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Biomedical subjects

Paolo Scrimin

Publications and source records attributed to Paolo Scrimin.

At least 19 recordsLinked to original sources
PubMed2006

Gold nanoparticles-based protease assay.

We describe here a simple assay that allows the visual detection of a protease. The method takes advantage of the high molar absorptivity of the plasmon band of gold colloids and is based on the color change of their solution when treated with dithiols. We used C- and N-terminal cysteinyl derivatives of a peptide substrate exploiting its selective recognition and cleavage by a specific protease. Contrary to the native ones, cleaved peptides are unable to induce nanoparticles aggregation; hence, the color of the solution does not change. The detection of two proteases is reported: thrombin (involved in blood coagulation and thrombosis) and lethal factor (an enzyme component of the toxin produced by Bacillus anthracis). The sensitivity of this nanoparticle-based assay is in the low nanomolar range.

Amino Acid Sequence↗
PubMed2006

C(alpha)-tetrasubstituted amino acid based peptides in asymmetric catalysis.

C(alpha)-tetrasubstituted alpha-amino acids constitute a powerful tool for controlling the conformation of short peptide sequences. Chiral peptides may be used in stereoselective reactions both for asymmetric induction and in kinetic resolution. By reviewing recent data from our own laboratories and by presenting new results on the stereoselective oxidation of chalcone to the corresponding oxide, this contribution shows that the control of peptide conformation is a critical issue in order to achieve successful stereoselective catalysis.

Acylation↗
PubMed2005

Effect of core size on the partition of organic solutes in the monolayer of water-soluble nanoparticles: an ESR investigation.

ESR spectroscopy has been used to study the interaction of para-pentylbenzyl hydroxyalkyl nitroxide with the monolayer of water-soluble protected gold clusters having a core diameter ranging from 1.6 to 5.3 nm. The solubilization of the nitroxide probe in the more hydrophobic environment of the monolayer strongly depends on the size of the gold core. In particular, the partition equilibrium constant increases as the nanoparticle diameter decreases. These results have been attributed to the different packing of the chains in the monolayer resulting from the different radius of curvature of the investigated nanoparticles. This represents, to the best of our knowledge, the first report demonstrating that the core size of metallic nanoparticles affects the solvating properties of the protective organic monolayer.

Journal Article↗
PubMed2005

Reversible aggregation/deaggregation of gold nanoparticles induced by a cleavable dithiol linker.

Aqueous solutions of Au colloids (12 +/- 4 nm size) when treated with a blend of mono- and dithiols aggregate forming stable clusters, as evidenced by the shift of their surface plasmon (SP) band from 512 to ca. 600 nm. The presence of carboxylate ester functions on the dithiol allows its cleavage by addition of a cleaving agent, such as hydrazine. The cleavage process results in the breaking down of the clusters of nanoparticles and the shift of the SP band back to lower wavelengths. Further addition of dithiol causes the formation of the clusters again. The aggregation/deaggregation process may be monitored visually by following the color change from pink-red to purple and vice versa in the forward and backward steps, respectively.

Journal Article↗
PubMed2005

Artificial metallonucleases.

The development of synthetic agents able to hydrolytically cleave DNA with high efficiency and selectivity is a fascinating challenge that will show the way to obtaining artificial nucleases able to compete with the natural enzymes. This Feature Article highlights the progress reported toward the realization of synthetic nucleases with particular attention to the strategies that can be pursued to improve efficiency and sequence selectivity.

Catalysis↗
PubMed2005

Carboxylate-imidazole cooperativity in dipeptide-functionalized gold nanoparticles with esterase-like activity.

We report here the first example of peptide-functionalized gold nanoparticles hydrolytically active against carboxylate esters. The active units are constituted by His-Phe-OH terminating thiols. The confinement of the catalytic units in the monolayer covering the nanoparticles triggers a cooperative hydrolytic mechanism operative at pH < 7 in which a carboxylate and an imidazolium ion act as general base and general acid, respectively. Such a mechanism is absent with an analogous monomeric dipeptide, and this results in a more than 300-fold rate acceleration of the hydrolytic process at low pH in the presence of the functional nanoparticles.

Butyrates↗
PubMed2004

De novo metallonucleases based on helix-loop-helix motifs.

Three new 42-mer peptides (PR I-III) designed to fold into a hairpin helix-loop-helix motif have been prepared. In the peptide sequence two (PR II-III) or four (PR I) copies of an unnatural amino acid bearing a triazacyclononane metal-ion binding site (ATANP) have been inserted in appropriate positions to allow the ligand subunits to face each other either within the same helix or between the two helices of the hairpin motif. Circular dichroism (CD) studies in solution have shown that the apopeptides adopt a well-defined helix-loop-helix tertiary structure that dimerizes in solution at concentrations above 200 microM to form a four-helix bundle. However, the helical content is strongly dependent on pH and metal-ion binding. Both protonation of the amines of the triazacyclononane units present in the ATANP lateral arm and complexation with Zn(II) ions cause a significant decrease of the helical content of the sequences. The Zn(II) complexes of the three peptides catalyze the transesterification of the RNA model substrate 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP) with different efficiency. The best catalyst appears to be PR I-4 Zn(II), that is, the peptide incorporating four ATANP units. Michaelis-Menten saturation kinetics allowed us to estimate that substrate fully bound to the catalyst reacts 380 times faster than in its absence. The kinetic evidence suggests cooperativity between (at least two) metal ions: one activating the nucleophilic species (directly or indirectly) and the other facilitating nucleophilic attack by coordination of the phosphate.

Catalysis↗
PubMed2004

EPR study of dialkyl nitroxides as probes to investigate the exchange of solutes between the ligand shell of monolayers of protected gold nanoparticles and aqueous solutions.

EPR spectroscopy has been used to study the interaction of para-substituted benzyl hydroxyalkyl nitroxides with the monolayer of water-soluble protected gold cluster made by a short alkyl chain and a triethylene glycol monomethyl ether unit. The inclusion of nitroxide probes in the more hydrophobic environment of the monolayer gave rise to a reduction of the value of both nitrogen and beta-proton hyperfine splittings. The spectra also showed selective line broadening attributed to modulation of the spectroscopic parameters as the result of exchange between free and complexed nitroxide. The rate constants were obtained by analyzing the EPR line shape variations as functions of nanoparticle concentration and temperature. This represents, to the best of our knowledge, the first determination of rate constants for the solubilization of organic substrates in a monolayer-protected cluster.

Electron Spin Resonance Spectroscopy↗
PubMed2004

Role of secondary structure in the asymmetric acylation reaction catalyzed by peptides based on chiral C alpha-tetrasubstituted alpha-amino acids.

In a recent series of papers, Miller and co-workers were able to show that His(pi-Me)-based, terminally protected peptides are potent catalysts of the asymmetric acyl transfer reaction, useful for the kinetic resolution of alcohols. In a structure-supporting solvent, one of the most active compounds, an Aib-containing tetrapeptide, is folded in a doubly intramolecularly H-bonded beta-hairpin motif incorporating a type-II' beta-turn conformation. In this work, we have expanded the study of the Miller tetrapeptide by examining a set of analogues and shorter sequences (dipeptide amides), characterized by chiral C(alpha)-tetrasubstituted alpha-amino acids of diverging bulkiness and optical configuration. Peptide synthesis in solution, conformational analysis by FT-IR absorption and (1)H NMR techniques, and screening of catalytic activity as well have been performed. Our results confirm the close relationship between the beta-hairpin 3D-structure and the catalytic activity of the peptides. A tetrapeptide analogue slightly more selective than the Miller compound has been found. However, the terminally protected, industrially more appealing, dipeptide amides are poorly effective.

Acylation↗
PubMed2002

Zinc(II) as an allosteric regulator of liposomal membrane permeability induced by synthetic template-assembled tripodal polypeptides.

Three copies of peptide sequences from the peptaibol family, known to affect the permeability of the lipid bilayer of membranes, were connected to tris(2-aminoethyl)amine (TREN), a tripodal metal ion ligand, to prepare functional peptides capable of modifying the permeability of liposomal membranes. Some of the resulting tripodal polypeptide derivatives are very effective in promoting carboxyfluorescein (CF) leakage from CF-loaded unilamellar vesicles composed of a 70:30 phosphatidylcholine/cholesterol blend. The activity of these novel compounds was shown to be tunable upon metal ion coordination of the TREN subunit; the tripodal apopeptide was far more effective than its ZnII complex. Leakage experiments showed that a minimum number of five amino acids per peptide chain is required to form active systems. A mechanism is proposed in which the ZnII ion changes the conformation of the template from extended to globular and thus acts as an allosteric regulator of the activity of the systems. Molecular modeling studies indicate that when the three peptide chains are connected to the template in the extended conformation, the resulting tripodal polypeptide is able to span across the membrane, thus allowing the formation of permeable channels made of a cluster of molecules. The same change of conformation induces, to some extent, fusion of the membranes of different liposomes.

Allosteric Regulation↗
PubMed2002

A peptide template as an allosteric supramolecular catalyst for the cleavage of phosphate esters.

The heptapeptide H-Iva-Api-Iva-ATANP-Iva-Api-Iva-NHCH(3) (P1a), where Iva is (S)-isovaline, Api is 4-amino-4-carboxypiperidine, and ATANP is (S)-2-amino-3-[1-(1,4,7-triazacyclononane)]propanoic acid, has been synthesized. Its conformation in aqueous solution is essentially that of a 3(10)-helix. By connecting three copies of P1a to a functionalized Tris(2-aminoethyl)amine (Tren) platform a new peptide template, [T(P1)(3)], was obtained. This molecule is able to bind up to four metal ions (Cu(II) or Zn(II)): one in the Tren subsite and three in the azacyclononane subunits. The binding of the metals to the Tren platform induces a change from an open to a closed conformation in which the three short, helical peptides are aligned in a parallel manner with the azacyclonane units pointing inward within the pseudocavity they define. T(P1)(3) shows a peculiar behavior in the transphosphorylation of phosphate esters; the tetrazinc complex is a catalyst of the cleavage of 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP), whereas the free ligand is a catalyst of the cleavage of an oligomeric RNA sequence with selectivity for pyrimidine bases. In the case of HPNP, Zn(II) acts as a positive allosteric effector by enhancing the catalytic efficiency of the system. In the case of the polyanionic RNA substrate, Zn(II) switches off the activity, thus behaving as a negative allosteric regulator. It is suggested that the opposite behavior of the catalyst induced by Zn(II) is associated with the change of conformation of the Tren platform, and consequently of the relative spatial disposition of the three linked peptides, that occurs after binding of the metal ion.

Allosteric Site↗