal-peptide-containing proteins to the secretory apparatus in the cell membrane. The 4.5S RNA increases the affinity of Ffh for signal peptides and is essential for the interaction between SRP and its receptor, protein FtsY. The 4.5S RNA also interacts with elongation factor G (EF-G) in the ribosome and this interaction is required for efficient translation.

RESULTS

We have determined by multiple anomalous dispersion (MAD) with Lu(3+) the 2.7 A crystal structure of a 4.5S RNA fragment containing binding sites for both Ffh and EF-G. This fragment consists of three helices connected by a symmetric and an asymmetric internal loop. In contrast to NMR-derived structures reported previously, the symmetric loop is entirely constituted by non-canonical base pairs. These pairs continuously stack and project unusual sets of hydrogen-bond donors and acceptors into the shallow minor groove. The structure can therefore be regarded as two double helical rods hinged by the asymmetric loop that protrudes from one strand.

CONCLUSIONS

Based on our crystal structure and results of chemical protection experiments reported previously, we predicted that Ffh binds to the minor groove of the symmetric loop. An identical decanucleotide sequence is found in the EF-G binding sites of both 4.5S RNA and 23S rRNA. The decanucleotide structure in the 4.5S RNA and the ribosomal protein L11-RNA complex crystals suggests how 4.5S RNA and 23S rRNA might interact with EF-G and function in translating ribosomes.

Probing non-selective cation binding in the hairpin ribozyme with Tb(III)

Catalysis by the hairpin ribozyme is stimulated by a wide range of both simple and complex metallic and organic cations. This independence from divalent metal ion binding unequivocally excludes inner-sphere coordination to RNA as an obligatory role for metal ions in catalysis. Hence, the hairpin ribozyme is a unique model to study the role of outer-sphere coordinated cations in folding of a catalytically functional RNA structure. Here, we demonstrate that micromolar concentrations of a deprotonated aqueous complex of the lanthanide metal ion terbium(III), Tb(OH)(aq)(2+), reversibly inhibit the ribozyme by competing for a crucial, yet non-selective cation binding site. Tb(OH)(aq)(2+) also reports a likely location of this binding site through backbone hydrolysis, and permits the analysis of metal binding through sensitized luminescence. We propose that the critical cation-binding site is located at a position within the catalytic core that displays an appropriately-sized pocket and a high negative charge density. We show that cationic occupancy of this site is required for tertiary folding and catalysis, yet the site can be productively occupied by a wide variety of cations. It is striking that micromolar Tb(OH)(aq)(2+) concentrations are compatible with tertiary folding, yet interfere with catalysis. The motif implicated here in cation-binding has also been found to organize the structure of multi-helix loops in evolutionary ancient ribosomal RNAs. Our findings, therefore, illuminate general principles of non-selective outer-sphere cation binding in RNA structure and function that may have prevailed in primitive ribozymes of an early "RNA world".

Calcium binding to the photosystem II subunit CP29

We have identified a Ca(2+)-binding site of the 29-kDa chlorophyll a/b-binding protein CP29, a light harvesting protein of photosystem II most likely involved in photoregulation. (45)Ca(2+) binding studies and dot blot analyses of CP29 demonstrate that CP29 is a Ca(2+)-binding protein. The primary sequence of CP29 does not exhibit an obvious Ca(2+)-binding site therefore we have used Yb(3+) replacement to analyze this site. Near-infrared Yb(3+) vibronic side band fluorescence spectroscopy (Roselli, C., Boussac, A., and Mattioli, T. A. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 12897-12901) of Yb(3+)-reconstituted CP29 indicated a single population of Yb(3+)-binding sites rich in carboxylic acids, characteristic of Ca(2+)-binding sites. A structural model of CP29 presents two purported extra-membranar loops which are relatively rich in carboxylic acids, one on the stromae side and one on the lumenal side. The loop on the lumenal side is adjacent to glutamic acid 166 in helix C of CP29, which is known to be the binding site for dicyclohexylcarbodiimide (Pesaresi, P., Sandonà, D., Giuffra, E. , and Bassi, R. (1997) FEBS Lett. 402, 151-156). Dicyclohexylcarbodiimide binding prevented Ca(2+) binding, therefore we propose that the Ca(2+) in CP29 is bound in the domain including the lumenal loop between helices B and C.

Lanthanide Complexes of the alpha-1 Isomer of the [P(2)W(17)O(61)](10-) Heteropolytungstate: Preparation, Stoichiometry, and Structural Characterization by (183)W and (31)P NMR Spectroscopy and Europium(III) Luminescence Spectroscopy

The alpha-1 and alpha-2 [P(2)W(17)O(61)](10)(-) isomers, derivatives of the Wells-Dawson molecule, [alpha-P(2)W(18)O(62)](6)(-), may be useful ligands for stabilizing high-valent metal ions and lanthanides and actinides. However, the potential utility of the [alpha1-P(2)W(17)O(61)](10)(-) ligand has not been realized. Specifically, for the lanthanides, the stoichiometry, structure, and purity of the lanthanide complexes of the [alpha1-P(2)W(17)O(61)](10)(-) isomer are ambiguous. We have prepared lanthanide (Ln) complexes of the [alpha1-P(2)W(17)O(61)](10)(-) isomer in >/=98% isomeric purity, according to (31)P NMR data. (183)W NMR data clearly showed, for the first time, that the C(1) symmetry of the [alpha1-P(2)W(17)O(61)](10)(-) lanthanide complexes was maintained in solution. We determined the stoichiometry of the lanthanide complexes of the [alpha1-P(2)W(17)O(61)](10)(-) isomer in solution by two different methods: a complexometric titration method and excited state lifetime measurements and luminescence titrations for the europium(III) analogue. All experiments show a 1:1 Ln:[alpha1-P(2)W(17)O(61)](10)(-) ratio. The (31)P NMR data showed that the lanthanides with smaller ionic radii (higher charge-size ratio) form stable complexes, even surviving crystallization from hot water. On the other hand, the lanthanum analogues were not stable in solutions of high lithium content. The tetrabutylammonium salt of the [Lu(alpha1-P(2)W(17)O(61))](7)(-) complex showed >/=98% isomeric purity and the C(1) symmetry required for a derivative of [alpha1-P(2)W(17)O(61)](10)(-). Also the tetrabutylammonium cation stabilized the [Lu(alpha1-P(2)W(17)O(61))](7)(-) complex; a mixed tetrabutylammonium, lithium salt was stable in water for weeks according to (31)P NMR spectroscopy.

Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb

Terbium(III) [Tb(III)] was shown to inhibit the hammerhead ribozyme by competing with a single magnesium(II) ion. X-ray crystallography revealed that the Tb(III) ion binds to a site adjacent to an essential guanosine in the catalytic core of the ribozyme, approximately 10 angstroms from the cleavage site. Synthetic modifications near this binding site yielded an RNA substrate that was resistant to Tb(III) binding and capable of being cleaved, even in the presence of up to 20 micromolar Tb(III). It is suggested that the magnesium(II) ion thought to bind at this site may act as a switch, affecting the conformational changes required to achieve the transition state.

Molecular tuning of an EF-hand-like calcium binding loop. Contributions of the coordinating side chain at loop position 3

Calcium binding and signaling orchestrate a wide variety of essential cellular functions, many of which employ the EF-hand Ca2+ binding motif. The ion binding parameters of this motif are controlled, in part, by the structure of its Ca2+ binding loop, termed the EF-loop. The EF-loops of different proteins are carefully specialized, or fine-tuned, to yield optimized Ca2+ binding parameters for their unique cellular roles. The present study uses a structurally homologous Ca2+ binding loop, that of the Escherichia coli galactose binding protein, as a model for the EF-loop in studies examining the contribution of the third loop position to intramolecular tuning. 10 different side chains are compared at the third position of the model EF-loop with respect to their effects on protein stability, sugar binding, and metal binding equilibria and kinetics. Substitution of an acidic Asp side chain for the native Asn is found to generate a 6,000-fold increase in the ion selectivity for trivalent over divalent cations, providing strong support for the electrostatic repulsion model of divalent cation charge selectivity. Replacement of Asn by neutral side chains differing in size and shape each alter the ionic size selectivity in a similar manner, supporting a model in which large-ion size selectivity is controlled by complex interactions between multiple side chains rather than by the dimensions of a single coordinating side chain. Finally, the pattern of perturbations generated by side chain substitutions helps to explain the prevalence of Asn and Asp at the third position of natural EF-loops and provides further evidence supporting the unique kinetic tuning role of the gateway side chain at the ninth EF-loop position.

Characterization of Eu(III) binding to a series of calmodulin binding site mutants using laser-induced Eu(III) luminescence spectroscopy

Laser-induced luminescence techniques were used in a rigorous evaluation of the Eu(3+)-binding behavior of a recombinant (Drosophila melanogaster) calmodulin and a series of calmodulin binding site mutants in which the bidentate glutamic acid residue in position 12 of each metal ion binding loop is systematically replaced with lysine. For the range of Ca2+ concentrations at which calmodulin functions (10(-5)-10(-6) M), Ca2+ binding is effectively eliminated at the mutated site; however, the luminescence studies show that the Eu3+ ion binds to the modified site with reduced affinity. The mutations do not significantly change the intermetal ion distances from their wild type values. These were determined by Eu3+-->Nd3+ Förster-type non-radiative energy transfer experiments. Consistent with the results of Ca(2+)-binding studies, mutation of sites II and IV in the N- and C-terminal domains, respectively, produces a larger alteration in the Eu(3+)-luminescence and Eu(3+)-binding behavior than does mutation of sites I and III. Modification of either of the sites in the C-terminus (III or IV, numbered from the amino terminus) causes two additional H2O molecules (four H2O molecules total) to bind to the Eu3+ ion in order to compensate for the loss of the bidentate glutamic acid residue. Consequently, the partner site in the domain loses an H2O molecule, thereby coordinating another ligand from the protein. Mutation of either of the high-affinity Ln(3+)-binding sites (I or II) has global effects on the Eu(3+)-binding behavior of the protein molecule.

Investigating the effects of posttranslational adenylylation on the metal binding sites of Escherichia coli glutamine synthetase using lanthanide luminescence spectroscopy

Lanthanide luminescence was used to examine the effects of posttranslational adenylylation on the metal binding sites of Escherichia coli glutamine synthetase (GS). These studies revealed the presence of two lanthanide ion binding sites of GS of either adenylylation extrema. Individual emission decay lifetimes were obtained in both H2O and D2O solvent systems, allowing for the determination of the number of water molecules coordinated to each bound Eu3+. The results indicate that there are 4.3 +/- 0.5 and 4.6 +/- 0.5 water molecules coordinated to Eu3+ bound to the n1 site of unadenylylated enzyme, GS0, and fully adenylylated enzyme, GS12, respectively, and that there are 2.6 +/- 0.5 water molecules coordinated to Eu3+ at site n2 for both GS0 and GS12. Energy transfer measurements between the lanthanide donor-acceptor pair Eu3+ and Nd3+, obtained an intermetal distance measurement of 12.1 +/- 1.5 A. Distances between a Tb3+ ion at site n2 and tryptophan residues were also performed with the use of single-tryptophan mutant forms of E. coli GS. The dissociation constant for lanthanide ion binding to site n1 was observed to decrease from Kd = 0.35 +/- 0.09 microM for GS0 to Kd = 0.06 +/- 0.02 microM for GS12. The dissociation constant for lanthanide ion binding to site n2 remained unchanged as a function of adenylylation state; Kd = 3.8 +/- 0.9 microM and Kd = 2.6 +/- 0.7 microM for GS0 and GS12, respectively. Competition experiments indicate that Mn2+ affinity at site n1 decreases as a function of increasing adenylylation state, from Kd = 0.05 +/- 0.02 microM for GS0 to Kd = 0.35 +/- 0.09 microM for GS12. Mn2+ affinity at site n2 remains unchanged (Kd = 5.3 +/- 1.3 microM for GS0 and Kd = 4.0 +/- 1.0 microM for GS12). The observed divalent metal ion affinities, which are affected by the adenylylation state, agrees with other steady-state substrate experiments (Abell LM, Villafranca JJ, 1991, Biochemistry 30:1413-1418), supporting the hypothesis that adenylylation regulates GS by altering substrate and metal ion affinities.

Elucidation of the metal-binding properties of the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase by lanthanide(III) luminescence spectroscopy

BACKGROUND

The exonuclease active site of the Klenow fragment (KF) of Escherichia coli DNA polymerase I has a double binding site for the two essential divalent metal ions in the presence of the nucleotide monophosphate dTMP.

RESULTS

The luminescence spectroscopy observed upon binding of Eu3+ to the exonuclease active site of T4 DNA polymerase was interpreted relative to the binding of Eu3+ or Tb3+ observed with KF. Both wild-type enzymes tightly bind a single Ln3+ ion but in two isomeric forms. The single mutants of KF (D424A) and T4 (D219A) also bind a single Eu3+ ion tightly, but the alignment of the coordinating ligands is altered. The KF double mutant (D355A, E357A) exhibits a markedly altered and weakened binding site (Kd = 20-26 microM). Eu3+ serves as a competitive inhibitor of Mg2+-induced polymerase and exonuclease activity, validating its use as a probe for these active sites.

CONCLUSIONS

Ln3+ luminescence spectroscopy is established as a sensitive way to determine the consequences of exonuclease binding-site mutations and to examine binding site similarities and differences among DNA polymerases from different sources. The binding sites of KF and T4 DNA polymerase are shown to be quite similar.