Use of NMR and fluorescence spectroscopy as well as theoretical conformational analysis in conformation-activity studies of cyclic enkephalin analogues.

In this review the conformational studies of natural enkephalins (H-Tyr-Gly-Gly-Phe-Met-OH; the [Met(5)]enkephalin and H-Tyr-Gly-Gly-Phe-Leu-OH; the [Leu(5)]enkephalin), their acyclic and cyclic analogues, including those carried out in our laboratory, performed by experimental and theoretical methods and their combination, are described. Emphasis is given on the role of conformational constraints introduced by cyclization on activity at the micro and delta opioid receptors. Comparison of the conformations of cyclic enkephalin analogues with high delta-receptor activity with those of potent rigid non-peptide delta-receptor agonists indicates that the proximity of the aromatic side chains in positions 1 and 4 as well as the N-terminal amino group is desirable for the activity at the delta opioid receptors; early conformational studies also suggested that spatial separation of the aromatic side chains and rigidity of the cyclic backbone is desirable for micro-receptor activity. The results of our recent conformational studies performed with the use of fluorescence and NMR spectroscopy as well as theoretical calculations indicate, however, that these structural features are not necessary for activity at the micro opioid receptors. Methods applied to the determination of the conformation of flexible peptides, such as Nuclear Magnetic Resonance (NMR), fluorescence spectroscopy, and theoretical conformational analysis are also discussed briefly.

Azapeptides structurally based upon inhibitory sites of cystatins as potent and selective inhibitors of cysteine proteases.

A series of azapeptides as potential inhibitors of cysteine proteases were synthesized. Their structures, based on the binding center of cystatins, contain an azaglycine residue (Agly) in place of the evolutionarily conserved glycine residue in the N-terminal part of the enzyme binding region of cystatins. Incorporation of Agly should lead to deactivation of the acyl-enzyme complex formed against nucleophilic attack by water molecules in the final step of peptide bond hydrolysis. The majority of synthesized azapeptides shows high inhibitory potency toward the investigated cysteine proteases, papain, cathepsin B, and cathepsin K. One of them, Z-Arg-Leu-Val-Agly-Ile-Val-OMe (compound 17), which contains in its sequence the amino acid residues from the N-terminal binding segment as well as the hydrophobic residues from the first binding loop of human cystatin C, proved to be a highly potent and selective inhibitor of cathepsin B. It inhibits cathepsin B with a K(i) value of 0.088 nM. To investigate the influence of the structure of compound 17 for its inhibitory properties, we determined its conformation by means of NMR studies and theoretical calculations. The Z-Arg-Leu-Val-Agly fragment, covalently linked to Cys29 of cathepsin B, was also developed and modeled, in the catalytic pocket of the enzyme, through a molecular dynamics approach, to analyze ligand-protein interactions in detail. Analysis of the simulation trajectories generated using the AMBER force field provided us with atomic-level understanding of the conformational variability of this inhibitor, which is discussed in the context of other experimental and theoretical data.

Possible involvement of copper(II) in Alzheimer disease.

The beta-amyloid (Abeta) peptide is a principal component of insoluble amyloid plaques that are characteristic neuropathological features of Alzheimer disease (AD). The amyloid peptide also exists as a normal soluble protein that undergoes a pathogenic transition to an aggregated, fibrous form. This transition can be affected by extraneous proteinaceous elements and nonproteinaceous elements such as copper ions, which may promote aggregation and/or stabilization of the fibrils. Copper has been found in abnormally high concentrations in amyloid plaques and AD-affected neuropil, and copper-selective chelators have been shown to dissolve Abeta peptide from postmortem brain specimens. Although Cu(2+) is an essential element for life and the function of numerous enzymes is basic to neurobiology, free or incorrectly bound Cu(2+) can also catalyze generation of the most damaging radicals, such as hydroxyl radical, giving a chemical modification of the protein, alternations in protein structure and solubility, and oxidative damage to surrounding tissue.

Coordination of copper(II) ions by the 11-20 and 11-28 fragments of human and mouse beta-amyloid peptide.

A potentiometric and spectroscopic (UV-vis, CD and EPR) study of Cu(II) binding to the (11-20), (11-28), (Ac-11-20H) and (Ac-11-28) fragments of human (H) and mouse (M) beta-amyloid peptide was carried out. The values of the protonation constants of the two lysine side chain amino groups for the (11-28) and (Ac-11-28) fragments of beta-amyloid peptide differ noticeably suggesting considerable interactions between the two residues. The N-terminal amino acid sequence Xaa-Yaa-His for the (11-20H) and (11-28H) fragments determines the coordination ability of the fragments studied to copper(II) ions. Addition of the (17-20) and (17-28) sequences to the (11-16) fragment of human and mouse beta-amyloid peptide does not change the coordination mode, and the stabilities of the complexes formed are comparable to those of the (11-16) peptide, although 1N complexes of the (11-28) fragments are stabilized by about one order of magnitude compared to those of the (11-16) peptides. The (Ac-11-28) peptides form complexes with the same coordination mode as those for the (Ac-11-16) fragments. The stability of the complexes for the (Ac-11-28H) fragment is one or two orders of magnitude higher compared to those of the (Ac-11-16H) fragment. This stabilization may result from structural organization of a peptide in copper(II) complexes.

Coordination abilities of the 1-16 and 1-28 fragments of beta-amyloid peptide towards copper(II) ions: a combined potentiometric and spectroscopic study.

Stoichiometry, stability constants and solution structures of the copper(II) complexes of the (1-16H), (1-28H), (1-16M), (1-28M), (Ac-1-16H) and (Ac-1-16M) fragments of human (H) and mouse (M) beta-amyloid peptide were determined in aqueous solution in the pH range 2.5-10.5. The potentiometric and spectroscopic data (UV-Vis, CD, EPR) show that acetylation of the amino terminal group induces significant changes in the coordination properties of the (Ac-1-16H) and (Ac-1-16M) peptides compared to the (1-16H) and (1-16M) fragments, respectively. The (Ac-1-16H) peptide forms the 3N [N(Im)(6), N(Im)(13), N(Im)(14)] complex in a wide pH range (5-8), while for the (Ac-1-16M) fragment the 2N [N(Im)(6), N(Im)(14)] complex in the pH range 5-7 is suggested. At higher pH values sequential amide nitrogens are deprotonated and coordinated to copper(II) ions. The N-terminal amino group of the (1-16) and (1-28) fragments of human and mouse beta-amyloid peptide takes part in the coordination of the metal ion, although, at pH above 9 the complexes with the 4N [N(Im), 3N(-)] coordination mode are formed. The phenolate -OH group of the Tyr(10) residue of the human fragments does not coordinate to the metal ion.

Products of Cu(II)-catalyzed oxidation in the presence of hydrogen peroxide of the 1-10, 1-16 fragments of human and mouse beta-amyloid peptide.

The interactions of proteins with reactive oxygen species (ROS) may result in covalent modifications of amino acid residues in proteins, formation of protein-protein cross-linkages, and oxidation of the protein backbone resulting in protein fragmentation. In an attempt to elucidate the products of the metal-catalyzed oxidation of the human (H) and mouse (M) (1-10H), (1-10M), (1-16H) and (1-16M) fragments of beta-amyloid peptide, the high performance liquid chromatography (HPLC) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) methods and Cu(II)/H(2)O(2) as a model oxidizing system were employed. Peptide solution (0.50 mM) was incubated at 37 degrees C for 24 h with metal:peptide:H(2)O(2) molar ratio 1:1:1 for the (1-16H), (1-16M) fragments, and 1:1:2 for the (1-10H), (1-10M) peptides in phosphate buffer, pH 7.4. Oxidation targets for all peptide studied are the histidine residues coordinated to the metal ions. For the (1-16H) peptide are likely His(13) and/or His(14), and for the (1-16M) fragment His(6) and/or His(14), which are converted to 2-oxo-His. Metal-binding residue, the aspartic acid (D(1)) undergoes the oxidative decarboxylation and deamination to pyruvate. The cleavages of the peptide bonds by either the diamide or alpha-amidation pathways were also observed.

Acyloxymethyl esterification of nodularin-R and microcystin-LA produces inactive protoxins that become reactivated and produce apoptosis inside intact cells.

We report the esterification of the carboxyl groups of the cyclic peptide toxins nodularin-R and microcystin-LA to produce stable diacetoxymethyl and dipropionyloxymethyl ester derivatives. The derivatives had no activity but were reactivated upon esterase treatment. When injected into cells, the acyloxymethyl moieties were cleaved off and apoptosis induced. Linking the acyloxymethyl-ester moiety of these potent toxins to carriers destined for endocytosis paves the way for selective apoptosis induction in target (e.g., cancer) cells.

Position-specific incorporation of a highly photodurable and blue-laser excitable fluorescent amino acid into proteins for fluorescence sensing.

A new fluorescent amino acid, L-2-acridonylalanine, was incorporated into proteins at specific positions using 4-base codon/anticodon strategy. The efficiency of the incorporation was high enough to obtain enough quantities of the mutants. The acridonyl group was highly fluorescent when it was excited at the wavelengths of blue-lasers and was highly photodurable compared with conventional fluorophores often used for biological analyses. The fluorescence intensity was sensitive to small changes in the polarity of the environment. When the nonnatural amino acid was incorporated into specific positions of streptavidin, the mutant protein worked as a fluorescent sensor to biotin. Similarly, when the amino acid was incorporated into camel single-chain antibody, the mutant protein sensitively responded to the antigen molecule. The high incorporation efficiency, the high photodurability, the excitability with blue-lasers, and high sensitivity to the environment make the acridonylalanine as the promising fluorescent amino acid for sensing small molecules when incorporated into specific positions of various antibodies, receptors, and enzymes.

O-Benzyl-N-tert-butoxycarbonyl-N-methyl-L-tyrosine.

The crystal structure of the title compound, alternatively called 3-[4-(benzyloxy)phenyl]-2-(N-tert-butoxycarbonyl-N-methylamino)propionic acid, C(22)H(27)NO(5), has been studied in order to examine the role of N-methylation as a determinant of peptide conformation. The conformation of the tert-butoxycarbonyl group is trans-trans. The side chain has a folded conformation and the two phenyl rings are effectively perpendicular to one another. The carboxylate hydroxyl group and the urethane carbonyl group form a strong intermolecular O[bond]H...O hydrogen bond.

Effect of antisense peptide binding on the dimerization of human cystatin C--gel electrophoresis and molecular modeling studies.

Human cystatin C (HCC) shows a tendency to dimerize. This process is particularly easy in the case of the L68Q HCC mutant and might lead to formation of amyloid deposits in brain arteries of young adults. Our purpose was to find ligands of monomeric HCC that can prevent its dimerization. Eleven antisense peptide ligands of monomeric HCC were designed and synthesized. The influence of these ligands on HCC dimerization was studied using gel electrophoresis and molecular modeling methods. The results suggest that all the designed peptides interact with monomeric HCC facilitating its dimerization rather than preventing it.

Identification of a novel high affinity copper binding site in the APP(145-155) fragment of amyloid precursor protein.

The copper(II) binding features of the APP(145-155) and APP(145-157) fragments of the amyloid precursor protein, Ac-Glu-Thr-His-Leu-His-Trp-His-Thr-Val-Ala-Lys-NH2 and Ac-Glu-Thr-His-Leu-His-Trp-His-Thr-Val-Ala-Lys-Glu-Thr-NH2 were studied by NMR spectroscopy and NMR findings were supported by UV-vis, CD and EPR spectra. Potentiometric measurements were performed only for the more soluble Ac-Glu-Thr-His-Leu-His-Trp-His-Thr-Val-Ala-Lys-Glu-Thr-NH2 peptide fragment. The following was shown: (i) the imidazole rings of all the three His residues are involved in metal coordination; (ii) metal binding induces ionisation of Leu-148 and His-149 amide nitrogens that complete the donor set to copper(II) in the species dominant at neutral pH; (iii) the unusual coordination scheme of the His-Xxx-His-Xxx-His consensus sequence justifies the high specificity for Cu(II) when compared to SOD-like or albumin-like peptides or even in amyloid Abeta fragments. The present findings may represent the key for interpreting the observed requirement of His residues conservation for the redox cycling between Cu(II) and Cu(I) by soluble APP.