Characterization of metal binding by a designed protein: single ligand substitutions at a tetrahedral Cys2His2 site

Benchmarking a computational design method for the incorporation of metal ion-binding sites at symmetric protein interfaces

The design of novel metal-ion binding sites along symmetric axes in protein oligomers could provide new avenues for metalloenzyme design, construction of protein-based nanomaterials and novel ion transport systems. Here, we describe a computational design method, symmetric protein recursive ion-cofactor sampling (SyPRIS), for locating constellations of backbone positions within oligomeric protein structures that are capable of supporting desired symmetrically coordinated metal ion(s) chelated by sidechains (chelant model). Using SyPRIS on a curated benchmark set of protein structures with symmetric metal binding sites, we found high recovery of native metal coordinating rotamers: in 65 of the 67 (97.0%) cases, native rotamers featured in the best scoring model while in the remaining cases native rotamers were found within the top three scoring models. In a second test, chelant models were crossmatched against protein structures with identical cyclic symmetry. In addition to recovering all native placements, 10.4% (8939/86013) of the non-native placements, had acceptable geometric compatibility scores. Discrimination between native and non-native metal site placements was further enhanced upon constrained energy minimization using the Rosetta energy function. Upon sequence design of the surrounding first-shell residues, we found further stabilization of native placements and a small but significant (1.7%) number of non-native placement-based sites with favorable Rosetta energies, indicating their designability in existing protein interfaces. The generality of the SyPRIS approach allows design of novel symmetric metal sites including with non-natural amino acid sidechains, and should enable the predictive incorporation of a variety of metal-containing cofactors at symmetric protein interfaces.

Probing the minimal determinants of zinc binding with computational protein design

Structure-based protein design tests our understanding of the minimal determinants of protein structure and function. Previous studies have demonstrated that placing zinc binding amino acids (His, Glu, Asp or Cys) near each other in a folded protein in an arrangement predicted to be tetrahedral is often sufficient to achieve binding to zinc. However, few designs have been characterized with high-resolution structures. Here, we use X-ray crystallography, binding studies and mutation analysis to evaluate three alternative strategies for designing zinc binding sites with the molecular modeling program Rosetta. While several of the designs were observed to bind zinc, crystal structures of two designs reveal binding configurations that differ from the design model. In both cases, the modeling did not accurately capture the presence or absence of second-shell hydrogen bonds critical in determining binding-site structure. Efforts to more explicitly design second-shell hydrogen bonds were largely unsuccessful as evidenced by mutation analysis and low expression of proteins engineered with extensive primary and secondary networks. Our results suggest that improved methods for designing interaction networks will be needed for creating metal binding sites with high accuracy.

β-Peptide bundles: Design. Build. Analyze. Biosynthesize

Peptides containing β-amino acids are unique non-natural polymers known to assemble into protein-like tertiary and quaternary structures. When composed solely of β-amino acids, the structures formed, defined assemblies of 14-helices called β-peptide bundles, fold cooperatively in water solvent into unique and discrete quaternary assemblies that are highly thermostable, bind complex substrates and metal ion cofactors, and, in certain cases, catalyze chemical reactions. In this Perspective, we recount the design and elaboration of β-peptide bundles and provide an outlook on recent, unexpected discoveries that could influence research on β-peptides and β-peptide bundles (and β-amino acid-containing proteins) for decades to come.

Revisiting and re-engineering the classical zinc finger peptide: consensus peptide-1 (CP-1)

Zinc plays key structural and catalytic roles in biology. Structural zinc sites are often referred to as zinc finger (ZF) sites, and the classical ZF contains a Cys2His2 motif that is involved in coordinating Zn(II). An optimized Cys2His2 ZF, named consensus peptide 1 (CP-1), was identified more than 20 years ago using a limited set of sequenced proteins. We have reexamined the CP-1 sequence, using our current, much larger database of sequenced proteins that have been identified from high-throughput sequencing methods, and found the sequence to be largely unchanged. The CCHH ligand set of CP-1 was then altered to a CAHH motif to impart hydrolytic activity. This ligand set mimics the His2Cys ligand set of peptide deformylase (PDF), a hydrolytically active M(II)-centered (M = Zn or Fe) protein. The resultant peptide [CP-1(CAHH)] was evaluated for its ability to coordinate Zn(II) and Co(II) ions, adopt secondary structure, and promote hydrolysis. CP-1(CAHH) was found to coordinate Co(II) and Zn(II) and a pentacoordinate geometry for Co(II)-CP-1(CAHH) was implicated from UV-vis data. This suggests a His2Cys(H2O)2 environment at the metal center. The Zn(II)-bound CP-1(CAHH) was shown to adopt partial secondary structure by 1-D (1)H NMR spectroscopy. Both Zn(II)-CP-1(CAHH) and Co(II)-CP-1(CAHH) show good hydrolytic activity toward the test substrate 4-nitrophenyl acetate, exhibiting faster rates than most active synthetic Zn(II) complexes.

Sequence Programmable Peptoid Polymers for Diverse Materials Applications

Polymer sequence programmability is required for the diverse structures and complex properties that are achieved by native biological polymers, but efforts towards controlling the sequence of synthetic polymers are, by comparison, still in their infancy. Traditional polymers provide robust and chemically diverse materials, but synthetic control over their monomer sequences is limited. The modular and step-wise synthesis of peptoid polymers, on the other hand, allows for precise control over the monomer sequences, affording opportunities for these chains to fold into well-defined nanostructures. Hundreds of different side chains have been incorporated into peptoid polymers using efficient reaction chemistry, allowing for a seemingly infinite variety of possible synthetically accessible polymer sequences. Combinatorial discovery techniques have allowed the identification of functional polymers within large libraries of peptoids, and newly developed theoretical modeling tools specifically adapted for peptoids enable the future design of polymers with desired functions. Work towards controlling the three-dimensional structure of peptoids, from the conformation of the amide bond to the formation of protein-like tertiary structure, has and will continue to enable the construction of tunable and innovative nanomaterials that bridge the gap between natural and synthetic polymers.

Designing hydrolytic zinc metalloenzymes

Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up.

Computational design of metalloproteins

A number of design strategies exist for the development of novel metalloproteins. These strategies often exploit the inherent symmetry of metal coordination and local topology. Computational design of metal binding sites in flexible regions of proteins is challenging as the number of conformational degrees of freedom is significantly increased. Additionally, without pre-organization of the primary shell ligands by the protein fold, metal binding sites can rearrange according to the coordination constraints of the metal center. Examples of metal incorporation into existing folds, full fold design exploiting symmetry, and fold design in asymmetric scaffolds are presented.

Influence of active site location on catalytic activity in de novo-designed zinc metalloenzymes

While metalloprotein design has now yielded a number of successful metal-bound and even catalytically active constructs, the question of where to put a metal site along a linear, repetitive sequence has not been thoroughly addressed. Often several possibilities in a given sequence may exist that would appear equivalent but may in fact differ for metal affinity, substrate access, or protein dynamics. We present a systematic variation of active site location for a hydrolytically active ZnHis3O site contained within a de novo-designed three-stranded coiled coil. We find that the maximal rate, substrate access, and metal-binding affinity are dependent on the selected position, while catalytic efficiency for p-nitrophenyl acetate hydrolysis can be retained regardless of the location of the active site. This achievement demonstrates how efficient, tailor-made enzymes which control rate, pKa, substrate and solvent access (and selectivity), and metal-binding affinity may be realized. These findings may be applied to the more advanced de novo design of constructs containing secondary interactions, such as hydrogen-bonding channels. We are now confident that changes to location for accommodating such channels can be achieved without location-dependent loss of catalytic efficiency. These findings bring us closer to our ultimate goal of incorporating the secondary interactions we believe will be necessary in order to improve both active site properties and the catalytic efficiency to be competitive with the native enzyme, carbonic anhydrase.

Computational approaches for rational design of proteins with novel functionalities

Proteins are the most multifaceted macromolecules in living systems and have various important functions, including structural, catalytic, sensory, and regulatory functions. Rational design of enzymes is a great challenge to our understanding of protein structure and physical chemistry and has numerous potential applications. Protein design algorithms have been applied to design or engineer proteins that fold, fold faster, catalyze, catalyze faster, signal, and adopt preferred conformational states. The field of de novo protein design, although only a few decades old, is beginning to produce exciting results. Developments in this field are already having a significant impact on biotechnology and chemical biology. The application of powerful computational methods for functional protein designing has recently succeeded at engineering target activities. Here, we review recently reported de novo functional proteins that were developed using various protein design approaches, including rational design, computational optimization, and selection from combinatorial libraries, highlighting recent advances and successes.

Triple stimulus-responsive polypeptide nanoparticles that enhance intratumoral spatial distribution

To address the limited tumor penetration of nanoparticle drug delivery vehicles, we report the first pH-responsive polypeptide micelle that dissociates at the low extracellular pH of solid tumors. This histidine-rich elastin-like polypeptide block copolymer self-assembles at 37 °C into spherical micelles that are stabilized by Zn(2+) and are disrupted as the pH drops from 7.4 to 6.4. These pH-sensitive micelles demonstrate better in vivo penetration and distribution in tumors than a pH-insensitive control.

Co(II)-substituted Haemophilus influenzae β-carbonic anhydrase: spectral evidence for allosteric regulation by pH and bicarbonate ion

Cobalt(II)-substituted Haemophilus influenzae β-carbonic anhydrase (HICA) has been produced by overexpression in minimal media supplemented with CoCl(2), enabling kinetic, structural, and spectroscopic characterization. Co(II)-substituted HICA (Co-HICA) has comparable catalytic activity to that of wild-type enzyme with k(cat)=82±19 ms(-1) (120% of wild-type). The X-ray crystal structure of Co-HICA was determined to 2.5Å resolution, and is similar to the zinc enzyme. The absorption spectrum of Co-HICA is consistent with four-coordinate geometry. pH-dependent changes in the absorption spectrum of Co-HICA, including an increase in molar absorptivity and a red shift of a 580 nm peak with decreasing pH, correlate with the pH dependence of k(cat)/K(m). The absence of isosbestic points in the pH-dependent absorption spectra suggest that more than two absorbing species are present. The addition of bicarbonate ion at pH 8.0 triggers spectral changes in the metal coordination sphere that mimic that of lowering pH, supporting its hypothesized role as an allosteric inhibitor of HICA. Homogeneously (99±1% Co) and heterogeneously (52±5% Co) substituted Co-HICA have distinctly different colors and absorption spectra, suggesting that the metal ions in the active sites in the allosteric dimer of Co-HICA engage in intersubunit communication.

Features of Rhodobacter sphaeroides ChrR required for stimuli to promote the dissociation of σ(E)/ChrR complexes

In the photosynthetic bacterium Rhodobacter sphaeroides, a transcriptional response to the reactive oxygen species singlet oxygen ((1)O(2)) is mediated by ChrR, a zinc metalloprotein that binds to and inhibits the activity of the alternative σ factor σ(E). We provide evidence that (1)O(2) promotes the dissociation of σ(E) from ChrR to activate transcription in vivo. To identify what is required for (1)O(2) to promote the dissociation of σ(E)/ChrR complexes, we analyzed the in vivo properties of variant ChrR proteins with amino acid changes in conserved residues of the C-terminal cupin-like domain (ChrR-CLD). We found that (1)O(2) was unable to promote the detectable dissociation of σ(E)/ChrR complexes when the ChrR-CLD zinc ligands (His141, His143, Glu147, and His177) were substituted with alanine, even though individual substitutions caused a 2-fold to 10-fold decrease in zinc affinity for this domain relative to that for wild-type ChrR (K(d)∼4.6×10(-)(10) M). We conclude that the side chains of these invariant residues play a crucial role in the response to (1)O(2). Additionally, we found that cells containing variant ChrR proteins with single amino acid substitutions at Cys187 or Cys189 exhibited σ(E) activity similar to those containing wild-type ChrR when exposed to (1)O(2), suggesting that these thiol side chains are not required for (1)O(2) to induce σ(E) activity in vivo. Finally, we found that the same aspects of R. sphaeroides ChrR needed for a response to (1)O(2) are required for the dissociation of σ(E)/ChrR complexes in the presence of the organic hydroperoxide t-butyl hydroperoxide.

Design of functional metalloproteins

Metalloproteins catalyse some of the most complex and important processes in nature, such as photosynthesis and water oxidation. An ultimate test of our knowledge of how metalloproteins work is to design new metalloproteins. Doing so not only can reveal hidden structural features that may be missing from studies of native metalloproteins and their variants, but also can result in new metalloenzymes for biotechnological and pharmaceutical applications. Although it is much more challenging to design metalloproteins than non-metalloproteins, much progress has been made in this area, particularly in functional design, owing to recent advances in areas such as computational and structural biology.

Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer

One of the long-term goals in developing advanced biomaterials is to generate protein-like nanostructures and functions from a completely nonnatural polymer. Toward that end, we introduced a high-affinity zinc-binding function into a peptoid (N-substituted glycine polymer) two-helix bundle. Borrowing from well-understood zinc-binding motifs in proteins, thiol and imidazole moieties were positioned within the peptoid such that both helices must align in close proximity to form a binding site. We used fluorescence resonance energy transfer (FRET) reporter groups to measure the change of the distance between the two helical segments and to probe the binding of zinc. We systematically varied the position and number of zinc-binding residues, as well as the sequence and size of the loop that connects the two helical segments. We found that certain peptoid two-helix bundles bind zinc with nanomolar affinities and high selectivity compared to other divalent metal ions. Our work is a significant step toward generating biomimetic nanostructures with enzyme-like functions.

Infrared Spectroscopy of Phenylalanine Ag(I) and Zn(II) Complexes in the Gas Phase

Infrared multiple-photon dissociation (IR-MPD) spectroscopy has been applied to singly-charged complexes involving the transition metals Ag(+) and Zn(2+) with the aromatic amino acid phenylalanine. These studies are complemented by DFT calculations. For [Phe+Ag](+) the calculations favor a tridentate charge solvation N/O/ring structure. The experimental spectrum strongly supports this as the predominant binding geometry and, in particular, rules out a significant presence of the salt-bridge conformation. Zn(2+) forms a deprotonated dimer complex with Phe, [Zn+Phe(2)-H](+), in which the +2 oxidation state serves as a useful biomimetic model for zinc protein sites. A number of low-energy conformations were located, of which the lowest-energy conformer predicted by the calculations involves a Phe ligand deprotonated on the carboxylic acid, while the other Phe ligand is in the tridentate charge solvation conformation. The calculated IR spectrum of this conformer gives a close fit to the experimental spectrum, strongly supporting this as the predominant binding geometry. This most stable calculated complex is characterized by N/ O/ring metal chelation with a tetrahedral-type coordination core of Zn(2+) to N and O of both ligands. Another similar tightly chelated structure shows a square-planar-type coordination core, but this structure is computed to be less stable and gives a less satisfactory match to the experimental spectrum. This preference for the tetrahedral geometry of the Lewis-basic atomic ligands parallels the common Zn(II) coordination geometry in proteins. The number of clearly identifiable peaks resolved in the IR-MPD spectra as well as the much-improved matches between the observed spectra and the DFT-calculated spectra of the most stable geometries compared to previous studies are noteworthy for systems of this size and complexity. These results demonstrate that IR spectroscopy of transition metal-amino acid complexes in combination with DFT calculations is a very powerful structural tool, readily applicable to biomimetic systems that model, for example, the reaction centers of proteins in the solvent-free environment. In addition, we present a novel ion-capturing method for Fourier transform ion cyclotron resonance mass spectrometry which removes the necessity of a buffer gas pulse, while allowing ion trapping at moderate voltages with apparently reduced collisional excitation of the ions.

Modulation of zinc- and cobalt-binding affinities through changes in the stability of the zinc ribbon protein L36

Cysteine-rich Zn(II)-binding sites in proteins serve two distinct functions: to template or stabilize specific protein folds, and to facilitate chemical reactions such as alkyl transfers. We are interested how the protein environment controls metal site properties, specifically, how naturally occurring tetrahedral Zn(II) sites are affected by the surrounding protein. We have studied the Co(II)- and Zn(II)-binding of a series of derivatives of L36, a small zinc ribbon protein containing a (Cys)(3)His metal coordination site. UV-vis spectroscopy was used to monitor metal binding by peptides at pH 6.0. For all derivatives, the following trends were observed: (1) Zn(II) binds tighter than Co(II), with an average K (A) (Zn) /K (A) (Co) of 2.8(+/-2.0)x10(3); (2) mutation of the metal-binding ligand His32 to Cys decreases the affinity of L36 derivatives for both metals; (3) a Tyr24 to Trp mutation in the beta-sheet hydrophobic cluster increases K (A) (Zn) and K (A) (Co) ; (4) mutation in the beta-hairpin turn, His20 to Asn generating an Asn-Gly turn, also increases K (A) (Zn) and K (A) (Co) ; (5) the combination of His20 to Asn and Tyr24 to Trp mutations also increases K (A) (Zn) and K (A) (Co) , but the increments versus C(3)H are less than those of the single mutations. Furthermore, circular dichroism, size-exclusion chromatography, and 1D and 2D (1)H NMR experiments show that the mutations do not change the overall fold or association state of the proteins. L36, displaying Co(II)- and Zn(II)-binding sensitivity to various sequence mutations without undergoing a change in protein structure, can therefore serve as a useful model system for future structure/reactivity studies.

Design, folding, and activities of metal-assembled coiled coil proteins

Metal ions serve many purposes in natural proteins, from the stabilization of tertiary structure to the direction of protein folding to crucial roles in electron transfer and catalysis. There is considerable interest in creating metal binding sites in designed proteins to understand the structural role of metal ions and to design new metalloproteins with useful functions. The de novo design of metalloproteins and the role of metals in the folding of designed proteins are reviewed here, with particular focus on the design, folding, and activities of the [M(bpy-peptide)(3)](2+) structure. This maquette is constructed by the covalent attachment of 2,2'-bipyridine to the N-termini of amphiphilic peptides, and it is assembled into a folded trimeric coiled coil by the addition of a six-coordinate transition metal ion and the resulting hydrophobic collapse of the peptides. The [M(bpy-peptide)(3)](2+) structure has been employed in diverse applications, ranging from electron transfer pathway studies to the study of optimal hydrophobic packing in a virtual library to the construction of receptors and biosensors.

Hydrolytic Reaction by Zinc Finger Mutant Peptides: Successful Redesign of Structural Zinc Sites into Catalytic Zinc Sites

To redesign a metal site originally required for the stabilization of a folded protein structure into a functional metal site, we constructed a series of zinc finger mutant peptides such as zf(CCHG) and zf(GCHH), in which one zinc-coordinating residue is substituted into a noncoordinating one. The mutant peptides having water bound to the zinc ion catalyzed the hydrolysis of 4-nitrophenyl acetate as well as the enantioselective hydrolysis of amino acid esters. All the zinc complexes of the mutant peptides showed hydrolytic activity, depending on their peptide sequences. In contrast, the zinc complex of the wild-type, zf(CCHH), and zinc ion alone exhibited no hydrolytic ability. These results clearly indicate that the catalytic abilities are predominantly attributed to the zinc center in the zinc complexes of the mutant peptides. Kinetic studies of the mutant peptides demonstrated that the catalytic hydrolysis is affected by the electron-donating ability of the protein ligands and the coordination environment. In addition, the pH dependence of the hydrolysis strongly suggests that the zinc-coordinated hydroxide ion participates the catalytic reaction. This report is the first successful study of catalytically active zinc finger peptides.

Spectropotentiometric analysis of metal binding to structural zinc-binding sites: accounting quantitatively for pH and metal ion buffering effects

Studies of the metal-binding affinity of protein sites are ubiquitous in bioinorganic chemistry and are valuable for the information that they can provide about metal speciation and exchange in biological systems. The potential for error in these studies is high, however, since many competing equilibria are present in solution and must be taken into consideration. Here, we report a new spectropotentiometric titration apparatus that allows pH and UV-vis absorption to be monitored simultaneously on small samples under inert atmosphere. In addition, we explain how data obtained from the complex equilibria can be combined with tabulated information about the protonation and metal-binding constants for common buffers to provide detailed, quantitative information about metal-protein interactions. Application of this approach to the investigation of metal binding to structural zinc-binding domains and common pitfalls encountered when performing these experiments are also discussed. We have used this approach to reevaluate the metal-binding constants of the N-terminal zinc-binding peptide from the HIV-1 nucleocapsid protein (10(-8)M</=K(d)(Co)</=10(-7)M; 10(-11)M</=K(d)(Zn)</=10(-10)M).

High affinity binding of serum histidine-rich glycoprotein to nickel-nitrilotriacetic acid: the application to microquantification

Histidine-rich glycoprotein (HRG) is a serum protein with possible pluripotent activities. In this study, a method for the quantification of rabbit histidine-rich glycoprotein (rHRG) was developed based upon the high affinity binding profile of rHRG to nickel-nitrilotriacetic acid (Ni-NTA), an improved chelation agent. When the binding profile of Ni-NTA for whole serum proteins was assessed by Western blotting, Ni-NTA exhibited the binding specificity only to rHRG even after washing with 20 mM imidazole, owing to the unusual amounts of histidine residues in rHRG. In the following experiments, the rHRG immobilized onto a microplate with specific antibody was determined spectrophotometrically with peroxidase-labeled Ni-NTA. This method permitted evaluation of rHRG concentrations ranging from 1.0 to 100 ng/ml, and was actually applicable to the monitoring of rHRG in Resource Q-fractionated serum preparations. Also, the co-addition of L-histidine into the incubation mixture significantly diminished the specific binding between rHRG and Ni-NTA. These findings indicate the potential usefulness of this method for the specific measurement of small amounts of rHRG and for understanding the roles of abundant histidine residues in rHRG-metal cation interaction.

Fluorescent zinc indicators for neurobiology

Mounting evidence indicates that zinc has multiple roles in cell biology, viz. as a part of metalloenzyme catalytic sites, as a structural component of gene regulatory proteins, and (like calcium) as a free signal ion, particularly in the cortex of the brain. While most Zn(II) in the brain is tightly bound, such that free Zn(II) levels extracellularly and intracellularly are likely to be picomolar, a subset of glutamatergic neurons possess weakly bound zinc in presynaptic boutons which is released at micromolar levels in response to a variety of stimuli. Key to further progress in understanding the multiple roles of zinc will be the availability of fluorescent indicator systems that will permit quantitative determination and imaging of zinc fluxes and levels over a broad concentration range both intracellularly and extracellularly using fluorescence microscopy. Towards that end, we have compared a variety of fluorescent indicators for their sensitivity to Zn(II) and Cu(II), selectivity for Zn(II) in the presence of potential interferents such as Ca(II) or Mg(II), and potential for quantitative imaging. The commercially available probes Fura-2, Mag-Fura-5, Newport Green DCF, and FuraZin-1 were compared with the carbonic anhydrase-based indicator systems for selectivity and sensitivity. In addition, intracellular levels of Zn following excitotoxic insult were determined by single pixel fluorescence lifetime microscopy of Newport Green DCF, and extracellular levels of free zinc following stimulus of rat hippocampal slices were determined ratiometrically with a carbonic anhydrase-based indicator system. These results suggest that zinc ion at high nM to microM levels can be accurately quantitated by FuraZin-1 ratiometrically or by Newport Green DCF by fluorescence lifetime; and at levels down to pM by intensity ratio, lifetime, or polarization using carbonic anhydrase-based systems.

Design and spectroscopic characterization of peptide models for the plastocyanin copper-binding loop

The Cu(II)- and Co(II)-binding properties of two peptides, designed on the basis of the active site sequence and structure of the blue copper protein plastocyanin, are explored. Peptide BCP-A, Ac-Trp-(Gly)(3)-Ser-Tyr-Cys-Ser-Pro-His-Gln-Gly-Ala-Gly-Met-(Gly )(3)-His-(Gly)(2)-Lys-CONH(2), conserves the Cu-binding loop of plastocyanin containing three of the four copper ligands and has a flexible (Gly)(3) linker to the second His ligand. Peptide BCP-B, Ac-Trp-(Gly)(3)-Cys-Gly-His-Gly-Val-Pro-Ser-His-Gly-Met-Gly-CONH(2), contains all four blue copper ligands, with two on either side of a beta-turn. Both peptides form 1:1 complexes with Cu(II) through His and Cys ligands. BCP-A, the ligand loop, binds to Cu(II) in a tetrahedrally distorted square plane with axial solvent ligation, while BCP-B-Cu(II) has no tetrahedral distortion in aqueous solution. In methanolic solution, distortion of the square plane is evident for both BCP-Cu(II) complexes. Tetrahedral Co(II) complexes are observed for both peptides in aqueous solution but with 4:2 peptide:Co(II) stoichiometries as estimated by ultracentrifugation. Cu(II) reduction potentials for the aqueous peptide-Cu(II) complexes were measured to be +75 +/- 30 mV vs NHE for BCP-A-Cu(II) and -10 +/- 20 mV vs NHE for BCP-B-Cu(II). The results indicate that the plastocyanin ligand loop can act as a metal-binding site with His and Cys ligands in the absence of the remainder of the folded protein but, by itself, cannot stabilize a type 1 copper site, emphasizing the role of the protein matrix in protecting the Cu binding site from solvent exposure and the Cys from oxidation.

N-Terminal domain of HTLV-I integrase. Complexation and conformational studies of the zinc finger

The HTLV-I integrase N-terminal domain [50-residue peptide (IN50)], and a 35-residue truncated peptide formed by residues 9-43 (IN35) have been synthesized by solid-phase peptide synthesis. Formation of the 50-residue zinc finger type structure through a HHCC motif has been proved by UV-visible absorption spectroscopy. Its stability was demonstrated by an original method using RP-HPLC. Similar experiments performed on the 35-residue peptide showed that the truncation does not prevent zinc complex formation but rather that it significantly influences its stability. As evidenced by CD spectroscopy, the 50-residue zinc finger is unordered in aqueous solution but adopts a partially helical conformation when trifluoroethanol is added. These results are in agreement with our secondary structure predictions and demonstrate that the HTLV-I integrase N-terminal domain is likely to be composed of an helical region (residues 28-42) and a beta-strand (residues 20-23), associated with a HHCC zinc-binding motif. Size-exclusion chromatography showed that the structured zinc finger dimerizes through the helical region.

De novo design and characterization of copper centers in synthetic four-helix-bundle proteins

The design and chemical synthesis of de novo metalloproteins on cellulose membranes with the structure of an antiparallel four-helix bundle is described. All possible combinations of three different sets of amphiphilic helices were assembled on cyclic peptide templates which were bound by a cleavable linker to the cellulose. In the hydrophobic interior, the four-helix bundle proteins carry a cysteine and several histidines at various positions for copper ligation. This approach was used successfully to synthesize, for the first time, copper proteins based on a four-helix bundle. UV-vis spectra monitored on the solid support showed ligation of copper(II) by about one-third out of the 96 synthesized proteins and tetrahedral complexes of cobalt(II) by most of these proteins. Three of the most stable copper-binding proteins were synthesized in solution and their structural properties analyzed by spectroscopic methods. Circular dichroism, one-dimensional NMR, and size-exclusion chromatography indicate a folding into a compact state containing a high degree of secondary structure with a reasonably ordered hydrophobic core. They displayed UV-vis absorption, resonance Raman, and EPR spectra intermediate between those of type 1 and type 2 copper centers. The present approach provides a sound basis for further optimizing the copper binding and its functional properties by using combinatorial protein chemistry guided by rational principles.

A de novo designed peptide ligase: a mechanistic investigation

A 33-residue de novo designed peptide ligase is reported which catalyzes the template-directed condensation of suitably activated short peptides with catalytic efficiencies in excess of 10(5) ([k(cat)/K(m)]/k(uncat)). The ligase peptide, derived from natural and designed alpha-helical coiled-coil proteins, presents a surface for substrate assembly via formation of a hydrophobic core at the peptide interface. Charged residues flanking the core provide additional binding specificity through electrostatic complementarity. Addition of the template to an equimolar fragment solution results in up to 4100-fold increases in initial reaction rates. Dramatic decreases in efficiency upon mutation of charged residues or increase in ionic strength establishes the importance of electrostatic recognition to ligase efficiency. Although most of the increase in reaction efficiency is due to entropic gain from binding of substrates in close proximity, mechanistic studies with altered substrates demonstrate that the system is highly sensitive to precise ordering at the point of ligation. Taken together these results represent the first example of a peptide catalyst with designed substrate binding sites which can significantly accelerate a bimolecular reaction and support the general viability of alpha-helical protein assemblies in artificial enzyme design.

One-step purification of rabbit histidine rich glycoprotein by dye-ligand affinity chromatography with metal ion requirement

A simple method for purification of the histidine rich glycoprotein (rHRG) from rabbit sera was developed. The rHRG was purified by one-step affinity chromatography using the triphenylmethane dye "acid fuchsin" as a specific ligand, which gave an overall yield above 80%. Interestingly, the binding of rHRG to the ligand required the divalent transition-metal ions such as Zn2+, Ni2+, and Co2+ at pH 9.5. In the presence of 0.5 mM ZnCl2, the binding was enhanced 15 times compared with that in the absence of ZnCl2. Bound rHRG was efficiently eluted from the affinity absorbent with 100 mM imidazole or histidine. Purified rHRG was homogeneous with an Mr of 94 kDa when analyzed by SDS-PAGE, whereas isoelectric focusing revealed microheterogeniety with pI values ranging from 6.3 to 6.8. Blotting analysis with lectins specific for carbohydrate moieties and treatment with glycosidases demonstrated that rHRG is a highly N-glycosylated protein with diverse carbohydrate structures.

De novo design and structural characterization of proteins and metalloproteins

De novo protein design has recently emerged as an attractive approach for studying the structure and function of proteins. This approach critically tests our understanding of the principles of protein folding; only in de novo design must one truly confront the issue of how to specify a protein's fold and function. If we truly understand proteins, it should be possible to design receptors, enzymes, and ion channels from scratch. Further, as this understanding evolves and is further refined, it should be possible to design proteins and biomimetic polymers with properties unprecedented in nature.

Utilization of a synthetic peptide as a tool to study the interaction of heavy metals with the zinc finger domain of proteins critical for gene expression in the developing brain

The zinc finger motif belonging to the Cys(2)/His(2) family provides a structural framework for a number of critical proteins which are essential for cellular function. To determine whether these domains are potential targets for heavy metal perturbation, we examined the interaction between various metals and a synthetic Cys(2)/His(2) finger peptide, of the type present in the transcription factor Sp1 and an intact recombinant human Sp1 protein (rhSp1). Sp1 has a DNA-binding domain composed of three contiguous zinc finger motifs which requires Zn(II) for its activity, and may be modulated by other transition metals. Using spectrophotometric methods, the incorporation of Zn(II) and a variety of other divalent metals into this zinc finger peptide was monitored, and their ability to displace zinc ion was evaluated. Furthermore, the DNA-binding activity of these various metal-peptide complexes and rhSp1 to their cognate DNA consensus sequence was examined electrophoretically. Our results suggested that group IIb metals [Zn(II), Cd(II), and Hg(II)] were able to complex with the peptide and bind the double-stranded DNA with high affinity as well as inhibiting Sp1 DNA-binding activity in a concentration-dependent manner. With the exception of Pb(II), non-transition-metal-peptide mixtures with Ca(II), Ba(II), and Sn(II) neither exhibited the binding spectra typical of zinc finger motifs nor bound the DNA; they also had little effect on DNA-binding ability of rhSp1. Therefore, we postulate that heavy metals may modulate zinc finger proteins through structural alterations of their zinc finger motifs and ultimately alter their function in terms of regulation of gene expression.

From genes to protein structure and function: novel applications of computational approaches in the genomic era

The genome-sequencing projects are providing a detailed 'parts list' of life. A key to comprehending this list is understanding the function of each gene and each protein at various levels. Sequence-based methods for function prediction are inadequate because of the multifunctional nature of proteins. However, just knowing the structure of the protein is also insufficient for prediction of multiple functional sites. Structural descriptors for protein functional sites are crucial for unlocking the secrets in both the sequence and structural-genomics projects.

Histidine placement in de novo-designed heme proteins

The effects of histidine residue placement in a de novo-designed four-alpha-helix bundle are investigated by placement of histidine residues at coiled coil heptad a positions in two distinct heptads and at each position within a single heptad repeat of our prototype heme protein maquette, [H10H24]2 [[Ac-CGGGELWKL x HEELLKK x FEELLKL x HEERLKK x L-CONH2]2]2 composed of a generic (alpha-SS-alpha)2 peptide architecture. The heme to peptide stoichiometry of variants of [H10H24]2 with either or both histidines on each helix replaced with noncoordinating alanine residues ([H10A24]2, [A10H24]2, and [A10A24]2) demonstrates the obligate requirement of histidine for biologically significant heme affinity. Variants of [A10A24]2, [[Ac-CGGGELWKL x AEELLKK x FEELLKL x AEERLKK x L-CONH2]2]2, containing a single histidine per helix in positions 9 to 15 were evaluated to verify the design based on molecular modeling. The bis-histidine site formed between heptad positions a at 10 and 10' bound ferric hemes with the highest affinity, Kd1 and Kd2 values of 1.5 and 800 nM, respectively. Placement of histidine at position 11 (heptad position b) resulted in a protein that bound a single heme with moderate affinity, Kd1 of 9.5 microM, whereas the other peptides had no measurable apparent affinity for ferric heme with Kd1 values >200 microM. The bis-histidine ligation of heme to [H10A24]2 and [H11A24]2 was confirmed by electron paramagnetic resonance spectroscopy. The protein design rules derived from this study, together with the narrow tolerances revealed, are applicable for improving future heme protein designs, for analyzing the results of randomized heme protein combinatorial libraries, as well as for implementation in automated protein design.

Selectivity and sensitivity of fluorescence lifetime-based metal ion biosensing using a carbonic anhydrase transducer

A key performance criterion for metal ion determinations in complex media like serum, cytoplasm of the cell, and sea water is selectivity: the ability to determine the analyte(s) of interest, in the presence of relatively high concentrations of interferents. Cu(II), Zn(II), Cd(II), Co(II), and Ni(II) may be determined by changes they induce in the fluorescence lifetime and intensity of site-specifically labeled fluorescent variants of apocarbonic anhydrase II. Free metal ion concentrations in the picomolar range (for Cu(II) and Zn(II)) and the nanomolar range (for Cd(II), Co(II), and Ni(II)) were determined, based on the affinity of the apoenzyme for these ions. Mg(II) at 50 mM and Ca(II) at 10 mM produced no effect. By the use of different fluorescent labels, transducers were made which responded well to Cu(II), Co(II), and Ni(II), but not to Zn(II) and Cd(II), and vice versa.

Determination of picomolar concentrations of metal ions using fluorescence anisotropy: biosensing with a "reagentless" enzyme transducer

Because of their high affinity and selectivity, metalloproteins can be used as transducers in novel sensors, i.e., biosensors, for the determination of trace levels of metal ions in solution. Here, we exploit carbonic anhydrase to determine picomolar to nanomolar concentrations of free transition metal ions by fluorescence anisotropy (polarization) in a reagentless format. Carbonic anhydrase variants engineered with a cysteine replacing a residue chosen near the active site (F131C and H64C) were covalently labeled with derivatives of benzoxadiazole sulfonamide. These labeled variants exhibited changes in anisotropy up to 0.07 upon binding free Cu(II), Co(II), and Zn(II) with apparent Kd's close to the values observed with wild-type apocarbonic anhydrase. The covalent attachment of the label has significant advantages over noncovalent labels we have described previously. Furthermore, the metal ion-dependent anisotropy changes were predictable using simple theory. The results demonstrate that free transition metal ions can be determined at trace levels in aqueous solution using inexpensive instruments.

The de novo design of a rubredoxin-like Fe site

A redox center similar to that of rubredoxin was designed into the 56 amino acid immunoglobulin binding B1 domain of Streptococcals protein G. The redox center in rubredoxin contains an iron ion tetrahedrally coordinated by four cysteine residues, [Fe(S-Cys)4](-1),(-2). The design criteria for the target site included taking backbone movements into account, tetrahedral metal-binding, and maintaining the structure and stability of the wild-type protein. The optical absorption spectrum of the Co(II) complex of the metal-binding variant is characteristic of tetrahedral chelation by four cysteine residues. Circular dichroism and nuclear magnetic resonance measurements reveal that the metal-free and Cd(II)-bound forms of the variant are folded correctly and are stable. The Fe(III) complex of the metal-binding mutant reproduces the optical and the electron paramagnetic resonance spectra of oxidized rubredoxin. This demonstrates that the engineered protein chelates Fe(III) in a tetrahedral array, and the resulting center is similar to that of oxidized rubredoxin.

A carboxyl-terminal Cys2/His2-type zinc-finger motif in DNA primase influences DNA content in Synechococcus PCC 7942

The DNA primase gene, dnaG, has been isolated from the cyanobacterium Synechococcus PCC 7942. It is not part of a macromolecular synthesis operon but is co-transcribed with pheT and located adjacent to the metallothionein divergon, smt. At the carboxyl terminus of this DnaG is a Cys2/His2 zinc-finger motif. The carboxyl-terminal 91 residues bound 65Zn and 0.95 g atom of Zn2+ mol-1 were detected with 4-(2-pyridylazo)resorcinol. Following exposure to Cd2+, 0.95 g atom of Cd2+ was displaced by 2 equivalents of p-(hydroxymercuri) phenylsulfonate mol-1, while only 0.03 g atom of Cd2+ was displaced mol-1 polypeptide missing the carboxyl-terminal (residue 592 onward) zinc-finger motif. Zn2+ caused an increase in intensity, and a reduction in wavelength, of Trp fluorescence at the tip of the predicted zinc-finger, while EDTA caused the converse. Cells containing a single chromosomal codon substitution (C597S), altering the zinc-finger, were generated by exploiting Zn2+-sensitive smt mutants and the proximity of dnaG to smt. Cells in which smt and dnaG(C597S) had integrated into the chromosome were selected via restored Zn2+ tolerance. Synechococcus PCC 7942 and its dnaG(C597S) mutant grew at equivalent rates, but the latter had a reduced number of chromosomes.

Computer search algorithms in protein modification and design

The computer-aided design of protein sequences requires efficient search algorithms to handle the enormous combinatorial complexity involved. A variety of different algorithms have now been applied with some success. The choice of algorithm can influence the representation of the problem in several important ways--the discreteness of the configuration, the types of energy terms that can be used and the ability to find the global minimum energy configuration. The use of dead end elimination to design the complete sequence for a small protein motif and the use of genetic and mean-field algorithms to design hydrophobic cores for proteins represent the major themes of the past year.

Effect of four helix bundle topology on heme binding and redox properties

We have designed two alternative four helix bundle protein scaffold topologies for maquette construction to examine the effect of helix orientation on the heme binding and redox properties of our prototype heme protein maquette, (alpha-SS-alpha)2, previously described as H10H24 [Robertson, D. E., Farid, R. S., Moser, C. C., Mulholland, S. E., Pidikiti, R., Lear, J. D., Wand, A. J., DeGrado, W. F., and Dutton, P. L. (1994) Nature 368, 425]. Conversion of the disulfide-bridged di-alpha-helical monomer of (alpha-SS-alpha)2 into a single polypeptide chain results in topological reorientation of the helix dipoles and side chains within a 62 amino acid helix-loop-helix monomer, (alpha-l-alpha), which self-associates to form (alpha-l-alpha)2. Addition of an N-terminal cysteine residue to (alpha-l-alpha) with subsequent oxidation yields a 126 amino acid single molecule four helix bundle, (alpha-l-alpha-SS-alpha-l-alpha). Gel permeation chromatography demonstrated that (alpha-SS-alpha)2 and (alpha'-SS-alpha')2, a uniquely structured variant of the prototype, as well as (alpha-l-alpha)2 and (alpha'-l-alpha')2 assemble into distinct four helix bundles as designed, whereas (alpha-l-alpha-SS-alpha-l-alpha) elutes as a monomeric four alpha-helix bundle. Circular dichroism (CD) spectroscopy proves that these peptides are highly alpha-helical, and incorporation of four hemes has little effect on the helical content of the secondary structure. Four heme dissociation constants were evaluated by UV-visible spectroscopy and ranged from the 15 nM to 25 microM range for each of the peptides. The presence of Cotton effects in the visible CD illustrated that the hemes reside within the protein architecture. The equilibrium redox midpoint potentials (Em8) of the four bound hemes in each peptide are between -100 and -280 mV, as determined by redox potentiometry. The heme affinity and spectroelectrochemical properties of the hemes bound to (alpha-l-alpha)2 and (alpha-l-alpha-SS-alpha-l-alpha) are similar to those of the prototype, (alpha-SS-alpha)2, and to bis-histidine ligated b-type cytochromes, regardless of the global architectural changes imposed by these topological rearrangements. The hydrophobic cores of these peptides support local electrostatic fields which result in nativelike heme chromophore properties (spectroscopy, elevated reduction potentials, heme-heme charge interaction, and reactivity with exogenous diatomics) illustrating the utility of these non-native peptides in the study of metalloproteins.

The construction of metal centers in proteins by rational design

Metalloprotein properties result from the interplay between coordination requirements of the metal center, protein stability, and modulation of the metal center by the surrounding protein matrix. Simple metal centers, which exercise control over the protein by affecting stability or enzyme activity, have been created by rational design. Complex centers, which require control by the protein matrix, have also been constructed.

Engineering enzyme specificity

Protein engineering is the application of knowledge to design and alter protein function and structure. Although powerful methods, from specific to random, have been developed for the redesign of protein architecture, their successful application is dependent on the information known about the protein. This database of information is providing a foundation for establishing rules that govern enzyme-substrate interactions.

Lessons from zinc-binding peptides

Zinc-finger domains are small metal-binding modules that are found in a wide range of gene regulatory proteins. Peptides corresponding to these domains have provided valuable model systems for examining a number of biophysical parameters entirely unrelated to their nucleic acid binding properties. These include the chemical basis for metal-ion affinity and selectivity, thermodynamic properties related to hydrophobic packing and beta-sheet propensities, and constraints on the generation of ligand-binding and potential catalytic sites. These studies have laid the foundation for applications such as the generation of optically detected zinc probes and the design of metal-binding peptides and proteins with desired spectroscopic and chemical properties.