113Cd NMR spectroscopy of coordination compounds and proteins

Zinc finger structure determination by NMR: Why zinc fingers can be a handful

Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.

Structural and Electronic Studies of Substituted m-Terphenyl Group 12 Complexes

The effects of para-substitution on the structural and electronic properties of four series of two-coordinate m-terphenyl Group 12 complexes (R-Ar^#)₂M (M = Zn, Cd, Hg; R = t-Bu 1–3, SiMe₃4–6, Cl 7–9, CF₃10–12, where R-Ar^# = 2,6-{2,6-Xyl}₂-4-R-C₆H₂ and 2,6-Xyl = 2,6-Me₂C₆H₃) have been investigated. X-ray crystallography shows little structural variation across the series, with no significant change in the C–M–C bond distances and angles. However, considerable electronic differences are revealed by heteronuclear nuclear magnetic resonance (NMR) spectroscopy; a linear correlation is observed between the ¹¹³Cd, ¹⁹⁹Hg, and ¹H (2,6-Xyl methyl protons) NMR chemical shifts of the para-substituted complexes and the Hammett constants for the R-substituents. Specifically, an upfield shift in the NMR signal is observed with increasingly electron-withdrawing R-substituents. Density functional theory (DFT) calculations are employed to attempt to rationalize these trends.

NMR spectroscopy of wastewater: A review, case study, and future potential

NMR spectroscopy is arguably the most powerful tool for the study of molecular structures and interactions, and is increasingly being applied to environmental research, such as the study of wastewater. With over 97% of the planet's water being saltwater, and two thirds of freshwater being frozen in the ice caps and glaciers, there is a significant need to maintain and reuse the remaining 1%, which is a precious resource, critical to the sustainability of most life on Earth. Sanitation and reutilization of wastewater is an important method of water conservation, especially in arid regions, making the understanding of wastewater itself, and of its treatment processes, a highly relevant area of environmental research. Here, the benefits, challenges and subtleties of using NMR spectroscopy for the analysis of wastewater are considered. First, the techniques available to overcome the specific challenges arising from the nature of wastewater (which is a complex and dilute matrix), including an examination of sample preparation and NMR techniques (such as solvent suppression), in both the solid and solution states, are discussed. Then, the arsenal of available NMR techniques for both structure elucidation (e.g., heteronuclear, multidimensional NMR, homonuclear scalar coupling-based experiments) and the study of intermolecular interactions (e.g., diffusion, nuclear Overhauser and saturation transfer-based techniques) in wastewater are examined. Examples of wastewater NMR studies from the literature are reviewed and potential areas for future research are identified. Organized by nucleus, this review includes the common heteronuclei (¹³C, ¹⁵N, ¹⁹F, ³¹P, ²⁹Si) as well as other environmentally relevant nuclei and metals such as ²⁷Al, ⁵¹V, ²⁰⁷Pb and ¹¹³Cd, among others. Further, the potential of additional NMR methods such as comprehensive multiphase NMR, NMR microscopy and hyphenated techniques (for example, LC-SPE-NMR-MS) for advancing the current understanding of wastewater are discussed. In addition, a case study that combines natural abundance (i.e. non-concentrated), targeted and non-targeted NMR to characterize wastewater, along with in vivo based NMR to understand its toxicity, is included. The study demonstrates that, when applied comprehensively, NMR can provide unique insights into not just the structure, but also potential impacts, of wastewater and wastewater treatment processes. Finally, low-field NMR, which holds considerable future potential for on-site wastewater monitoring, is briefly discussed. In summary, NMR spectroscopy is one of the most versatile tools in modern science, with abilities to study all phases (gases, liquids, gels and solids), chemical structures, interactions, interfaces, toxicity and much more. The authors hope this review will inspire more scientists to embrace NMR, given its huge potential for both wastewater analysis in particular and environmental research in general.

Conformational Dynamics from Ambiguous Zinc Coordination in the RanBP2-Type Zinc Finger of RBM5

The multi-domain RNA binding protein RBM5 is a molecular signature of metastasis. RBM5 regulates alternative splicing of apoptotic genes including the cell death receptor Fas and the initiator Caspase-2. The RBM5 RanBP2-type zinc finger (Zf1) is known to specifically recognize single-stranded RNAs with high affinity. Here, we study the structure and conformational dynamics of the Zf1 zinc finger of human RBM5 using NMR. We show that the presence of a non-canonical cysteine in Zf1 kinetically destabilizes the protein. Metal-exchange kinetics show that mutation of the cysteine establishes high-affinity coordination of the zinc. Our data indicate that selection of such a structurally destabilizing mutation during the course of evolution could present an opportunity for functional adaptation of the protein.

Loading across the Periodic Table: Introducing 14 Different Metal Ions To Enhance Metal-Organic Framework Performance

Loading metal guests within metal-organic frameworks (MOFs) via secondary functional groups is a promising route for introducing or enhancing MOF performance in various applications. In this work, 14 metal ions (Li⁺, Na⁺, K⁺, Mg²⁺, Ca²⁺, Ba²⁺, Zn²⁺, Co²⁺, Mn²⁺, Ag⁺, Cd²⁺, La³⁺, In³⁺, and Pb²⁺) have been successfully introduced within the MIL-121 MOF using a cost-efficient route involving free carboxylic groups on the linker. The local and long-range structure of the metal-loaded MOFs is characterized using multinuclear solid-state NMR and X-ray diffraction methods. Li/Mg/Ca-loaded MIL-121 and Ag nanoparticle-loaded MIL-121 exhibit enhanced H₂ and CO₂ adsorption; Ag nanoparticle-loaded MIL-121 also demonstrates remarkable catalytic activity in the reduction of 4-nitrophenol.

Crystalline Superlattices of Nanoscopic CdS Molecular Clusters: An X-ray Crystallography and 111Cd SSNMR Spectroscopy Study

Systematic ¹¹¹Cd solid-state (SS) NMR experiments were performed to correlate X-ray crystallographic data with SSNMR parameters for a set of CdS-based materials, varying from molecular crystals of small complexes [Cd(SPh)₄]^2- and [Cd₄(SPh)₁₀]^2- to superlattices of large monodisperse clusters [Cd₅₄S₃₂(SPh)₄₈(dmf)₄]^4- and 1.9 nm CdS. Methodical data analysis allowed for assigning individual resonances or resonance groups to particular types of cadmium sites residing in different chemical and/or crystallographic environments. For large CdS frameworks, ¹¹¹Cd resonances were found to form three groups. This result is noteworthy, since for related systems with size polydispersity and variations in composition, such as CdS or CdSe nanoparticles protected with an organic ligand shell, typically only two groups of resonances were observed. The generalized information obtained in this work can be used for the interpretation of ^111/113Cd SSNMR data for large CdS clusters and nanoparticles, for which crystal structure analysis remains inaccessible. Comparison of the powder X-ray diffraction patterns for freshly prepared and dried superlattices of large CdS clusters revealed an interesting superstructure rearrangement that was not observed for the smaller frameworks.

Incorporation of second coordination sphere D-amino acids alters Cd(II) geometries in designed thiolate-rich proteins

We use a de Novo protein design strategy to demonstrate that the second coordination sphere of a metal site plays a key role in controlling coordination geometries of Cd(II)-tris-thiolate complexes. Specifically, we show that alteration of chirality within the core hydrophobic packing region of a three-stranded coiled coil (3SCC) can control the coordination number of Cd(II) by limiting steric encumbrance to the metal center. Within a specific class of 3SCCs [Ac-G-(LKALEEK) _n -G-NH₂], where n = 4 is TRI and n = 5 is GRAND, one L-Leu may be substituted by L-Cys to generate a planar tris-thiolate array capable of metal binding. In the native peptide containing only the L-configuration of leucine, the three-Cys ligand site leads to a mixture of 3- and 4-coordinate Cd(II). When the L-Leu above (toward the N-terminus) the tris-Cys site is substituted with D-Leu, solely a 3-coordinate structure [Cd(II)S₃] was obtained. When D-Leu is located below (toward the C-terminus), a mixture of two coordination geometries, presumably Cd(II)S₃O and Cd(II)S₃O₂, is observed, while substitution with D-Leu both above and below the tris-Cys plane yields a higher percentage of 4-coordinate Cd(II)S₃O species. Thus, the use of D-amino acids around a metal's coordination sphere provides a powerful tool for controlling the properties of future designed metalloproteins.

From discrete molecule, to polymer, to MOF: mapping the coordination chemistry of Cd(II) using (113)Cd solid-state NMR

Studies of three related Cd(II) systems (a discrete [Cd(II)2] unit, a one-dimensional [Cd(II)2]n coordination polymer and a Cd(II)-based MOF) all derived from the ligand 2,4,6-tris(2-pyrimidyl)-1,3,5-triazine, reveal an exceptionally rare example of (113)Cd-(113)Cd J coupling in the polymer that is detectable by solid-state NMR ((2)JCd-Cd = ∼65 Hz).

Isoskeletal Schiff base polynuclear coordination clusters: synthetic and theoretical aspects

This work addresses and enlightens synthetic aspects derived from our effort to systematically construct isoskeletal tetranuclear coordination clusters (CCs) of the general formula [TR₂Ln₂(LX)₄(NO₃)₂(solv)₂] possessing a specific defected dicubane topology.

A comparison of the amorphization of zeolitic imidazolate frameworks (ZIFs) and aluminosilicate zeolites by ball-milling

Amorphization of zeolitic imidazolate frameworks during ball-milling is much more rapid than that of aluminosilicate zeolites.

Mechanistic insights into the role of alkylamine in the synthesis of CdSe nanocrystals

This paper reports a detailed mechanistic study of the effect of alkylamine on the synthesis of CdSe nanocrystals. Alkylamines are one of the most important additives for the synthesis of colloidal semiconductor nanocrystals. However, their effect on the monomer production as well as nanocrystal nucleation and growth are not well understood, as indicted by inconsistent and contradictory conclusions in the literature. We found that alkylamines slow down the reaction between cadmium oleate and trialkyl phosphine selenide by binding to cadmium and preventing the activation of trialkyl phosphine selenide. A linear correlation was observed between the observed reaction rate constant and the (31)P NMR chemical shift or (1)J(P-Se) of phosphine selenide. In the presence of alkylamine, an alkylaminophosphonium intermediate was observed. Mechanistic study suggests that the cleavage of P═Se bond is through nucleophilic attack by carboxylate instead of alkylamine. Interestingly, although alkylamines decrease the rate of monomer production, it increases the rate of CdSe nanocrystal growth. Although seemingly contradictory, this is due to a drastic decrease in the nanocrystal nucleation events in the presence of alkylamines. As a result, each nucleus is fed with more monomers and grows faster in the presence of alkylamine than in its absence.

Crystal-to-crystal transformations and photoluminescence changes in the Cu(i) coordination networks based on a formamidinate ligand

While the syn-complexes show broad emission bands, those of the anti-complexes are not detectable, indicating that cuprophilicity is unlikely to play a significant role in determining the emission.

Auxiliary ligand-aided tuning of aggregation of transition metal benzoates: isolation of four different types of coordination polymers

The position of benzoic acid substituents and the ability of the auxiliary ligand to act as a chelating or a bridging ligand drive metal benzoates to assemble either as discrete or as polymeric complexes.

Spectroscopic and mechanistic studies of dinuclear metallohydrolases and their biomimetic complexes

An enhanced understanding of the metal ion binding and active site structural features of phosphoesterases such as the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ), and the organophosphate degrading agent from Agrobacterium radiobacter (OpdA) have important consequences for potential applications. Coupled with investigations of the metalloenzymes, programs of study to synthesise and characterise model complexes based on these metalloenzymes can add to our understanding of structure and function of the enzymes themselves. This review summarises some of our work and illustrates the significance and contributions of model studies to knowledge in the area.

Molecular architecture and therapeutic potential of lectin mimics

Lectins are proteins of non-immune origin that bind specific carbohydrates without chemical modification. Coupled with the emerging biological and pathological significance of carbohydrates, lectins have become extensively used as research tools in glycobiology. However, lectin-based drug development has been impeded by high manufacturing costs, low chemical stability, and the potential risk of initiating an unfavorable immune response. As alternatives to lectins, non-protein small molecules having carbohydrate-binding properties (lectin mimics) are currently attracting a great deal of attention because of their ease of preparation and chemical modification. Lectin mimics of synthetic origin are divided roughly into two groups, boronic acid-dependent and boronic acid-independent lectin mimics. This article outlines their representative architectures and carbohydrate-binding properties, and discusses their therapeutic potential by reviewing recent attempts to develop antiviral and antimicrobial agents using their architectures. We also focus on the naturally occurring lectin mimics, pradimicins and benanomicins. They are the only class of non-protein natural products having a C-type lectin-like ability to recognize d-mannopyranosides in the presence of Ca^2 + ions. Their molecular basis of carbohydrate recognition and therapeutic potential are also discussed.

Lateral cis-1,3,5,7-tetraazadecalin podands and their complexes: synthesis, structure, and strong binding with Pb(II) and other heavy metal ions

The chemistry and complexation behavior of diaminal podands based on cis-1,3,5,7-tetraazadecalin (cis-TAD) were elaborated, reassessed, and extended. The synthesis of 2,6-bis(hydroxymethylene)-cis-TAD (9) and 2,6-bis(α,α'-dimethyl-β- hydroxyethyl)-cis-TAD (10) as well as of suitably substituted 2,6-diaryl-cis-TAD podands is laid out. For the latter, the effect of electron donating or withdrawing substituents on the benzaldehyde reagents was examined while 9 and 10 were probed and showed considerable propensity for heavy metal-ion chelation. The [Cd(II)·(9)] and [Pb(II)·(9)] complexes stood out indeed, and their structure and properties show a particularly interesting 5-amino-1,3-diazane chelation type and strong ligand-ion binding mode, with intramolecular donor exchange in solution, all strongly influenced by the anomeric effect in the ligand.

Lessons on the critical interplay between zinc binding and protein structure and dynamics

Zinc is one of the most important micronutrients for virtually all living organisms, and hence, it is important to understand the molecular mechanisms for its homeostasis. Besides proteins involved in transmembrane transport, both extra- and intracellular zinc-binding proteins play important roles in the respective metabolic networks. Important examples for extracellular zinc transporters are mammalian serum albumins, and for intracellular zinc handling, certain metallothioneins are of relevance. The availability of protein structures including relevant metal binding sites is a fundamental prerequisite to decipher the mechanisms that govern zinc binding dynamics in these proteins, but their determination can prove to be surprisingly challenging. Due to the spectroscopic silence of Zn(2+), combinations of biophysical techniques including electrospray ionisation mass spectrometry (ESI-MS) and multinuclear NMR, isothermal titration calorimetry (ITC) and extended X-ray absorption fine structure (EXAFS) spectroscopy, coupled with site-directed mutagenesis and molecular modelling have proven to be valuable approaches to understand not only the zinc-binding properties of metallothioneins and albumins, but also the influence of other physiologically relevant competing agents. These studies have demonstrated why the bacterial metallothionein SmtA contains a site inert towards exchange with Cd(2+), why the plant metallothionein EC from wheat is partially unfolded in the presence of Cd(2+), and how fatty acids impact on the zinc-binding ability of mammalian serum albumins.

Natural and artificial proteins containing cadmium

This chapter describes an approach using designed proteins to understand the structure, spectroscopy, and dynamics of proteins that bind Cd(II). We will show that three-stranded coiled coils (3SCCs) based on the parent peptides TRI (Ac-G(LKALEEK)(4)G-NH(2)) or GRAND (Ac-G(LKALEEK)(5)G-NH(2)) have been essential for understanding how Cd(II) binds to thiolate-rich environments in proteins. Examples are given correlating physical properties such as the binding constants or deprotonation constants relating to structure. We present a scale that relates (113)Cd NMR chemical shifts to structures extracted from (111m)Cd PAC experiments. In addition, we describe motional processes that help transport from the helical interface of proteins into the hydrophobic interior of helical bundles. These studies help clarify the chemistry of Cd(II) in relation to metal-regulated gene expression and detoxification.

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

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

Pseudopeptidic ligands: exploring the self-assembly of isophthaloylbisglycine (H2IBG) and divalent metal ions

We present a systematic study of the complexation of the new pseudopeptidic ligand isophthaloylbisglycine (H(2)IBG) with divalent metal ions of varying ionic radius. This work represents the initial employment of H(2)IBG in the coordination chemistry of alkaline earth, 3d transition, Zn(II) and Cd(II) metal elements. Infrared, NMR, thermal, magnetic, adsorption and theoretical studies of these compounds are also discussed.

Cadmium(II) complex formation with selenourea and thiourea in solution: an XAS and 113Cd NMR study

The complexes formed in methanol solutions of Cd(CF(3)SO(3))(2) with selenourea (SeU) or thiourea (TU), for thiourea also in aqueous solution, were studied by combining (113)Cd NMR and X-ray absorption spectroscopy. At low temperature (~200 K), distinct (113)Cd NMR signals were observed, corresponding to CdL(n)(2+) species (n = 0-4, L = TU or SeU) in slow ligand exchange. Peak integrals were used to obtain the speciation in the methanol solutions, allowing stability constants to be estimated. For cadmium(II) complexes with thione (C═S) or selone (C═Se) groups coordinated in Cd(S/Se)O(5) or Cd(S/Se)(2)O(4) (O from MeOH or CF(3)SO(3)(-)) environments, the (113)Cd chemical shifts were quite similar, within 93-97 ppm and 189-193 ppm, respectively. However, the difference in the chemical shift for the Cd(SeU)(4)(2+) (578 pm) and Cd(TU)(4)(2+) (526 ppm) species, with CdSe(4) and CdS(4) coordination, respectively, shows less chemical shielding for the coordinated Se atoms than for S, in contrast to the common trend with increasing shielding in the following order: O > N > Se > S. In solutions dominated by mono- and tetra-thiourea/selenourea complexes, their coordination and bond distances could be evaluated by Cd K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy. At ~200 K and high excess of thiourea, a minor amount (up to ~30%) of [Cd(TU)(5-6)](2+) species was detected by an upfield shift of the (113)Cd NMR signal (up to 423 ppm) and an amplitude reduction of the EXAFS oscillation. The amount was estimated by fitting linear combinations of simulated EXAFS spectra for [Cd(TU)(4)](2+) and [Cd(TU)(6)](2+) complexes. At room temperature, [Cd(TU)(4)](2+) was the highest complex formed, also in aqueous solution. Cd L(3)-edge X-ray absorption near edge structure (XANES) spectra of cadmium(II) thiourea solutions in methanol were used to follow changes in the CdS(x)O(y) coordination. The correlations found from the current and previous studies between (113)Cd NMR chemical shifts and different Cd(II) coordination environments are generally useful for evaluating cadmium coordination to thione-containing or Se-donor ligands in biochemical systems or for monitoring speciation in solution.

Synthesis, characterization, thermal and antioxidant studies of potassium dihydrobisphenothiazinyl borate and its transition metal complexes

The bidentate borate anion H(2)B(ptz)(2)(-) and its transition metal complexes have been synthesized and characterized by elemental analyses, magnetic susceptibility, electronic, IR, (1)H and (13)C NMR data. The molar conductance of 10(-3) M solution for all the complexes supports their non-ionic nature. The TGA profile of borate anion shows a single stage unlike that of two stage decomposition plot of the metal complexes. On the basis of spectroscopic studies the geometry of all the complexes have been proposed to be distorted-tetrahedral. The in vitro antioxidant and lipid oxidation inhibition of the ligand and its complexes have also been studied. The Cu[B(ptz)(2)](2) complex was found to be most effective in all the studies.

Cd2+ complex of a triazole-based calix[4]arene conjugate as a selective fluorescent chemosensor for Cys

An N,N-Dimethylamine ethylimino-appended triazole-linked calix[4]arene conjugate, L, has been synthesized and characterized, and its Cd(2+) complex has been isolated and characterized. The structure of [CdL] was established by computational calculation using B3LYP/LANL2DZ. Time-dependent density functional theory calculations were performed to demonstrate the electronic properties of [CdL]. This highly fluorescing [CdL] has been used to recognize Cys selectively among the 20 naturally occurring amino acids. [CdL] exhibits a minimum detection limit of 58 ppb for Cys, with reusability and reversibility being imparted to the system during sensing. Thus, the sensing of Cys was well demonstrated using various techniques, viz., fluorescence, absorption, visual color change, electrospray ionization MS, (1)H NMR, and live cell imaging experiments.

Experimental and theoretical evaluation of multisite cadmium(II) exchange in designed three-stranded coiled-coil peptides

An important factor that defines the toxicity of elements such as cadmium(II), mercury(II), and lead(II) with biological macromolecules is metal ion exchange dynamics. Intriguingly, little is known about the fundamental rates and mechanisms of metal ion exchange into proteins, especially helical bundles. Herein, we investigate the exchange kinetics of Cd(II) using de novo designed three-stranded coiled-coil peptides that contain metal complexing cysteine thiolates as a model for the incorporation of this ion into trimeric, parallel coiled coils. Peptides were designed containing both a single Cd(II) binding site, GrandL12AL16C [Grand = AcG-(LKALEEK)(5)-GNH(2)], GrandL26AL30C, and GrandL26AE28QL30C, as well as GrandL12AL16CL26AL30C with two Cd(II) binding sites. The binding of Cd(II) to any of these sites is of high affinity (K(A) > 3 × 10(7) M(-1)). Using (113)Cd NMR spectroscopy, Cd(II) binding to these designed peptides was monitored. While the Cd(II) binding is in extreme slow exchange regime without showing any chemical shift changes, incremental line broadening for the bound (113)Cd(II) signal is observed when excess (113)Cd(II) is titrated into the peptides. Most dramatically, for one site, L26AL30C, all (113)Cd(II) NMR signals disappear once a 1.7:1 ratio of Cd(II)/(peptide)(3) is reached. The observed processes are not compatible with a simple "free-bound" two-site exchange kinetics at any time regime. The experimental results can, however, be simulated in detail with a multisite binding model, which features additional Cd(II) binding site(s) which, once occupied, perturb the primary binding site. This model is expanded into differential equations for five-site NMR chemical exchange. The numerical integration of these equations exhibits progressive loss of the primary site NMR signal without a chemical shift change and with limited line broadening, in good agreement with the observed experimental data. The mathematical model is interpreted in molecular terms as representing binding of excess Cd(II) to surface Glu residues located at the helical interfaces. In the absence of Cd(II), the Glu residues stabilize the three-helical structure though salt bridge interactions with surface Lys residues. We hypothesize that Cd(II) interferes with these surface ion pairs, destabilizing the helical structure, and perturbing the primary Cd(II) binding site. This hypothesis is supported by the observation that the Cd(II)-excess line broadening is attenuated in GrandL26AE28QL30C, where a surface Glu(28), close to the metal binding site, was changed to Gln. The external binding site may function as an entry pathway for Cd(II) to find its internal binding site following a molecular rearrangement which may serve as a basis for our understanding of metal complexation, transport, and exchange in complex native systems containing α-helical bundles.

Towards the role of metal ions in the structural variability of proteins: CdII speciation of a metal ion binding loop motif

A de novo designed dodecapeptide (HS), inspired by the metal binding loops of metal-responsive transcriptional activators, was synthesized. The aim was to create a model system for structurally promiscuous and intrinsically unstructured proteins, and explore the effect of metal ions on their structure and dynamics. The interaction with Cd(II) was investigated by UV, synchrotron radiation CD, (1)H NMR, and perturbed angular correlation (PAC) of γ-rays spectroscopy, pH-potentiometry, and molecular modelling. The peptide mainly displays characteristics of random coil in the CD spectra, and the molecular dynamics simulations demonstrate that it is unstructured with transient and varying helical content. The spectroscopic studies revealed the formation of loop structures with the coordination of the two Cys-thiolates close to each end of the HS peptide, in the presence of one equivalent of Cd(II) per ligand. The imidazole moiety from histidine is also bound to Cd(II) at neutral pH and above. In the presence of 0.5 equivalent of Cd(II) per HS metal bridged structures with e.g. CdS(2)N(2) and possibly CdS(4) coordination geometries are formed above pH ~6. In an equilibrium of several co-existing species the peptide is exchanging between a number of structures also in its metal ion bound state(s), as indicated by NMR and PAC data.