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Indole oxidation represents a real challenge for selectivity because it typically leads to complex mixtures of products even when highly selective enzymes are used. Here, we describe the catalytic potential of an artificial enzyme, Mn-Mimochrome VI*a (Mn-MC6*a), in promoting indole oxidation. This mini-enzyme contains a manganese-deuteroporphyrin active site within a scaffold of two synthetic small peptides covalently linked to porphyrin. Mn-MC6*a promotes the selective oxidation of indole at its C3 position, leading to a 3-oxindole derivative (2-TFE-3-oxindole) with unprecedented product selectivity (86% at pH 8.5) compared to native or artificial heme-enzymes. We also suggest a possible reaction mechanism based on the effect of pH, cosolvent, and indole substitution on the reaction outcome. These studies demonstrate that Mn-MC6*a is an excellent artificial peroxygenase for the production of 3-oxindole-containing compounds as key building blocks for the synthesis of fine chemicals.

Metalloproteins are crucial for life. The mutual relationship between metal ions and proteins makes metalloproteins able to accomplish key processes in biological systems, often very difficult to reproduce with inorganic coordination compounds under mild conditions. Taking inspiration from nature, many efforts have been devoted to developing artificial molecules as metalloprotein mimics. We have witnessed an explosion of protein design strategies leading to designed metalloproteins, ranging from stable structures to functional molecules. This review illustrates the most recent results for inserting metalloprotein functions in designed and engineered protein scaffolds. The selected examples highlight the potential of different approaches for the construction of artificial molecules capable of simulating and even overcoming the features of natural metalloproteins.

Fe-Mimochrome VI*a is a synthetic peroxidase and peroxygenase, featuring two different peptides that are covalently-linked to deuteroheme. To perform a systematic structure/function correlation, we purposely shortened the distance between the distal peptide and the heme, allowing for the separation and characterization of two regioisomers. They differ in both His axial-ligand orientation, as determined by paramagnetic NMR shifts, and activity. These findings highlight that synthetic metalloenzymes may provide an efficient tool for disentangling the role of axial ligand orientation over peroxidase activity.

Advanced oxidation processes represent a viable alternative in water reclamation for potable reuse. Sensing methods of hydrogen peroxide are, therefore, needed to test both process progress and final quality of the produced water. Several bio-based assays have been developed so far, mainly relying on peroxidase enzymes, which have the advantage of being fast, efficient, reusable, and environmentally safe. However, their production/purification and, most of all, batch-to-batch consistency may inherently prevent their standardization. Here, we provide evidence that a synthetic de novo miniaturized designed heme-enzyme, namely Mimochrome VI*a, can be proficiently used in hydrogen peroxide assays. Furthermore, a fast and automated assay has been developed by using a lab-bench microplate reader. Under the best working conditions, the assay showed a linear response in the 10.0–120 μM range, together with a second linearity range between 120 and 500 μM for higher hydrogen peroxide concentrations. The detection limit was 4.6 μM and quantitation limits for the two datasets were 15.5 and 186 μM, respectively. In perspective, Mimochrome VI*a could be used as an active biological sensing unit in different sensor configurations.

Cationic antimicrobial peptides (CAMPs) are a promising alternative to treat multidrug-resistant bacteria, which have developed resistance to all the commonly used antimicrobial, and therefore represent a serious threat to human health. One of the major drawbacks of CAMPs is their sensitivity to proteases, which drastically limits their half-life. Here we describe the design and synthesis of three nine-residue CAMPs, which showed high stability in serum and broad spectrum antimicrobial activity. As for all peptides a very low selectivity between bacterial and eukaryotic cells was observed, we performed a detailed biophysical characterization of the interaction of one of these peptides with liposomes mimicking bacterial and eukaryotic membranes. Our results show a surface binding on the DPPC/DPPG vesicles, coupled with lipid domain formation, and, above a threshold concentration, a deep insertion into the bilayer hydrophobic core. On the contrary, mainly surface binding of the peptide on the DPPC bilayer was observed. These observed differences in the peptide interaction with the two model membranes suggest a divergence in the mechanisms responsible for the antimicrobial activity and for the observed high toxicity toward mammalian cell lines. These results could represent an important contribution to unravel some open and unresolved issues in the development of synthetic CAMPs.

Synthetic proteins represent useful tools for reproducing metalloprotein functions in minimal, well-defined scaffolds. Herein, we describe the rational refinement of function into heme-protein models from the Mimochrome family. Originally designed to mimic the bis-His cytochrome b, the Mimochrome structure was modified to introduce a peroxidase-like activity, by creating a distal cavity on the heme. The success with the first asymmetric system, Mimochrome VI (MC6), gave the opportunity to explore further modifications in order to improve the catalytic activity. Starting from ferric MC6, single amino acid substitutions were introduced in the peptide chains to obtain four compounds, which were screened for peroxidase activity. The detailed structural and functional analysis of the best analogue, Fe(III)-E(2)L(TD)-MC6, indicates that an arginine residue in proximity to the heme-distal site could assist with catalysis by favoring the formation of the intermediate "compound I", thus mimicking R(38) in HRP. This result highlights the potential of using small scaffolds for exploring the main factors that tune the heme-protein activity, and for programming new desired functions.

Metalloproteins utilize O-2 as an oxidant, and they often achieve a 4-electron reduction without H2O2 or oxygen radical release. Several proteins have been designed to catalyze one or two-electron oxidative chemistry, but the de novo design of a protein that catalyzes the net 4-electron reduction of O-2 has not been reported yet. We report the construction of a diiron-binding four-helix bundle, made up of two different covalently linked (2) monomers, through click chemistry. Surprisingly, the prototype protein, DF-C1, showed a large divergence in its reactivity from earlier DFs (DF: due ferri, two iron). DFs release the quinone imine and free H2O2 in the oxidation of 4-aminophenol in the presence of O-2, whereas Fe-III-DF-C1 sequesters the quinone imine into the active site, and catalyzes inside the scaffold an oxidative coupling between oxidized and reduced 4-aminophenol. The asymmetry of the scaffold allowed a fine-engineering of the substrate binding pocket, that ensures selectivity.

Bioconjugation is a rapidly expanding field because of the numerous potential applications of bioconjugate materials. We explored the usefulness of branched porphyrins as rigid scaffolds, bearing multiple sites for bioconjugation. To this end, we first selected the tetrakis(p-(aminomethyl) phenyl) porphyrin (TAMPP) macrocycle and developed a straightforward synthetic protocol, able to provide the desired tetraphenylporphyrin, carrying four functional amino groups. The partially protection of the amino groups by tert-butoxy-carbonyl allowed the selective and specific decoration of the porphyrin with different peptide sequences. To explore the utility of the macrocycle as molecular scaffold for bioconjugation, we selected peptide sequences able to function as thrombin inhibitors. In particular, two peptide sequences, named CS3 and ES7, able to interact, respectively, with the thrombin catalytic site and the fibrinogen recognition exosite, were joined onto the porphyrin macrocycle, providing the multisite-directed inhibitor CS3-TAMPP-ES7. This multisite inhibitor and its Mn III complex are able to inhibit α-thrombin-catalyzed hydrolysis of Tos-Gly-Pro-Arg-nitroanilide with inhibition constants in the micromolar range, as well as the hydrolysis of the natural substrate fibrinogen. The inhibitor is resistant against enzymatic degradation by thrombin and is highly selective. The Mn III complex is capable of interacting with clot-bound thrombin and partially inhibits clot growth in the presence of fibrinogen. The results herein reported are very promising, suggesting the potential of the newly developed conjugate as new imaging agents for clot detection. C

Glycosylation is an important PTM in proteins, and it is of paramount importance for the manufacture and efficacy of therapeutic glycoproteins. The elucidation of the glycosylation patterns is greatly hampered by the structural heterogeneity, which involves the oligosaccharide moieties, and sometimes also the protein chain. Several strategies are used to map the glycosylation state of glycoproteins: they generally involve analysis of the glycopeptides obtained upon glycoprotein proteolytic digestion, and/or analysis of the glycans, enzymatic or chemically released from the glycoproteins. These approaches are efficient in determining the total glycan content, as well as the glycan structures; nevertheless, information regarding the whole protein is lost. Recent advances in MS allowed us to directly analyze human follicle stimulating hormone (hFSH). RP-HPLC/IT-TOF MS, coupled to bioinformatic algorithms, was used to determine the glycan content of intact hFSH preparations, either urinary-derived or recombinant. More traditional and complementary analytical methods (oligosaccharide profiling, IEF, and peptide mapping analyses) were employed to compare the obtained results. Our analysis shows a predominance of highly sialylated, highly branched glycans in a urinary hFSH preparation as compared to recombinant hFSH expressed in rodent cell lines. Noteworthy, high-resolution mass spectra may allow to evaluate the glycosylation profile during the manufacturing process of different preparations.

The chemokine receptor CCR5 is utilized as a critical coreceptor by most primary HIV-1 strains. While the lack of structural information on CCR5 has hampered the rational design of specific inhibitors, mimetics of the chemokines that naturally bind CCR5 can be molecularly engineered. We used a structure-guided approach to design peptide mimetics of the N-loop and β1-strand regions of regulated on activation normal T-cell-expressed and secreted (RANTES)/CCL5, which contain the primary molecular determinants of HIV-1 blockade. Rational modifications were sequentially introduced into the N-loop/β1-strand sequence, leading to the generation of mimetics with potent activity against a broad spectrum of CCR5-specific HIV-1 isolates (IC50 range: 104–640 nM) but lacking activity against CXCR4-specific HIV-1 isolates. Functional enhancement was initially achieved with the stabilization of the N loop in the β-extended conformation adopted in full-length RANTES, as confirmed by nuclear magnetic resonance (NMR) analysis. However, the most dramatic increase in antiviral potency resulted from the engraftment of an in silico-optimized linker segment designed using de novo structure-prediction algorithms to stabilize the C-terminal α-helix and experimentally validated by NMR. Our mimetics exerted CCR5-antagonistic effects, demonstrating that the antiviral and proinflammatory functions of RANTES can be uncoupled. RANTES peptide mimetics provide new leads for the development of safe and effective HIV-1 entry inhibitors.—Lusso, P., Vangelista, L., Cimbro, R., Secchi, M., Sironi, F., Longhi, R., Faiella, M., Maglio, O., Pavone, V. Molecular engineering of RANTES peptide mimetics with potent anti-HIV-1 activity.

Many efforts are continuously devoted to the construction of hybrid biomaterials for specific applications, by immobilizing enzymes on different types of surfaces and/or nanomaterials. In addition, advances in computational, molecular and structural biology have led to a variety of strategies for designing and engineering artificial enzymes with defined catalytic properties. Here, we report the conjugation of an artificial heme enzyme (MIMO) with lipoic acid (LA) as a building block for the development of gold-based biomaterials. We show that the artificial MIMO@LA can be successfully conjugated to gold nanoparticles or immobilized onto gold electrode surfaces, displaying quasi-reversible redox properties and peroxidase activity. The results of this work open interesting perspectives toward the development of new totally-synthetic catalytic biomaterials for application in biotechnology and biomedicine, expanding the range of the biomolecular component aside from traditional native enzymes.

The dodecapeptide Ac-Asp-Lys-Asp-Gly-Asn-Gly-Tyr-Ile-Ser-Ala-Ala-Gaba-OH is a modified calmodulin calcium binding domain III. The synthesis of the peptide by the solid phase method with a total protection scheme using PAM-resin is reported. The purified compound has been characterized by 1H n.m.r. spectroscopy, both in the presence and in the absence of calcium ions, at various pHs. No strong specific interaction seems to occur between the peptide and Ca++ ions in water solutions.

A major objective in protein science is the design of enzymes with novel catalytic activities that are tailored to specific applications. Such enzymes may have great potential in biocatalysis and biosensor technology, such as in degradation of pollutants and biomass, and in drug and food processing. To reach this objective, investigations into the basic biochemical functioning of metalloproteins are still required. In this perspective, metalloprotein design provides a powerful approach first to contribute to a more comprehensive understanding of the way metalloproteins function in biology, with the ultimate goal of developing novel biocatalysts and sensing devices. Metalloprotein mimetics have been developed through the introduction of novel metal-binding sites into naturally occurring proteins as well as through de novo protein design. We have approached the challenge of reproducing metalloprotein active sites by using a miniaturization process. We centered our attention on iron-containing proteins, and we developed models for heme proteins and diiron–oxo proteins. In this paper we summarize the results we obtained on the design, structural, and functional properties of DFs, a family of artificial diiron proteins.

A single polypeptide chain may provide an astronomical number of conformers. Nature selected only a trivial number of them through evolution, composing an alphabet of scaffolds, that can afford the complete set of chemical reactions needed to support life. These structural templates are so stable that they allow several mutations without disruption of the global folding, even having the ability to bind several exogenous cofactors. With this perspective, metal cofactors play a crucial role in the regulation and catalysis of several processes. Nature is able to modulate the chemistry of metals, adopting only a few ligands and slightly different geometries. Several scaffolds and metal-binding motifs are representing the focus of intense interest in the literature. This review discusses the widespread four-helix bundle fold, adopted as a scaffold for metal binding sites in the context of de novo protein design to obtain basic biochemical components for biosensing or catalysis. In particular, we describe the rational refinement of structure/function in diiron–oxo protein models from the due ferri (DF) family. The DF proteins were developed by us through an iterative process of design and rigorous characterization, which has allowed a shift from structural to functional models. The examples reported herein demonstrate the importance of the synergic application of de novo design methods as well as spectroscopic and structural characterization to optimize the catalytic performance of artificial enzymes.

Peptide-based metalloprotein models represent useful systems to help understand how metalloproteins can support different functions, by the use of similar metal ion cofactors. In order to shed light on the role of the protein matrix in modulating the heme properties, we developed new models: mimochromes. They are pseudo-C(2) symmetric systems, composed of two helical peptides covalently linked to the deuteroporphyrin. The use of C(2) symmetry is particularly advantageous, because it simplifies the design, synthesis and characterization. However, it leaves the problem of possible diastereomeric forms. In the cobalt complex of the first derivative, mimochrome I, Lambda and Delta isomers were indeed experimentally observed. All the insights derived from the Co(III)-mimochrome I structure were used to obtain a re-designed molecule, mimochrome IV. The spectroscopic characterization of the iron and cobalt derivatives suggested the presence of the Lambda isomer as unique species. The NMR solution structure of the diamagnetic Co(III)-mimochrome IV confirmed the ability of the molecule to adopt a unique topology, and revealed the peptide chains to be in helical conformation, as designed. The insertion of intramolecular, inter-chain interactions was successful in favoring the formation of one of the two possible diastereomers. The stereochemically stable structure of mimochrome IV provides an attractive model for modulating the redox potential of the heme, by simple changing the peptide chain composition around the heme.

A fully protected tripeptide containing a novel Cα,α-disubstituted glycine—α,α-di(2-pyridyl)glycine (2Dpy)—in the central position and Cα,α-dimethylglycine (Aib) in positions 1 and 3 was synthesized and structurally characterized by single crystal X-ray analysis. The 2Dpy residue bears two 2-pyridyl moieties, which may coordinate metal ions, and promote self-assembly of peptide units. The tripeptide Z-Aib1-2Dpy2-Aib3-OCH3 (Z: benzyloxycarbonyl) adopts in the solid state a folded type III (III′) β-turn conformation (with Aib1-2Dpy2 as corner residues), stabilized by an i ← i + 3 hydrogen bond between the Aib3 NH and the urethane CO group. The peptide was able to self-assemble in the presence of Cu(II) ions, giving rise to an octahedral complex with a 2 : 1 peptide/Cu(II) stoichiometry, which has been structurally characterized. The metal ion, arranged on a crystallographic symmetry centre, is coordinated by two symmetry related 2Dpy residues, which act as tridentate ligands: each 2Dpy residue donates to the Cu(II) the N atoms of both pyridyl moieties in the equatorial positions, and the carbonyl oxygen atom in the axial positions. A very similar folded conformation characterizes the peptide in both the free and metal-bound states. This indicates that the overall peptide structure is ready to coordinate the metal ion without substantial conformational changes. Metal binding of the tri-peptide toward copper ions was analyzed by UV-visible spectroscopy performed in methanol solution. The experimental data agree with an equilibrium between two species in solution, one in the ratio Cu/peptide 1 : 1, the other 1 : 2. The formation constants are 9.7 × 103 M−1 and 3.5 × 102 M−1, respectively. The molar extinction coefficients are 66 ± 3 M−1 cm−1 (590 nm) for the 2 : 1 complex and 17 ± 2 M−1 cm−1 (690 nm) for the other. All the data obtained in the present work suggest that the 2Dpy residue is well suited to be accommodated into folded conformations. The spontaneous formation of an ordered structure by the 2Dpy containing tri-peptide and copper ions may guide toward the design of more elaborate self-assembling systems.

We have investigated the conformational preferences of a newly synthesized C(alpha,alpha) symmetrically disubstituted glycine, namely alpha,alpha-dicyclopropylglycine (Dcp). We report here the crystal structure of a fully protected dipeptide containing Dcp, namely Z-Dcp(1)-Dcp(2)-OCH(3). Both Dcp residues are in a folded conformation. The overall peptide structural organization corresponds to an alpha-pleated sheet conformation, similar to that observed in linear peptides made up of alternating D- and L-residues and in Z-Aib-Aib-OCH(3) (Aib: alpha,alpha-dimethylglycine). These preliminary data suggest that the Dcp could represent an alternative as molecular tool to stabilize folded conformations.

Recent studies on the conformational preferences of the Dphig (C(alpha,alpha)-diphenylglycine) residue showed that this C(alpha,alpha)-disubstituted glycine has a structural versatility. In fact, depending on the nature of the following or preceding residue, Dphig can assume either folded or extended conformations. We have carried out the analysis of the conformational preferences of the Dphig residue in tripeptides containing consecutive Dphig residues. The crystal structures of Z-Dphig-Dphig -Dphig-OMe (a; Z = benzyloxycarbonyl; OMe = methyl ester), Z-Aib-Dphig-Dphig-OMe (b; Aib = alpha-aminoisobutyric acid), and Z-Ac(3)c-Dphig-Dphig-OMe (c; Ac(3)c = alpha-amino-cyclopropan carboxylic acid), are here reported. The Dphig residues adopt the fully extended conformation in the three tripeptides examined. Together with our previous findings on Dphig containing peptides, the structures of the peptides here examined, indicate that the presence of adjacent Dphig residue in the sequence further stabilizes the extended conformation.

The crystal structures of three fully protected tripeptides containing the Dϕg residue (Cα,α-diphenylglycine) in the central position are reported, namely Z-Gly-Dϕg-Gly-OMe (a), Z-Gly-Dϕg-Aib-OMe (b) and Z-Aib-Dϕg-Aib-OMe (c). The molecular conformations are quite unusual because the Dϕg residue adopts a folded conformation in the 310-helical region when the following residue adopts a folded conformation of opposite handedness (peptidesbandc). In contrast, the Dϕg residue adopts the more frequently observed fully extended conformation when the following residue adopts a semi-extended conformation (peptidea). These findings are in agreement with the theoretical calculations on Ac-Dϕg-Aib-NHCH3 and Ac-Aib-Dϕg-NHCH3 also reported in this work. © 1998 European Peptide Society and John Wiley & Sons, Ltd.

The 2,2,8-triisopropyl-4,5,7,8-tetrahydroimidazo[1,2-a]pyrazin-3,6-dione molecule, C15H25N3O2, has a double bond and two partial double bonds in the bicyclic skeleton, with some π-delocalization along C'1—N3—C'2. The conformation parameters of the diisopropyl (Dip) residue reveals that it is in an unusually high energy conformation. The peptide bond between the glycine and valine residues is cis [Cα3—C'3—N1—Cα1 = −7.0 (3)°]. In the crystal, the molecules are held together in the ac plane of the P2/n space group by intermolecular hydrogen bonds formed around a twofold axis by molecules related by symmetry centres.

We recently reported the rational design, synthetics, and structural characterization of the most potent and selective peptide-based neurokinin A antagonist thus far described: cyclo(Met1-Asp2-Trp3-Phe4-Dap5-Leu6)cyclo(2 beta-5 beta). Its bicyclic structure is characterized by a type I and a type II two beta-turn around Trp3-Phe4 and Leu6-Met1, respectively. In order to understand whether the two different beta-turned structures are determined by the bicyclic structure or by the amino acid type at the corner positions, we have synthesized the pseudo-symmetrical analogue cyclo(Phe1-Asp2-Trp3-Phe4-Dap5-Trp6)cyclo(2 beta-5 beta). The structural characterization in the crystal state and in solution, here reported, gives an experimental evidence that the backbone of the bicyclic structure is a rigid scaffold that can be used to build both a type I and type II beta-turn independently from the amino acid composition.

The cyclic octapeptide cyclo[‐Pro1‐Pro‐Phe‐Phe‐Ac6c‐Ile‐ala‐Val8‐] [C8‐Ac6c], containing the Pro1‐Pro‐Phe‐Phe sequence, followed by a bulky helicogenic Cα,α‐dialkylated glycine residue Ac6c (1‐aminocyclohexane‐1‐carboxylic acid), and a D‐Ala residue at position 7 has been synthesized. This cyclic peptide is a deletion analogue of the naturally occurring cyclic nonapeptide cyclolinopeptide A (CLA). It has been designed with the aim of studying the role that the Ac6c and D‐Ala residues play on the conformational behaviour of the whole molecule and their influence on the conformation of the Pro1‐Pro‐Phe‐Phe sequence when compared with cyclolinopeptide A. C8Ac6c has been investigated in chloroform and acetonitrile solutions by 2D NMR techniques. Only one set of sharp signals is observed in both solvents. This evidence strongly supports the hypothesis that only one conformational state exists in the chosen solvents. The interpretation of the experimental data points to the existence for C8‐Ac6c of a very rigid structure stabilized by intramolecular hydrogen bonds. The measured NOE effects allow the calculation of internuclear distances, which have been used as restraints in molecular dynamic calculations. The proposed conformation of the molecule shows that the Pro‐Pro‐Phe segment retains the conformation observed in natural CLA both in solution and in the solid state and that the Ac6c residue indeed reinforces the ring rigidity not permitting the formation of any appropriate cavity in which inorganic cations could be complexed. Copyright © 1995 European Peptide Society and John Wiley & Sons Ltd.

The Bridging Sheet domain of HIV-1 gp120 is highly conserved among the HIV-1 strains and allows HIV-1 binding to host cells via the HIV-1 coreceptors. Further, the bridging sheet domain is a major target to neutralize HIV-1 infection. We rationally designed four linear peptide epitopes that mimic the three-dimensional structure of bridging sheet by using molecular modeling. Chemically synthesized peptides BS3 and BS4 showed a fair degree of antigenicity when tested in ELISA with IgG purified from HIV+ broadly neutralizing sera while the production of synthetic peptides BS1 and BS2 failed due to their high degree of hydrophobicity. To overcome this limitation, we linked all four BS peptides to the COOH-terminus of GST protein to test both their antigenicity and immunogenicity. Only the BS1 peptide showed good antigenicity, however, no envelope specific antibodies were elicited upon mice immunization. Therefore we performed further analyses by linking BS1 peptide to the NH2-terminus of the E2 scaffold from the Geobacillus Stearothermophylus PDH complex. The E2-BS1 fusion peptide showed good antigenic results, however only one immunized rabbit elicited good antibody titers towards both the monomeric and oligomeric viral envelope glycoprotein (Env). In addition, moderate neutralizing antibodies response was elicited against two HIV-1 clade B and one clade C primary isolates. These preliminary data validate the peptide mimotope approach as a promising tool to obtain an effective HIV-1 vaccine.

In the present paper we describe the synthesis, purification, single crystal x-ray analysis, and nmr solution characterization, combined with restrained molecular dynamic simulations, of the cyclic hexapeptide cyclo-(L-Pro-L-Phe-β-Ala)2. The peptide was synthesized by classical solution methods and the cyclization of the free hexapeptide was accomplished in good yields in diluted methylene chloride solution using N,N-dicyclohexyl-carbodiimide. The compound crystallizes in the monoclinic space group P21 from methanol-dichloro-methane solution. The two identical halves of the molecule adopt in the solid state two different conformations. One β-Ala-L-Pro peptide bond is trans, while the second is cis. The molecule is present in dimethylsulfoxide d6 solutions as a mixture of conformational families. One of these corresponds to a C2 symmetrical molecule with both β-Ala-Pro cis peptide bonds, while the second major conformation is very similar to that observed in the solid state. All Pro-Phe segments, both in the solid state and the symmetrical and unsym-metrical solution conformations, display ϕ,ψ angles close to that of position i + 1 and i + 2 of type II β-turns. In addition, the segments preceeded by a trans β-Ala-Pro peptide bond are characterized by a typical i i + 3 hydrogen bond, which is absent in the conformer containing a cis β-Ala-Pro peptide bond. The latter conformation corresponds to a new structural domain we define as the “pseudo type II β-turn.” © 1994 John Wiley & Sons, Inc.

The fully blocked pentapeptide Tfa‐(Deg)2‐L‐Abu‐(Deg)2‐OtBu (Tfa:triflouroacetyl; Deg: Cα,α‐diethylglycine; OtBu: tert‐butoxy) adopts in the crystal state a regular, right‐handed 310‐helical structure stabilized by three N  H … O  C intramolecular 1 ← 4 (or C10) H bonds, as determined by an x‐ray diffraction analysis. However, a Fourier transform ir absorption and 1H‐nmr study strongly supports the view that in deuterochloroform solution the four Deg residues at both termini of the peptide main chain are involved in successive, fully extended C5 forms. A comparison with the stable, fully developed, multiple C5 conformation of Tfa‐(Deg)5‐OtBu indicates that incorporation of an Abu guest residue, interrupting the side‐chain uniformity of the host (Deg)5 homopeptide, while altering only marginally the conformation in a solvent of low polarity, is responsible for a dramatic perturbation of the crystal‐state structure. © 1994 John Wiley & Sons, Inc. Copyright © 1994 John Wiley & Sons, Inc.

In the present paper we describe the synthesis, purification, single-crystal x-ray analysis, solution conformational characterization, and conformational energy calculations of the cyclic tetrapeptide cyclo- (β-Ala-L-Pro-β-Ala-L-Val). The peptide was synthesized by classical solution methods and the cyclization of the free tetrapeptide was accomplished in good yields in diluted methylene chloride solution using N,N-dicyclohexyl-carbodiimide. The compound crystallizes in the monoclinic space group P21 from ethanol with two independent molecules in the unit cell. All peptide bonds are trans. The nmr molecular conformation in the acetonitrile solution as well as that derived from the molecular dynamic simulation in vacuo is quite different from those observed in the solid state and is very similar to that previously observed for the parent compound cyclo-(β-Ala-L-Pro-β-Ala-L-Pro). © 1993 John Wiley & Sons, Inc.

Mimicking enzymes with alternative molecules represents an important objective in synthetic biology, aimed to obtain new chemical entities for specific applications. This objective is hampered by the large size and complexity of enzymes. The manipulation of their structures often leads to a reduction of enzyme activity. Herein, we describe the spectroscopic and functional characterization of Fe(III)-mimochrome VI, a 3.5 kDa synthetic heme-protein model, which displays a peroxidase-like catalytic activity. By the use of hydrogen peroxide, Fe(III)-mimochrome VI efficiently catalyzes the oxidation of several substrates, with a typical Michaelis-Menten mechanism and with several multiple turnovers. The catalytic efficiency of Fe(III)-mimochrome VI in the oxidation of 2,2'-azino-di(3-ethyl-benzothiazoline-6-sulfonic acid (ABTS) and guaiacol (k(cat)/K(m)=4417 and 870 mM(-1) s(-1), respectively) is comparable to that of native horseradish peroxidase (HRP, k(cat)/K(m)=5125 and 500 mM(-1) s(-1), respectively). Fe(III)-mimochrome VI also converts phenol to 4- and 2-nitrophenol in the presence of NO(2) (-) and H(2) O(2) in high yields. These results demonstrate that small synthetic peptides can impart high enzyme activities to metal cofactors, and anticipate the possibility of constructing new biocatalysts tailored to specific functions.

Mimochrome VI (MC-VI) is a synthetic heme peptide containing a helix-heme-helix sandwich motif designed to reproduce the catalytic activity of heme oxidases. The thermodynamics of Fe(III) to Fe(II) reduction and the kinetics of the electron-transfer process for MC-VI immobilized through hydrophobic interactions on a gold electrode coated with a nonpolar SAM of decane-1-thiol have been determined through cyclic voltammetry. Immobilization slightly affects the reduction potential of MC-VI, which under these conditions electrocatalytically turns over molecular oxygen. This work sets the premise for the exploitation of totally synthetic mimochrome-modified electrode surfaces for clinical and pharmaceutical biosensing.

The 2,2,8-triisopropyl-4,5,7,8-tetrahydroimidazo[1,2-a]pyrazin-3,6-dione molecule, C15H25N3O2, has a double bond and two partial double bonds in the bicyclic skeleton, with some π-delocalization along C'1—N3—C'2. The conformation parameters of the diisopropyl (Dip) residue reveals that it is in an unusually high energy conformation. The peptide bond between the glycine and valine residues is cis [Cα3—C'3—N1—Cα1 = −7.0 (3)°]. In the crystal, the molecules are held together in the ac plane of the P2/n space group by intermolecular hydrogen bonds formed around a twofold axis by molecules related by symmetry centres.

We report here the synthesis and preliminary pharmacological characterization of a novel Neurokinin A receptor antagonist. This molecule contains a dehydroalanine residue. It displays a high conformational rigidity and possesses very high activity. Its pharmacological properties as a neurokinin A receptor antagonist were assessed in in vitro experiments on rat vas deferens and were compared to those of Neuronorm and MEN10627.

The design, synthesis, and metal-binding properties of DF3, a new de novo designed di-iron protein model are described (‘‘DF’’ represents due ferri, Italian for ‘‘two iron,’’ ‘‘di-iron’’). DF3 is the latest member of the DF family of synthetic proteins. They consist of helix–loop– helix hairpins, designed to dimerize and form an antiparallel four-helix bundle that encompasses a metal-binding site similar to those of non-heme carboxylate-bridged di-iron proteins. Unlike previous DF proteins, DF3 is highly soluble in water (up to 3 mM) and forms stable complexes with several metal ions (Zn, Co, and Mn), with the desired secondary structure and the expected stoichiometry of two ions per protein. UV–vis studies of Co(II) and Fe(III) complexes confirm a metal-binding environment similar to previous di- Co(II)- and di-Fe(III)-DF proteins, including the presence of a l-oxo-di-Fe(III) unit. Interestingly, UV–vis, EPR, and resonance Raman studies suggest the interaction of a tyrosine adjacent to the di-Fe(III) center. The design of DF3 was aimed at increasing the accessibility of small molecules to the active site of the four-helix bundle. Indeed, binding of azide to the di-Fe(III) site demonstrates a more accessible metal site compared with previous DFs. In fact, fitting of the binding curve to the Hill equation allows us to quantify a 150% accessibility enhancement, with respect to DF2. All these results represent a significant step towards the development of a functional synthetic DF metalloprotein.

The conformational analysis of [Aib 5,6 -D-Ala 8 ]cyclolinopeptide A, in the solid state and solution, has been carried out by X-ray diffraction and NMR spectroscopy. The structure of the orthorhombic form, obtained from methanol-water mixture [a=29.92 (3) A b=19.85 (3) A, c=9.90 (1) A, space group P2 1 2 1 2 1 Z=4], shows the presence of five in N-H...O=C hydrogen bonds, with formation of one C 17 ring structure, one α-turn (C 13 ), one γ-turn (C 7 ), and two β-turns (C 10 , one of type III and one of type I)

The trans-[Cl2-Pt-(H-Aib-OH)2] and trans-[Pt-(H-Aib-O−)2] complexes have been synthesized and characterized in solution and in the solid state. Their crystal and molecular structures have been determined by X-ray diffraction analyses. The complexes show a distorted planar coordination around the heavy atom. The organic moiety in the two complexes shows different conformations: in trans-[Pt-(H-Aib-O−)2] the amino acid residue, acting as a bidentate, is forced to assume an unusual conformation. On the other hand, in trans-[Cl2-Pt-(H-Aib-OH)2], in which the amino acid acts as a monodentate ligand, the α-aminoisobutyric acid assumes an extended conformation, which in general for α-monosubstituted amino acid residues coordinated to the platinum should be the preferred conformation. In both crystal structures hydrogen bonds are formed between the donor and acceptor groups with further stabilization deriving from van der Waals interactions between hydrophobic moieties.

A survey of literature for the various types of helices experimentally observed in high-resolution single crystal x-ray diffraction analyses of peptides has allowed to determine accurate conformational and helical parameters for the various secondary structures such as the alpha-helix, the 3(10)-helix, the fully extended conformation (2(5)-helix) and the beta-bend ribbon spiral. For each of these structures the characteristic phi, psi conformational parameters, n, the number of residues per turn, h, the height per residues and p, the pitch of the helix are described.

In the present paper we describe the synthesis, purification, single crystal x-ray analysis, and solution conformational characterization of the cyclic tetrapeptide cyclo-(L-Pro-beta-Ala-L-Pro-beta-Ala). This peptide was synthesized by classical solution methods and the cyclization of the free tetrapeptide was accomplished in good yields in diluted methylene chloride solution using N,N-dicyclohexyl-carbodiimide (DCCI). The compound crystallizes in the orthorombic space group P2(1)2(1)2(1) from ethyl acetate. All peptide bonds are trans. The molecular conformation is stabilized by two intramolecular hydrogen bonds between the CO and NH groups of the two beta-alanine residues. These hydrogen bonds take place in a C7 structure in which both proline residues occupy the 2 position of an inverse gamma-turn. The two beta-alanine residues have a typical folded conformation (around the C alpha-C beta bond) observed in other cyclic peptides containing this residue. A detailed 1H-nmr analysis in CD3CN solution has been carried out. The molecule assumes a twofold symmetry in solution with a molecular conformation consistent with that observed in the solid state.

Urokinase receptor (uPAR) plays a key role in physiological and pathological processes sustained by an altered cell migration. We have developed peptides carrying amino acid substitutions along the Ser 88 -Arg-Ser-Arg-Tyr 92 (SRSRY) uPAR chemotactic sequence. The peptide pyro glutamic acid (pGlu)-Arg-Glu-Arg-Tyr-NH2 (pERERY-NH 2 ) shares the same binding site with SRSRY and competes with N -formyl-Met-Leu-Phe (fMLF) for binding to the G-protein-coupled N -formyl-peptide receptor (FPR). pERERY-NH 2 is a dose-dependent inhibitor of both SRSRY- and fMLF-directed cell migration, and prevents agonist-induced FPR internalization and fMLF-dependent ERK1/2 phosphorylation. pERERY-NH 2 is a new and potent uPAR inhibitor which may suggest the generation of new pharmacological treatments for pathological conditions involving increased cell migration.

The solid state conformational analysis of the ionophoric homodetic bicyclic cyclo(Glu-Leu-Pro-Gly-Lys-Leu-Pro-Gly)cyclo(1γ-5ϵ)Gly (BCP3) has been carried out by x-ray diffraction. It crystallizes with 4.5 molecules of water per peptide molecule in the monoclinic system, space group P21, with a = 11.425 A, b = 16.616 A, c = 13.931 A, β = 109.24°, and Z = 2. The structure has been determined by direct methods and refined to an R factor of 0.061 for 2448 observed reflections. The structure characterized by all trans peptide bonds is stabilized by three intramolecular hydrogen bonds: a type II β-turn, a mixed type I-type III β-turn, and a pseudo γ-turn, which involves the side chain CO and the main-chain NH groups of the Glu1 residue. The resulting globular molecule presents a rather hydrophilic surface with most of the CO groups available to hydration of the solvent molecules, which are linked through hydrogen bonds of the NH … O or OH … O types in a complicated H-bonding scheme. The conformation observed in the solid state is rather different from the conformation proposed in solution for both the free and the Ca2+-complexed BCP3 molecule.

HIV initiates its infectious cycle by docking to CD4 and a chemokine receptor, most commonly CCR5. RANTES, a natural CCR5 ligand, is a potent inhibitor of HIV-1. Despite the lack of structural information on the RANTES-CCR5 complex, determinants of HIV blockade were previously identified within the RANTES N-loop and beta1-strand regions. A prototype N-loop/beta1-strand peptide, named R11-29, contains two terminal hydrophobic stretches separated by a central hydrophilic region. Here, the role of the terminal hydrophobic clusters was investigated by means of amino acid substitutions or deletions. Most hydrophobic residues in these clusters were shown to be fundamental for the anti-HIV activity. However, increasing the hydrophobicity of the two clusters using non-natural amino acids did not significantly improve the potency of the peptides. These results may provide instrumental knowledge for the rational design of RANTES-derivative molecules with increased anti-HIV activity.

Calmodulin (CaM) is an acidic protein of 148 amino acid residues that plays a central role in cellular regulation by relating the levels of cellular calcium to the activities of regulatory proteins, such as kinases, phosphatases, etc. Recent studies with synthetic models and natural peptides have shown that CaM recognizes positively charged, amphiphilic peptides [1]. There is no exact sequence homology in the CaM binding proteins, but they frequently contain segments rich in basic residues (Arg, Lys, His) and are capable of adopting, when they bind to CaM, an amphiphilic conformation. These observations demonstrated that this structural feature is important for binding, and that hydrophobic and electrostatic interactions both play a relevant role. We report here our approach for the design of an dimer covalently linked in a parallel or antiparallel orientation that is able to specifically interact with only one of the target enzymes recognized by CaM and form three stranded coiled coils. The target sequence that we chose for binding was the CaM binding domain of calcineurin. This important enzyme is the target of immunosuppressive drugs, such as cyclosporin A and FK506. A peptide that specifically binds to calcineurin could be expected to be either an immune-stimulant or an immune-suppressant, depending on whether it activates or inhibits activation of the enzyme.

The properties of mimochrome II, a hemoprotein model compound, were evaluated in relation to the peptide chain composition and length and its importance in controlling heme properties.

We previously identified the major structural determinants of CCR5 binding and HIV blockade in RANTES, describing linear RANTES-derived peptides with biological activity in the low micromolar range (Nardese et al., 2001). To deepen our understanding of RANTES structure-function relations and obtain more potent antiviral peptido-mimetics, we have extensively mutagenized the prototypic peptide, R11-29. This presents two clusters of hydrophobic residues at its termini, (corresponding to RANTES N-loop and b1-strand) connected by a positivelycharged linker. Single or multiple alanine substitutions within the Nor C-terminal hydrophobic clusters resulted in a dramatic loss of antiviral activity, whereas deletion of selected residues within the hydrophilic linker had no major functional consequences. Based on RANTES 3D structure, we designed a series of modified peptides, resulting in a progressive increase in specific antiviral activity. These peptides also displayed anti-inflammatory properties blocking RANTES-elicited lymphocyte chemotaxis. Through serial passages in culture in the presence of increasing concentrations of the most effective antiviral peptides, we have derived variants of the R5 HIV-1 isolate BaL resistant to the peptide inhibitory activity. Complete sequencing of the envelope genes from such variants is currently underway. Our results provide new insights into the structure of the receptor-binding region of RANTES and identify new antiviral peptides that may be instrumental in the development of effective HIV-1 entry inhibitors. from 2005 International Meeting of The Institute of Human Virology Baltimore, USA, 29 August – 2 September 2005

Peptide-based models have an enormous impact for the development of metalloprotein models, as they seem appropriate candidates to mimic both the structural characteristics and reactivity of the natural systems. Through the de novo design of four-helix bundles, we developed the DF (Due Ferri) family of artificial proteins, as models of di-iron and di-manganese metalloproteins. The goal of our research is to elucidate how the electrostatic environment, polarity and solvent accessibility of the metal-binding site, influence the functional properties of di-iron proteins. The first two subsets of the DF protein family, DF1 and DF2, consist of two non-covalently associated helix-loop-helix motifs, which bind the di-metal cofactor near the center of the structure. The DF2 subset was designed to improve the properties of DF1: DF2 and DF2t have several changes in their sequences to improve solubility and metal ion access, as well as a change in the loop connecting the two helices. In order to evaluate how these changes affect the overall structure of the model proteins, we solved the NMR structures of the di-Zn(II) complexes of DF2 and DF2t, and compared these structures with those recently obtained from X-ray crystallography. Further, we examined the thermodynamic consequences associated with the mutations, by measuring the stability of DF2t in the presence of different metal ions, and comparing the results with the data already obtained for DF2. Taken together, analysis of all the data showed the importance of the turn conformation in the design and stability of four-helix bundle.

De novo protein design provides an attractive approach for the construction of models to probe the features required for the function of complex metalloproteins. These minimal models contain the essential elements believed necessary for activity of the protein. Here, the authors summarize the design, structure detn., and functional properties of a family of artificial diiron proteins which include DF1, DF2, DF2t, and DFsc.

The miniaturization process applied to rubredoxins generated a class of peptide-based metalloprotein models, named METP ( m iniaturized e lectron t ransfer p rotein). The crystal structure of Desulfovibrio vulgaris rubredoxin was selected as a template for the construction of a tetrahedral (S γ -Cys) 4 iron-binding site. Analysis of the structure showed that a sphere of 17 Å in diameter, centered on the metal, circumscribes two unconnected approximately C 2 symmetry related β-hairpins, each containing the -Cys-(Aaa) 2 -Cys- sequence. These observations provided a starting point for the design of an undecapeptide, which self assembles in the presence of tetrahedrally coordinating metal ions. The METP peptide was synthesized in good yield by standard methodologies. Successful assembly of the METP peptide with Co(II), Zn(II), Fe(II/III), in the expected 2:1 stoichiometry, was proven by UV-visible and circular dichroism spectroscopies. UV-visible analysis of the metal complexes indicated the four Cys ligands tetrahedrally arrange around the metal ion, as designed. Circular dichroism measurements on both the free and metal-bound forms revealed that the metal coordination drives the peptide chain to fold into a turned conformation. NMR characterization of the Zn(II)-METP complex fully supported the structure of the designed model. These results prove that METP reproduces the main features of rubredoxin.

In this paper we have reported a preliminary analysis of the functional and structural properties of a rationally designed DNA-binding peptide. Finger 4 is able to bind a DNA target sequence. More remarkably, the peptide sequence shows a high helical content, thus demonstrating the effectiveness of the Aib residue in inducing helical structures even in highly charged, water-solubles peptides.

The X-ray crystal structure of the human alpha-thrombin-hirunorm IV complex has been determined at 2.5 A resolution, and refined to an R-factor of 0.173. The structure reveals an inhibitor binding mode distinctive of a true hirudin mimetic, which justifies the high inhibitory potency and the selectivity of hirunorm IV. This novel inhibitor, composed of 26 amino acids, interacts through the N-terminal end with the alpha-thrombin active site in a nonsubstrate mode, and binds specifically to the fibrinogen recognition exosite through the C-terminal end. The backbone of the N-terminal tripeptide Chg1"-Arg2"-2Na13" (Chg, cyclohexyl-glycine; 2Na1, beta-(2-naphthyl)-alanine) forms a parallel beta-strand to the thrombin main-chain segment Ser214-Gly216. The Chg1" side chain occupies the S2 site, Arg2" penetrates into the S1 specificity site, while the 2Na13" side chain occupies the aryl binding site. The Arg2" side chain enters the S1 specificity pocket from a position quite apart from the canonical P1 site. This notwithstanding, the Arg2" side chain establishes the typical ion pair with the carboxylate group of Asp189.