Electrochemical and spectroscopic investigations of immobilized de novo designed heme proteins on metal electrodes.

On the basis of rational design principles, template-assisted four-helix-bundle proteins that include two histidines for coordinative binding of a heme were synthesized. Spectroscopic and thermodynamic characterization of the proteins in solution reveals the expected bis-histidine coordinated heme configuration. The proteins possess different binding domains on the top surfaces of the bundles to allow for electrostatic, covalent, and hydrophobic binding to metal electrodes. Electrostatic immobilization was achieved for proteins with lysine-rich binding domains (MOP-P) that adsorb to electrodes covered by self-assembled monolayers of mercaptopropionic acid, whereas cysteamine-based monolayers were employed for covalent attachment of proteins with cysteine residues in the binding domain (MOP-C). Immobilized proteins were studied by surface-enhanced resonance Raman (SERR) spectroscopy and electrochemical methods. For all proteins, immobilization causes a decrease in protein stability and a loosening of the helix packing, as reflected by a partial dissociation of a histidine ligand in the ferrous state and very low redox potentials. For the covalently attached MOP-C, the overall interfacial redox process involves the coupling of electron transfer and heme ligand dissociation, which was analyzed by time-resolved SERR spectroscopy. Electron transfer was found to be significantly slower for the mono-histidine-coordinated than for the bis-histidine-coordinated heme. For the latter, the formal heterogeneous electron-transfer rate constant of 13 s(-1) is similar to those reported for natural heme proteins with comparable electron-transfer distances, which indicates that covalently bound synthetic heme proteins provide efficient electronic communication with a metal electrode as a prerequisite for potential biotechnological applications.     

Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase

The de novo molecular design program SPROUT has been used in conjunction with the X-ray crystal structure of RNA polymerase (RNAP) from Thermus aquaticus to produce a novel enzyme inhibitor scaffold. A short and efficient synthesis of molecules corresponding to this scaffold has been developed and in keeping with the design predictions, the resulting inhibitors displayed useful levels of inhibition of Escherichia coli RNAP.     

Structure of a de novo designed protein model of radical enzymes

The use of side chains as catalytic cofactors for protein mediated redox chemistry raises significant mechanistic issues as to how these amino acids are activated toward radical chemistry in a controlled manner. De novo protein design has been used to examine the structural basis for the creation and maintenance of a tryptophanyl radical in a three-helix bundle protein maquette. Here we report the detailed structural analysis of the protein by multidimensional NMR methods. An interesting feature of the structure is an apparent pi-cation interaction involving the sole tryptophan and a lysine side chain. Hybrid density functional calculations support the notion that this interaction raises the reduction potential of the W degrees /WH redox pair and helps explain the redox characteristics of the protein. This model protein system therefore provides a powerful model for exploring the structural basis for controlled radical chemistry in protein.     

Control of metal coordination number in de novo designed peptides through subtle sequence modifications

Substitution of an alanine for leucine (shown in light blue) in the hydrophobic interior of designed three-stranded coiled coils allows for the control of metal ion coordination number and geometry. The influence of this perturbation by a noncoordinating residue can be monitored by the dramatic impact on the 113Cd NMR spectrum. The structural effect occurs even when the residue substitution is as much as 7 A from the metal binding site.     

Zinc-bacteriochlorophyllide dimers in de novo designed four-helix bundle proteins. A model system for natural light energy harvesting and dissipation

Photosynthetic organisms utilize interacting pairs of chlorophylls and bacteriochlorophylls as excitation energy donors and acceptors in light harvesting complexes, as photosensitizers of charge separation in reaction centers, and maybe as photoprotective quenching centers that dissipate excess excitation energy under high light intensities. To better understand how the pigment's local environment and spatial organization within the protein tune its ground- and excited-state properties to perform different functions, we prepared and characterized the simplest possible system of interacting bacteriochlorophylls within a protein scaffold. Using HP7, a high-affinity heme-binding protein of the HP class of de novo designed four-helix bundles, we incorporated 13(2)-OH-zinc-bacteriochlorophyllide-a (ZnBChlide), a water-soluble bacteriochlorophyll derivative, into specific binding sites within the four-helix bundle protein core. We capitalized on the rich and informative optical spectrum of ZnBChlide to rigorously characterize its complexes with HP7 and two variants, in which a single heme-binding site is eliminated by replacing histidine residues at positions 7 or 42 by phenylalanine. Surprisingly, we found the ZnBChlide binding capacity of HP7 and its variants to be higher than for heme: up to three ZnBChlide pigments bind per HP7, or two per each single histidine variant. The formation of dimers within HP7 results in dramatic quenching of ZnBChlide fluorescence, reducing its quantum yield by about 80%, and the singlet excited-state lifetime by 2 orders of magnitudes compared to the monomer. Thus, HP7 and its variants are the first examples of a simple protein environment that can isolate a self-quenching pair of photosynthetic pigments in pure form. Unlike its complicated natural analogues, this system can be constructed from the ground up, starting with the simplest functional element, increasing the complexity as needed.     

Synthesis and alkali metal ion-binding properties of a chromium(III) triacetylide complex

A simple triacetylide complex of chromium(III) is synthesized for use as a potential precursor to metal-dicarbide clusters. Reaction of Me(3)SiCCLi with [(Me(3)tacn)Cr(CF(3)SO(3))(3)] (Me(3)tacn = N,N',N"-trimethyl-1,4,7-triazacyclononane) in THF generates [(Me(3)tacn)Cr(CCSiMe(3))(3)], which subsequently reacts with Bu(4)NF to supply [(Me(3)tacn)Cr(CCH)(3)] as an air-stable orange solid. The crystal structure of this unprecedented triacetylide complex reveals octahedral coordination of the chromium center, with linear Cr-C(triple bond)C bond angles and C(triple bond)C bond distances essentially identical to the corresponding distance in acetylene. Crystallization of the complex from a DMF solution containing K(CF(3)SO(3)) leads to the sandwich complex ([(Me(3)tacn)Cr(CCH)(3)](2)K)(+), in which the K(+) ion is coordinated in a side-on fashion by each of the six C(triple bond)C units. With the larger Cs(+) cation, a triangular ([(Me(3)tacn)Cr(CCH)(3)](3)Cs)(+) complex is instead observed. The magnetic properties of these alkali metal complexes are indicative of weak antiferromagnetic exchange between Cr(III) centers, with J = -0.8 and -0.3 cm(-1), respectively.     

Membrane binding and structure of de novo designed alpha-helical cationic coiled-coil-forming peptides.

We introduce a de novo designed peptide model system that enables the systematic study of 1) the role of a membrane environment in coiled-coil peptide folding, 2) the impact of different domains of an alpha-helical coiled-coil heptad repeat on the interaction with membranes, and 3) the dynamics of coiled-coil peptide-membrane interactions depending on environmental conditions. Starting from an ideal alpha-helical coiled-coil peptide sequence, several positively charged analogues were designed that exhibit a high propensity toward negatively charged lipid membranes. Furthermore, these peptides differ in their ability to form a stable alpha-helical coiled-coil structure. The influence of a membrane environment on peptide folding is studied. All positively charged peptides show strong interactions with negatively charged membranes. This interaction induces an alpha-helical structure of the former random-coil peptides, as revealed by circular dichroism measurements. Furthermore, vesicle aggregation is induced by a coiled-coil interaction of vesicle-bound peptides. Dynamic light scattering experiments show that the strength of vesicle aggregation increases with the peptide's intrinsic ability to form a stable alpha-helical coiled coil. Thus, the peptide variant equipped with the strongest inter- and intra-helical coiled-coil interactions shows the strongest effect on vesicle aggregation. The secondary structure of this peptide in the membrane-bound state was studied as well as its effect on the phospholipids. Peptide conformation within the peptide-lipid aggregates was analyzed by (13)C cross-polarization magic-angle spinning NMR experiments. A uniformly (13)C- and (15)N-labeled Leu residue was introduced at position 12 of the peptide chain. The (13)C chemical shift and torsion angle measurements support the finding of an alpha-helical structure of the peptide in its membrane-bound state. Neither membrane leakage nor fusion was observed upon peptide binding, which is unusual for amphiphatic peptide structures. Our results lay the foundation for a systematic study of the influence of the alpha-helical coiled-coil folding motif in membrane-active events on a molecular level.     

Slipping of a histidine improved the peroxidase activity of a de novo designed polypeptide packing an iron porphyrin

Polypeptides with two histidines and an iron porphyrin (1H⁴⁰-7H⁴⁶) were synthesized with a variety of positions of a histidine. In 4H⁴³, histidine (H⁴³) was in the hydrophobic region of an α-helix. The other polypeptides were of slightly or substantially distorted conformation. In the pH 7.2 buffer solution, two histidines of the polypeptide coordinated the iron porphyrin regardless of their positions. Some polypeptides (1H⁴⁰, 3H⁴², and 5H⁴⁴) showed an enhanced catalytic activity in the peroxidase reaction using cumene hydroperoxide compared to that of 4H⁴³, whereas some polypeptides (2H⁴¹ and 6H⁴⁵) were ineffective catalysts. The distortion of the peptide conformation by the addition of MeOH was also effective for the peroxidase reaction.     

Controlling and fine tuning the physical properties of two identical metal coordination sites in de novo designed three stranded coiled coil peptides

Herein we report how de novo designed peptides can be used to investigate whether the position of a metal site along a linear sequence that folds into a three-stranded α-helical coiled coil defines the physical properties of Cd(II) ions in either CdS(3) or CdS(3)O (O-being an exogenous water molecule) coordination environments. Peptides are presented that bind Cd(II) into two identical coordination sites that are located at different topological positions at the interior of these constructs. The peptide GRANDL16PenL19IL23PenL26I binds two Cd(II) as trigonal planar 3-coordinate CdS(3) structures whereas GRANDL12AL16CL26AL30C sequesters two Cd(II) as pseudotetrahedral 4-coordinate CdS(3)O structures. We demonstrate how for the first peptide, having a more rigid structure, the location of the identical binding sites along the linear sequence does not affect the physical properties of the two bound Cd(II). However, the sites are not completely independent as Cd(II) bound to one of the sites ((113)Cd NMR chemical shift of 681 ppm) is perturbed by the metalation state (apo or [Cd(pep)(Hpep)(2)](+) or [Cd(pep)(3)](-)) of the second center ((113)Cd NMR chemical shift of 686 ppm). GRANDL12AL16CL26AL30C shows a completely different behavior. The physical properties of the two bound Cd(II) ions indeed depend on the position of the metal center, having pK(a2) values for the equilibrium [Cd(pep)(Hpep)(2)](+) → [Cd(pep)(3)](-) + 2H(+) (corresponding to deprotonation and coordination of cysteine thiols) that range from 9.9 to 13.9. In addition, the L26AL30C site shows dynamic behavior, which is not observed for the L12AL16C site. These results indicate that for these systems one cannot simply assign a "4-coordinate structure" and assume certain physical properties for that site since important factors such as packing of the adjacent Leu, size of the intended cavity (endo vs exo) and location of the metal site play crucial roles in determining the final properties of the bound Cd(II).     

Thermally reversible hydrogels via intramolecular folding and consequent self-assembly of a de novo designed peptide

A small de novo designed peptide (MAX3) is described that exhibits complete thermoreversible self-assembly into a hydrogel network. Importantly, a prerequisite to hydrogelation is that the peptide must first fold into a conformation conducive to self-assembly. At ambient temperature, MAX3 is unfolded, resulting in a low viscosity aqueous solution. On increasing the temperature, the peptide undergoes a unimolecular folding event, affording an amphiphilic beta-hairpin that consequently self-assembles into a hydrogel network. Increasing the temperature serves to dehydrate the nonpolar residues of the unfolded peptide and trigger folding via hydrophobic collapse. Cooling the resultant hydrogel results in beta-hairpin unfolding and consequent complete dissolution of the hydrogel. The temperature at which folding and consequent self-assembly into a rigid hydrogel occur can be tuned by altering the hydrophobicity of the peptides.     

Synthesis of new 14- and 16-membered macrocycles and their transition metal complexes

Summary Benzoylacetic acid (1 mol) interacts with ethylenediamine or with propanediamine (2 mol) to yield new N₄ macrocycles 1,5,8,12-tetraazacyclotetradeca-2,4,9,11-tetraphenyl-3, 10-dicarboxylic-4,11-diacetic acid- 1,8-diene (L¹) and 1,5,9,13-tetraazacyclohexadeca-2,4,10,12-tetraphenyl-3, 11-dicarboxylic-4,12-diacetic acid-1,9-diene (L²), respectively. These macrocycles have been successfully complexed with Cr^III, Fe^III, Mn^II, Co^II, Ni^II, Cu^II and Zn^II. The complexes of the divalent metal ions are non-electrolytes, while those of Fe^III and Cr^III are 1:1 electrolytes in DMSO. On the basis of ligand field spectra and magnetic moments an octahedral geometry has been proposed for all the complexes.     

Specific isolation of N-terminal fragments from proteins and their high-fidelity de novo sequencing

A new method to determine N-terminal amino acid sequences of multiple proteins at low pmol level by a parallel processing has been developed. The method contains the following five steps: (1) reduction, S-alkylation and guanidination for targeted proteins; (2) coupling with sulfosucccimidyl-2-(biotinamido)ethyl-1,3-dithiopropionate(sulfo-NHS-SS-biotin) to N(alpha)-amino groups of proteins; (3) digestion of the modified proteins by an appropriate protease; (4) specific isolation of N-terminal fragments of proteins by affinity capture using the biotin-avidin system; (5) de novo sequence analysis of peptides by MALDI-TOF-/MALDI-TOF-PSD mass spectrometry with effective utilization of the CAF (chemically assisted fragmentation) method.1 This method is also effective for N-terminal sequencing of each protein in a mixture of several proteins, and for sequencing components of a multiprotein complex. It is expected to become an essential proteomics tool for identifying proteins, especially when used in combination with a C-terminal sequencing method.     

Synthesis and characterization of diazonium functionalized nanoparticles for deposition on metal surfaces

Silica nanoparticles were surface-functionalized with diazonium groups. The reaction steps leading to the formation of the diazonium functionality were followed with IR and XPS, and the structure of the diazonium-functionalized nanoparticle was confirmed with solid state NMR. Nanoparticle size distribution was determined with DLS, SEM, and TEM. The nanoparticles were then covalently bonded to gold and iron surfaces. Their spatial distribution over the metal surface was analyzed by SEM. Diazonium modification of nanoparticles represents a new method for the covalent attachment of nanoparticles to metal surfaces.     

Synthesis and potent cytotoxic activity of 8- and 9-anilinophenanthridine-7,10-diones

A series of 8-anilino and 9-anilinophenanthridine-7,10-diones was prepared and screened against various cancer cell lines to measure anti-proliferative activity. The compounds tested display potent cytotoxic activity in the micromolar and sub-micromolar range. These compounds are promising new leads for developing anticancer compounds.     

Synthesis and characterization of dimaleimide fluorogens designed for specific labeling of proteins

A series of aromatic compounds were prepared bearing two maleimide groups attached directly to the fluorescent cores. The resulting derivatives do not fluoresce until the maleimide groups undergo their typical thiol addition reaction, thus removing their ability to quench fluorescence, as shown by kinetic and spectral characterization studies. In this way, the title compounds serve as fluorogens capable of detection of small thiols or appropriately sized dithiols. Recombinant alpha-helical proteins were then designed to bear two cysteine residues capable of regioselective dithiol addition reaction with the dimaleimide fluorogens, thus acting as spatially encoded substrates that form specifically labeled covalent complexes. The efficiency of this in vitro fluorescent protein-labeling reaction demonstrates the feasibility of the development of a method for the fluorescent labeling of specific recombinant proteins.     

Cucurbit[8]uril induced heterodimerization of methylviologen and naphthalene functionalized proteins

Cucurbit[8]uril is a supramolecular inducer of protein heterodimerization for proteins appended with methylviologen and naphthalene host elements. Two sets of fluorescent protein pairs, which visualize the specific protein assembly process, enabled the interplay of the supramolecular elements with the proteins to be established.     

Synthesis and electrochemical sensing behaviour of a new ferrocene functionalized tet ‘a’ macrocyclic receptor towards transition metal ions

A new ferrocene functionalized macrocyclic receptor 1,8‐bis(ferrocenylmethyl)‐5,5,7,12,12,14‐hexamethyl‐1,4,8,11‐tetraazacyclotetradecane (R) has been designed and synthesized to study its potential application as chemosensor. The receptor has been characterized by spectral techniques and X‐ray diffraction. The compound crystallizes in the orthorhombic space group Pcab with four molecules in a unit cell (half‐a‐molecule in the asymmetric unit). The electrochemical studies of the receptor in dioxane–water (7:3 v/v, 25 °C) indicate that the receptor is pH‐dependent with a displacement of E_1/2 to more anodic potentials with a decrease in the pH from 12 to 5. The electrochemical behaviour of R was also studied in the presence of Mn²⁺, Co²⁺, Ni²⁺, Cu²⁺ and Zn²⁺ in dioxane–water (7:3 v/v, 25 °C, [Buⁿ₄N][ClO₄]), showing that upon complexation the ferrocene–ferrocenium half‐wave potential shifts anodically in relation to that of the free receptor. The maximum electrochemical shift (ΔE_1/2) of 46 mV was found in the presence of Cu²⁺, followed by Co²⁺ (20 mV), Mn²⁺ (15 mV), Ni²⁺ (13 mV) and Zn²⁺ (9 mV). Moreover, the receptor R is able to electrochemically and selectively sense Cu²⁺ in the presence of the other transition metal cations studied. Copyright © 2007 John Wiley & Sons, Ltd.     

Preparation, characterization and catalytic activity towards green reactions of sulfonic functionalized SBA-15

Acidic heterogeneous catalysts based on the anchorage of sulfonic groups on SBA-15 mesoporous silica were synthesized. In a first synthesis step, samples containing mercapto groups were prepared by co-condensation of tetraethylorthosilicate with 3-mercaptopropyltrimethoxysilane, in presence of ethylene-propylene block copolymer as mesoporous silica structure director. In other samples, mercapto groups were introduced by post-functionalization of the traditional calcined SBA-15. In a second step, these mercapto groups were oxidized in order to get sulfonic acid groups on the surface. Characterization of the samples was carried out by N₂ adsorption-desorption, FTIR, XPS and acid-base titration. Spectroscopic techniques showed that the effective incorporation of sulfonic groups depends on the synthesis methodology used. In turn, the SBA-15 post-synthesis functionalization produces changes in structural characteristics like a decrease in BET surface and changes in the pore size distribution. The as-prepared materials were tested as acid catalysts in the alkylation of isobutane with 1-butene, and in the esterification of free fatty acids with methanol. The results obtained show a lack of activity in the alkylation reaction which can be associated with the formation and stabilization of the intermediate carbocation species.     

Synthesis and cytotoxicity of methyl-and methoxy-substituted metal 8-quinolinethiolates

It has been found that the nature of the substituent, its position in the quinoline ring, and the nature of the metal significantly affect the antitumor activity and toxicity of metal 8-quinolinethiolates. The most cytotoxic towards human fibrosarcoma HT-1080 and mouse hepatoma MG-22A tumor cells are the 6-methoxy-8-quinolinethiolates of rhodium, osmium, iridium, indium, antimony, and bismuth, however these are highly toxic towards normal mouse embryonic NIH 3T3 fibroblasts. The iridium 5-methyl-8-quinolinethiolate is somewhat less active to MG-22A cells but shows quite good selectivity of action because of its markedly lower toxicity. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 711–717, May, 2008.