Metallocyclopeptide complexes with MII(S.Cys)4 chromophores

Methods to identify and characterize iron-sulfur oligopeptides in water

Iron-sulfur clusters are ubiquitous cofactors that mediate central biological processes. However, despite their long history, these metallocofactors remain challenging to investigate when coordinated to small (≤ six amino acids) oligopeptides in aqueous solution. In addition to being often unstable in vitro, iron-sulfur clusters can be found in a wide variety of forms with varied characteristics, which makes it difficult to easily discern what is in solution. This difficulty is compounded by the dynamics of iron-sulfur peptides, which frequently coordinate multiple types of clusters simultaneously. To aid investigations of such complex samples, a summary of data from multiple techniques used to characterize both iron-sulfur proteins and peptides is provided. Although not all spectroscopic techniques are equally insightful, it is possible to use several, readily available methods to gain insight into the complex composition of aqueous solutions of iron-sulfur peptides.

The curious case of peptide-coordinated iron-sulfur clusters: prebiotic and biomimetic insights

Iron-sulfur clusters are among the most ancient biological cofactors and are thought to have had an ancient role in mediating the chemical reactions that led to life. Two different, yet complementary approaches, based on bioinorganic chemistry and prebiotic chemistry, have already provided important clues for the formation and activity of biomimetic iron-sulfur analogues in aqueous solution. This frontier article discusses the efforts spent in the last 50 years in the context of peptide-coordinated iron-sulfur clusters, with a particular emphasis on insightful contributions from recent prebiotic chemistry research.

Nickel−Cysteine Binding Supported by Phosphine Chelates

The effect of chelating phosphines was tested on the structure and pH-dependent stability of nickel-cysteine binding. (1,2-Bis(diphenylphosphino)ethane (dppe) and 1,1,1-tris[(diphenylphosphino)methyl]ethane (triphos) were used with three different cysteine derivatives (L-cysteine, Cys; L-cysteine ethyl ester, CysEt; cystamine, CysAm) to prepare complexes of the form (dppe)NiCysR(n+) and (triphos)NiCysR(n+) (n = 0 for Cys; n = 1 for CysEt and CysAm). Similar 31P {1H} NMR spectra for all (dppe)NiCysRn+ confirmed their square-planar P2NiSN coordination spheres. The structure of [(dppe)NiCysAm]PF6 was also confirmed by single-crystal X-ray diffraction methods. The (triphos)NiCysAm+ and (triphos)NiCysEt+ complexes were fluxional at room temperature by 31P NMR. Upon cooling to -80 degrees C, all gave spectra consistent with a P2NiSN coordination sphere with the third phosphorus uncoordinated. Temperature-dependent 31P NMR spectra showed that a trans P-Ni-S pi interaction controlled the scrambling of the coordinated triphos. In aqueous media, (dppe)NiCys was protonated at pH approximately 4-5, leading to possible formation of a nickel-cysteinethiol and eventual cysteine loss at pH < 3. The importance of N-terminus cysteine in such complexes was demonstrated by preparing (dppe)NiCys-bead and trigonal-bipyramidal Tp*NiCys-bead complexes, where Cys-bead represents cysteine anchored to polystyrene synthesis beads and Tp*- = hydrotris(3,5-dimethylpyrazolyl)borate. Importantly, results with these heterogeneous systems demonstrated the selectivity of these nickel centers for cysteine over methionine and serine and most specifically for N-terminus cysteine. The role of Ni-S pi bonding in nickel-cysteine geometries will be discussed, including how these results suggest a mechanism for the movement of electron density from nickel onto the backbone of coordinated cysteine.

Description of the ground-state covalencies of the bis(dithiolato) transition-metal complexes from X-ray absorption spectroscopy and time-dependent density-functional calculations

The electronic structures of [M(L(Bu))(2)](-) (L(Bu)=3,5-di-tert-butyl-1,2-benzenedithiol; M=Ni, Pd, Pt, Cu, Co, Au) complexes and their electrochemically generated oxidized and reduced forms have been investigated by using sulfur K-edge as well as metal K- and L-edge X-ray absorption spectroscopy. The electronic structure content of the sulfur K-edge spectra was determined through detailed comparison of experimental and theoretically calculated spectra. The calculations were based on a new simplified scheme based on quasi-relativistic time-dependent density functional theory (TD-DFT) and proved to be successful in the interpretation of the experimental data. It is shown that dithiolene ligands act as noninnocent ligands that are readily oxidized to the dithiosemiquinonate(-) forms. The extent of electron transfer strongly depends on the effective nuclear charge of the central metal, which in turn is influenced by its formal oxidation state, its position in the periodic table, and scalar relativistic effects for the heavier metals. Thus, the complexes [M(L(Bu))(2)](-) (M=Ni, Pd, Pt) and [Au(L(Bu))(2)] are best described as delocalized class III mixed-valence ligand radicals bound to low-spin d(8) central metal ions while [M(L(Bu))(2)](-) (M=Cu, Au) and [M(L(Bu))(2)](2-) (M=Ni, Pd, Pt) contain completely reduced dithiolato(2-) ligands. The case of [Co(L(Bu))(2)](-) remains ambiguous. On the methodological side, the calculation led to the new result that the transition dipole moment integral is noticeably different for S(1s)-->valence-pi versus S(1s)-->valence-sigma transitions, which is explained on the basis of the differences in radial distortion that accompany chemical bond formation. This is of importance in determining experimental covalencies for complexes with highly covalent metal-sulfur bonds from ligand K-edge absorption spectroscopy.

Model peptides based on the binding loop of the copper metallochaperone Atx1: selectivity of the consensus sequence MxCxxC for metal ions Hg(II), Cu(I), Cd(II), Pb(II), and Zn(II)

The amino acid sequence MxCxxC is conserved in many soft-metal transporters that are involved in the control of the intracellular concentration of ions such as Cu(I), Hg(II), Zn(II), Cd(II), and Pb(II). A relevant task is thus the selectivity of the motif MxCxxC for these different metal ions. To analyze the coordination properties and the selectivity of this consensus sequence, we have designed two model peptides that mimic the binding loop of the copper chaperone Atx1: the cyclic peptide P(C) c(GMTCSGCSRP) and its linear analogue P(L) (Ac-MTCSGCSRPG-NH2). By using complementary analytical and spectroscopic methods, we have demonstrated that 1:1 complexes are obtained with Cu(I) and Hg(II), whereas 1:1 and 1:2 (M:P) species are successively formed with Zn(II), Cd(II), and Pb(II). The complexation properties of the cyclic and linear peptides are very close, but the cyclic compound provides systematically higher affinity constants than its unstructured analogue. The introduction of a xPGx motif that forms a type II beta turn in P(C) induces a preorganization of the binding loop of the peptide that enhances the stabilities of the complexes (up to 2 orders of magnitude difference for the Hg complexes). The affinity constants were measured in the absence of any reducing agent that would compete with the peptides and range in the order Hg(II) > Cu(I) >> Cd(II) > Pb(II) > Zn(II). This sequence is thus highly selective for Cu(I) compared to the essential ion Zn(II) that could compete in vivo or compared to the toxic ions Cd(II) and Pb(II). Only Hg(II) may be an efficient competitor of Cu(I) for binding to the MxCxxC motif in metalloproteins.

Femtomolar Zn(II) affinity in a peptide-based ligand designed to model thiolate-rich metalloprotein active sites

Metal-ligand interactions are critical components of metalloprotein assembly, folding, stability, electrochemistry, and catalytic function. Research over the past 3 decades on the interaction of metals with peptide and protein ligands has progressed from the characterization of amino acid-metal and polypeptide-metal complexes to the design of folded protein scaffolds containing multiple metal cofactors. De novo metalloprotein design has emerged as a valuable tool both for the modular synthesis of these complex metalloproteins and for revealing the fundamental tenets of metalloprotein structure-function relationships. Our research has focused on using the coordination chemistry of de novo designed metalloproteins to probe the interactions of metal cofactors with protein ligands relevant to biological phenomena. Herein, we present a detailed thermodynamic analysis of Fe(II), Co(II), Zn(II), and[4Fe-4S]2(+/+) binding to IGA, a 16 amino acid peptide ligand containing four cysteine residues, H2N-KLCEGG-CIGCGAC-GGW-CONH2. These studies were conducted to delineate the inherent metal-ion preferences of this unfolded tetrathiolate peptide ligand as well as to evaluate the role of the solution pH on metal-peptide complex speciation. The [4Fe-4S]2(+/+)-IGA complex is both an excellent peptide-based synthetic analogue for natural ferredoxins and is flexible enough to accommodate mononuclear metal-ion binding. Incorporation of a single ferrous ion provides the FeII-IGA complex, a spectroscopic model of a reduced rubredoxin active site that possesses limited stability in aqueous buffers. As expected based on the Irving-Williams series and hard-soft acid-base theory, the Co(II) and Zn(II) complexes of IGA are significantly more stable than the Fe(II) complex. Direct proton competition experiments, coupled with determinations of the conditional dissociation constants over a range of pH values, fully define the thermodynamic stabilities and speciation of each MII-IGA complex. The data demonstrate that FeII-IGA and CoII-IGA have formation constant values of 5.0 x 10(8) and 4.2 x 10(11) M-1, which are highly attenuated at physiological pH values. The data also evince that the formation constant for ZnII-IGA is 8.0 x 10(15) M-1, a value that exceeds the tightest natural protein Zn(II)-binding affinities. The formation constant demonstrates that the metal-ligand binding energy of a ZnII(S-Cys)4 site can stabilize a metalloprotein by -21.6 kcal/mol. Rigorous thermodynamic analyses such as those demonstrated here are critical to current research efforts in metalloprotein design, metal-induced protein folding, and metal-ion trafficking.

Structural, spectroscopic and magnetic properties of M[R2P(E)NP(E)R′2]2complexes, M = Co, Mn, E = S, Se and R, R′ = Ph oriPr. Covalency of M–S bonds from experimental data and theoretical calculations

The S/Se-containing bidentate ligands LH of the type R2P(E)NHP(E)R'2, E = S, Se and R, R' = Ph or iPr have been employed to synthesize ML2 (M = Mn, Co) complexes which contain the biologically important MS4 core. Theoretical calculations on the LH and L- forms of the ligands probe the geometric and electronic changes induced by the deprotonation of the LH form, which are correlated with structural data from X-ray crystallography. These results reflect the flexibility of the ligands, which enables them to be rather versatile with respect to the formation of ML2 complexes with varied geometries and MEPNPE metallacycle conformations. A series of old and new ML2 complexes have been synthesized and their structural, spectroscopic and magnetic properties characterized in detail. The nephelauxetic ratio beta of the CoL2 complexes provides evidence of covalent interactions, whereas the EPR properties of the MnL2 complexes are interpreted on the basis of predominant ionic interactions, between the metal center and the ligands, respectively. Additional evidence for the existence of covalent interactions in the CoL2 complexes (R = Ph, iPr, or mixed Ph/iPr), is offered by comparisons between their 31P NMR. The aforementioned notations are supported by extensive theoretical calculations on the ML2 (E = S, R = Me) modelled structures, which probe the covalent and ionic character of the M-S bonds when M = Co or Mn. Wider implications of the findings of the present study on the M-S covalency and its importance in the active sites of various metalloenzymes are also discussed.

De novo design of a redox-active minimal rubredoxin mimic

Metal-binding sites in metalloproteins frequently occur at the interfaces of elements of secondary structure, which has enabled the retrostructural analysis of natural proteins and the de novo design of helical bundles that bind metal ion cofactors. However, the design of metalloproteins containing beta-structure is less well developed, despite the frequent occurrence of beta-conformations in natural metalloproteins. Here, we describe the design and construction of a beta-protein, RM1, that forms a stable, redox-active 4-Cys thiolate Fe(II/III) site analogous to the active site of rubredoxin. The protein folds into a beta-structure in the presence and absence of metal ions and binds Fe(II/III) to form a redox-active site that is stable to repeated cycles of oxidation and reduction, even in an aerobic environment.

Metal-Binding Properties of the Peptide APP170-188: A Model of the ZnII-Binding Site of Amyloid Precursor Protein (APP)

Amyloid precursor protein (APP) plays a key role in Alzheimer's disease (AD), although the function of this membrane protein is still unclear. Metal ions are implicated in AD and they also interact with APP. APP possesses a strong ZnII binding site, which is evolutionary conserved. In this paper a synthetic peptide, APP170-188, with a sequence corresponding to the conserved ZnII-binding domain of APP, was synthesised and its metal-binding properties analysed. Titration experiments pointed to the binding of a stoichiometric amount of divalent ions. Further studies indicated that the binding of divalent metals like ZnII, CdII and CoII induces the dimerisation of the peptide. This dimer contains a dinuclear cluster in which the two divalent metals are bridged by two thiolate ligands from cysteine residues. The other two ligands of the tetrahedral coordination sites of each metal ion are terminal thiolate ligands. This structure was supported by the following arguments. The complex formed with CoII presents the characteristic features for tetrahedral tetrathiolate coordination in its UV-visible spectrum. The sequence of APP170-188 contains only three cysteine residues, which is incompatible with a monomeric CoII-APP170-188 complex. EPR measurements of the complex with one equivalent of CoII show almost no signal at 4 K, which is compatible with an antiferromagnetic spin-coupling of the metal ions in a cluster structure. Size-exclusion chromatography indicated that the elution time for the complexes with ZnII and CdII corresponds to the expected molecular weight of a dimer. The circular dichroism (CD) spectrum of the complex with one equivalent of CdII shows a band at 265 nm+, and an ellipticity similar to those observed for similar CdII-thiolate clusters. Possible biological implications of the ZnII binding site and the metal-induced dimerisation are discussed.

Comparison of cysteine and penicillamine ligands in a Co(II) maquette

l-Penicillamine (Pen) has been investigated as a ligand for metalloprotein design by examining the binding of Co(II) to the sequence NH(2)-KL(Pen)EGG.(Pen)IG(Pen)GA(Pen).GGW-CONH(2). For comparison, we have studied Co(II) binding to the analogous sequence with Cys ligands, the ferredoxin maquette ligand IGA that was originally designed to bind a [4Fe-4S] cluster. The Co(II) affinity and UV-vis spectroscopic properties of IGA indicate formation of a pseudotetrahedral tetrathiolate ligated Co(II). In contrast, IGA-Pen showed formation of a pseudotetrahedral complex with Co(II) bound by three Pen ligands and an exogenous H(2)O. EXAFS data on both Co(II) complexes confirms not only the proposed primary coordination spheres but also shows six Co(II)-C(beta) methyl group distances in Co(II)-IGA-Pen. These results demonstrate that ligand sterics in simple peptides can be designed to provide asymmetric coordination spheres such as those commonly observed in natural metalloproteins.

Cobalt(II) and zinc(II) binding to a ferredoxin maquette

We have examined the Co(II) and Zn(II) affinity of the prototype ferredoxin maquette ligand, NH(2)-KLCEGG.CIACGAC.GGW-CONH2 (IAA), which was originally designed to bind a [4Fe-4S] cluster. UV-Vis spectroscopy demonstrates tight 1:1 complex formation between Co(II) and IAA. The intensity of the S-->Co(II) charge transfer bands at 304 and 340 nm and the ligand field bands between 630 and 728 nm indicate Co(II) coordination by the four cysteine thiolates of IAA in a pseudo-tetrahedral geometry. A dissociation constant value of 5.3 microM was determined for the Co(II)-IAA complex at pH 6.5. Zn(II) readily displaces Co(II) from IAA as evinced by loss of the Co(II) spectral features. The dissociation constant for Zn(II), 20 pM at pH 6.5, was determined be competition experiments with Co(II)-IAA. These results demonstrate that the ferredoxin maquette ligand is an excellent ligand for Zn(II).

Cys-Gly-Cys Tripeptide Complexes of Nickel: Binuclear Analogues for the Catalytic Site in Acetyl Coenzyme A Synthase

The tripeptide, Ac-CysGlyCys-CONH2, is utilized as a ligand to bind Ni in a fashion identical to that found at the active site of acetyl coenzyme A synthase. The Ni-peptide construct is a suitable metalloligand for the preparation of larger structures formed via bridging Cys side chains. The complexes Ni(CysGlyCys)Ni(dppe) and Ni(CysGlyCys)Ni(depe) serve as close structural representations for the binuclear subcluster, exhibiting electrochemical properties that demonstrate facile access to the reduced mixed valent Ni(II)Ni(I) state, which binds CO.

Structural characterization of metallopeptides designed as scaffolds for the stabilization of nickel(II)-Fe(4)S(4) bridged assemblies by X-ray absorption spectroscopy

In earlier work, de novo designed peptides with a helix-loop-helix motif and 63 residues have been synthesized as potential scaffolds for stabilization of the [Ni(II)-X-Fe(4)S(4)] bridged assembly that is the spectroscopically deduced structure of the A-Cluster in clostridial carbon monoxide dehydrogenase. The 63mers contain a consensus tricysteinyl ferredoxin domain in the loop for binding an Fe(4)S(4) cluster and Cys and His residues proximate to the loop for binding Ni(II), with one Cys residue designed as the bridge X. The metallopeptides HC(4)H(2)-[Fe(4)S(4)]-Ni and HC(5)H-[Fe(4)S(4)]-M, containing three His and one Cys residue for Ni(II) coordination and two His and two Cys residues for binding M = Ni(II) and Co(II), have been examined by Fe-, Ni-, and Co-K edge spectroscopy and EXAFS. All peptides bind an [Fe(4)S(4)](2+) cubane-type cluster. Interpretation of the Ni and Co data is complicated by the presence of a minority population of six-coordinate species with low Z ligands, designated for simplicity as [M(OH(2))(6)](2+). Best fits of the data were obtained with ca. 20% [M(OH(2))(6)](2+) and ca. 80% M(II) with mixed N/S coordination. The collective XAS results for HC(4)H(2)-[Fe(4)S(4)]-Ni and HC(5)H-[Fe(4)S(4)]-M demonstrate the presence of an Fe(4)S(4) cluster and support the existence of the distorted square-planar coordination units [Ni(II)(S.Cys)(N.His)(3)] and [Ni(II)(S.Cys)(2)(N.His)(2)] in the HC(4)H(2) and HC(5)H metallopeptides, respectively. In the HC(5)H metallopeptide, tetrahedral [Co(II)(S.Cys)(2)(N.His)(2)] is present. We conclude that the designed scaffolded binding sites, including Ni-(mu(2)-S.Cys)-Fe bridges, have been achieved. This is the first XAS study of a de novo designed metallopeptide intended to stabilize a bridged biological assembly, and one of a few XAS analyses of metal derivatives of designed peptides. The scaffolding concept should be extendable to other bridged metal assemblies.

Helix-loop-helix peptides as scaffolds for the construction of bridged metal assemblies in proteins: the spectroscopic A-cluster structure in carbon monoxide dehydrogenase

Four helix-loop-helix 63mer peptides were designed and synthesized in order to assess the utility of peptides as scaffolds for the stabilization of complex metal sites in proteins. Bridged assembly [Ni(II)-(mu(2)-S.Cys)-Fe(4)S(4)], consistent with spectroscopic information on the A-cluster of carbon monoxide dehydrogenase, was chosen as the target assembly. The peptides consist of two helices with approximately 20 residues connected by a flexible loop containing the ferredoxin consensus sequence Cys-Ile-Ala-Cys-Gly-Ala-Cys to bind the Fe(4)S(4) cluster. A fourth cysteine was positioned to serve as the bridging ligand between the cluster and Ni(II). Three other binding residues were incorporated in appropriate positions to constitute a binding site for Ni(II). One of the peptides was designed with an N(3)S (His(3)Cys) site, and each of the other three with N(2)S(2) (His(2)Cys(2)) sites. A detailed account of the synthesis and characterization of the peptides and their metalloderivatives is presented. The four peptides were synthesized using an Fmoc/t-Bu-based solid-phase strategy, purified by reversed-phase HPLC, and characterized by ES-MS. On the basis of size-exclusion chromatography and circular dichroism spectropolarimetry, these peptides appear to dimerize in solution to form four-helix bundles of high helical contents. Reactions of the peptides with preformed cluster [Fe(4)S(4)(SCH(2)CH(2)OH)(4)](2)(-) and subsequent purification by column chromatography yield a product consistent with the incorporation of one [Fe(4)S(4)](2+) cluster per 63mer, as judged from absorption and Mössbauer spectra. Addition of a Ni(II) salt to the [Fe(4)S(4)]-peptides results in an apparent equilibrium between free Ni(II) and a peptide-bound nickel form, as established by column chromatography studies. Nickel EXAFS data (Musgrave, K. B.; Laplaza, C. E.; Holm, R. H.; Hedman, B.; Hodgson, K. O. Results to be published.) provide strong evidence that the peptide-bound nickel binds in the desired site in two of the metallopeptides. This work represents the first exploration of peptides as scaffolds for the support of biologically relevant bridged assemblies containing iron-sulfur clusters.

Absence of Mn-centered oxidation in the S(2) --> S(3) transition: implications for the mechanism of photosynthetic water oxidation

A key question for the understanding of photosynthetic water oxidation is whether the four oxidizing equivalents necessary to oxidize water to dioxygen are accumulated on the four Mn ions of the oxygen-evolving complex (OEC), or whether some ligand-centered oxidations take place before the formation and release of dioxygen during the S(3) --> [S(4)] --> S(0) transition. Progress in instrumentation and flash sample preparation allowed us to apply Mn Kbeta X-ray emission spectroscopy (Kbeta XES) to this problem for the first time. The Kbeta XES results, in combination with Mn X-ray absorption near-edge structure (XANES) and electron paramagnetic resonance (EPR) data obtained from the same set of samples, show that the S(2) --> S(3) transition, in contrast to the S(0) --> S(1) and S(1) --> S(2) transitions, does not involve a Mn-centered oxidation. On the basis of new structural data from the S(3)-state, manganese mu-oxo bridge radical formation is proposed for the S(2) --> S(3) transition, and three possible mechanisms for the O-O bond formation are presented.

Absence of Mn-centered oxidation in the S(2) --> S(3) transition: implications for the mechanism of photosynthetic water oxidation

A key question for the understanding of photosynthetic water oxidation is whether the four oxidizing equivalents necessary to oxidize water to dioxygen are accumulated on the four Mn ions of the oxygen-evolving complex (OEC), or whether some ligand-centered oxidations take place before the formation and release of dioxygen during the S(3) --> [S(4)] --> S(0) transition. Progress in instrumentation and flash sample preparation allowed us to apply Mn Kbeta X-ray emission spectroscopy (Kbeta XES) to this problem for the first time. The Kbeta XES results, in combination with Mn X-ray absorption near-edge structure (XANES) and electron paramagnetic resonance (EPR) data obtained from the same set of samples, show that the S(2) --> S(3) transition, in contrast to the S(0) --> S(1) and S(1) --> S(2) transitions, does not involve a Mn-centered oxidation. On the basis of new structural data from the S(3)-state, manganese mu-oxo bridge radical formation is proposed for the S(2) --> S(3) transition, and three possible mechanisms for the O-O bond formation are presented.

Designing metal-peptide models for protein structure and function

Recent progress in the rational design of metal sites within peptide model systems shows increasing control in the placement of metals within helical bundles and inclusion of sophisticated elements such as second-sphere ligand interactions. A crystallographically characterized two-metal peptide model for diiron proteins represents a major achievement in de novo design methodologies. Increasingly complex and robust models for electron transfer through and between helices, and electrode-supported electron-transfer peptides, have been constructed. Design elements for peptide-supported ferredoxins and mononuclear Fe(II) and Zn(II) sites have been refined.