Alteration of protein structure induced by low-energy (<18 eV) electrons. I. The peptide and disulfide bridges

We present measurements of low-energy (<18 eV) electron-stimulated desorption of anions from acetamide (CH(3)CONH(2)) and dimethyl disulfide [DMDS: (CH(3)S)(2)] films. Electron irradiation of physisorbed CH(3)CONH(2) produces H(-), CH(3)(-) and O(-) anions, whereas the H(-), CH(2)(-), CH(3)(-), S(-), SH(-) and SCH(3)(-) anions are observed to desorb from the DMDS film. Below 12 eV, the dependence of the anion yields on the incident electron energy exhibits structures that indicate that a resonant process (i.e. dissociative electron attachment) is responsible for molecular fragmentation. Within the range of 1-18 eV, it is found that (1.7 and 1.4) x 10(7) H(-) ions/incident electron and (7.8 x 10(-11) and 4.3 x 10(-8)) of the other ions/incident electron are desorbed from acetamide and DMDS films, respectively. These results suggest that, within proteins, the disulfide bond is more sensitive to low-energy electron attack than the peptide bond. In biological cells, some proteins interact closely with nucleic acid. Therefore, the observed fragments, when produced from secondary low-energy electrons generated by high-energy radiation, not only may denature proteins, but may also induce reactions with the nearby nucleic acid and damage DNA.     

ESR an optical absorption studies on the copper(II) interaction with small peptides containing aromatic amino acids.

The interaction of Cu(II) with di- and tripeptides each containing phenylalanine, tryptophan or histidine in the amino acid chain has been investigated by means of electron spin resonance (ESR) and optical absorption spectroscopy. Cu(II) complexes of dipeptides and tripeptides exhibit different magnetic and optical parameters. Dipeptide complexes have larger gparallel-values and smaller A parallel values than tripeptide complexes. When compared to dipeptide complexes, the d-d band of the central metal ion is blue shifted for tripeptide complexes. There are no significant difference in the behavior of Cu(II) peptide complexes containing phenylalanine or tryptophan. Complexes of histidine containing peptides, however, show modified spectra caused by the participation of the imidazole nitrogen in the coordination to Cu(II). The imidazole nitrogen seems to coordinate in-plane with other coordinating atoms or in an axial position depending on the kind of peptide.     

Suppression of epimerization by cupric (II) salts in peptide synthesis using free amino acids as amino components.

An epimerization-free system for coupling N-protected peptides with free amino acids was developed. A number of inorganic substances were tested as epimerization suppressant additives during the coupling by various methods (carbodiimide plus additives, uronium salts, Woodward's reagent-K, isobutyl-chloroformate, etc.). Some of them (ZnCl2, RbClO4, LiCl, SnCl4, AlCl3, etc.) in combination with some coupling methods can guarantee coupling with minimal epimerization (D-epimer < 1%). But only a simultaneous use of 1-hydroxybenzotriazole and Cu2+ ions as additives in carbodiimide-mediated peptide couplings appeared to give a standard result (D-epimer < 0.1%). There was no epimerization even in the case when N-methyl amino acid (sarcosine) was used as an amino component, while in the absence of Cu2+ ions an unacceptable level of epimerization was observed (D-epimer, 22% for carbodiimide with the 1-hydroxybenzotriazole method). So far it has been considered that Cu2+ ions prevent obtaining peptides in high yields (< 90%) by various coupling methods. We have found that the use of 1-hydroxybenzotriazole, CuCl2 and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide instead of dicyclohexylcarbodiimide provides a possible method for obtaining the desired peptides in 90-99% yields without epimerization. All these results were shown by employing several model peptide couplings with free amino acids as amino components dissolved in an effective solvent system which readily dissolved them.     

Analysis of epitope structure of PSP94 (prostate secretory protein of 94 amino acids): (II) epitope mapping by monoclonal antibodies

PSP94 has shown potential to be a serum biomarker for evaluating prostate cancer. Studies of the epitope structure is crucial for this endeavour. In this article, we have used 15 different monoclonal antibodies (MAb) to analyse the epitope structure of PSP94 and to compare with the results obtained from our previous work using polyclonal antibody and recombinant PSP94. Firstly, we determined the relative activities of the 15 MAb population by direct and competitive ELISA. The two predominant MAbs (MAb PSP-6 and -19) in 15 MAbs were selected for further studies of the epitope structure. By comparing the binding activities of recombinant GST-PSP94 and natural PSP94 with MAbs, and by comparing their affinity with MAbs in an in vitro denaturing experiment, PSP94 was shown to have a similar, prevalently linear epitope structure as we demonstrated by polyclonal antibody. Using recombinant GST fusion protein with PSP94 and with each half of the N- and C-terminal 47 amino acids (GST-PSP-N47/C47) in E. coli cells, the different epitopes recognized by 15 monoclonal antibodies were delineated and the polar distribution of the epitope structure of PSP94 was characterized. Results of direct ELISA of recombinant N47 and C47 and their competitive binding against natural PSP94 (competitive ELISA) showed that the N- and C-termini represent the immuno-dominant and immuno-recessive area separately. A majority of the monoclonal antibodies (12/15) showed preferential binding of the N-terminal sequence of the PSP94 protein. Using GST-PSP-N47 as a standard protein, an epitope map of the 15 monoclonal antibodies was obtained. The results of this study will help to define the clinical utility of PSP94. J. Cell. Biochem. 65:186–197. © 1997 Wiley-Liss, Inc.     

Photophysics of ruthenium(II) complexes carrying amino acids in the ligand 2,2′-bipyridine and intramolecular electron transfer from methionine to photogenerated Ru(III)

New ruthenium(II) complexes carrying methionine and phenylalanine in the bipyridine ligand, [Ru(bpy)₂(4-Me-4′-(CONH-l-methionine methyl ester)-2,2′-bipyridine)](PF₆)₂ (IV) and [Ru(bpy)₂(4-Me-4′-(CONH-l-phenylalanine ethyl ester)-2,2′-bpy)](PF₆)₂(V) have been synthesized and characterized and their photophysical properties studied. Flash photolysis measurements of complex IV, in the presence of an electron acceptor, methyl viologen (MV²⁺) show that an intermolecular electron transfer from the excited state of Ru(II) in complex IV, to MV²⁺ takes place, forming Ru(III) and the methyl viologen cation radical, MV⁺. The formation of MV⁺ in this system is confirmed using time-resolved transient absorption spectroscopy. This intermolecular electron transfer is followed by intramolecular electron transfer from the thioether moiety (methionine) to the photogenerated Ru(III), regenerating Ru(II).     

Whitebellied sunbirds (<Emphasis Type="Italic">Nectarinia talatala</Emphasis>, Nectariniidae) do not prefer artificial nectar containing amino acids

Amino acids are the most abundant class of compounds in nectar after sugars. Like its sugar concentration, the amino acid concentration of nectar has been linked to pollinator type, and it has been suggested that amino acid concentrations are high in the floral nectars of plant species pollinated by passerine birds compared to those pollinated by hummingbirds. We investigated the feeding response of whitebellied sunbirds (Nectarinia talatala) to the inclusion of amino acids in artificial nectar (0.63 M sucrose solution). The response to asparagine, glutamine, phenylalanine, proline, serine and valine, amino acids commonly found in floral nectars, was tested individually and using a mixture of all six amino acids, at two different concentrations (2 and 15 mM). Sunbirds showed no significant preference for amino acids in nectar, or avoided them, especially at the higher concentration. We discuss these findings in the light of the nitrogen requirements of nectarivorous birds and data on amino acids in floral nectars.     

Dinuclear bis(terpyridine)ruthenium(II) complexes by amide coupling of ruthenium amino acids: Synthesis and properties

Two redox-asymmetric amide-bridged bis(terpyridine)ruthenium(II) complexes (3a, 3b) have been prepared by amide coupling of a carboxylic acid functionalized complex with an amine substituted complex and they were fully characterized by spectroscopic analyses. They emit at 692 and 750 nm at room temperature in fluid solution with quantum yields larger than 10⁻³ and ³MLCT lifetimes of 22 ns. Ru···Ru distances were estimated from DFT models as 17.7 and 13.4 Å for 3a and 3b, respectively. Cyclic voltammetry gives two oxidation potentials for the differently substituted ruthenium sites with splittings of 0.10 and 0.23 V for 3a and 3b, respectively. Oxidation of 3b with Ce^IV ions gives the corresponding mixed-valent Ru^II-Ru^III system which is valence-localized according to NIR spectroscopic and theoretical analyses.     

Involvement of organic acids and amino acids in ameliorating Ni(II) toxicity induced cell cycle dysregulation in Caulobacter crescentus: a metabolomics analysis

Applied Microbiology and Biotechnology - Nickel (Ni(II)) toxicity is addressed by many different bacteria, but bacterial responses to nickel stress are still unclear. Therefore, we studied the...     

Photochemical cross-linking of Escherichia coli Fpg protein to DNA duplexes containing phenyl(trifluoromethyl)diazirine groups.

Formamidopyrimidine-DNA glycosylase (Fpg protein) of Escherichia coli is a DNA repair enzyme that excises oxidized purine bases, most notably the mutagenic 7-hydro-8-oxoguanine, from damaged DNA. In order to identify specific contacts between nucleobases of DNA and amino acids from the E. coli Fpg protein, photochemical cross-linking was employed using new reactive DNA duplexes containing 5-[4-[3-(trifluoromethyl)-3H-diazirin-3-yl]phenyl]-2'-deoxyuridine dU* residues near the 7-hydro-8-oxoguanosine (oxoG) lesion. The Fpg protein was found to bind specifically and tightly to the modified DNA duplexes and to incise them. The nicking efficiency of the DNA duplex containing a dU* residue 5' to the oxoG was higher as compared to oxidized native DNA. The conditions for the photochemical cross-linking of the reactive DNA duplexes and the Fpg protein have been optimized to yield as high as 10% of the cross-linked product. Our results suggest that the Fpg protein forms contacts with two nucleosides, one 5' adjacent to oxoG and the other 5' adjacent to the cytidine residue pairing with oxoG in the other strand. The approaches developed may be applicable to pro- and eukaryotic homologues of the E. coli Fpg protein as well as to other repair enzymes.     

Changes in protein profile and amino acids in <Emphasis Type="Italic">Cladophora vagabunda</Emphasis> (Chlorophyceae) in response to salinity stress

The aim of the present study was to detect organic substances functioning as osmoticants that are used by the intertidal alga, Cladophora vagabunda (L.) Hoek (Chlorophyceae), to adapt to a wide range of salinity. The major constituents of the amino acid pool were aspartate, glutamate, glycine, valine, lysine, histidine, arginine, and proline. There were concomitant increases in the acidic amino acids: aspartate and the glutamate and the basic amino acids: lysine, histidine and arginine in response to salinity stress. The appearance of proline at hypersalinity alone showed that it acts as an osmoticant. As salinity increased, there was a progressive shift in the electrophoretic pattern of protein bands. New peptide bands appeared under hyposalinity (10‰) and hypersalinity (65‰) stress conditions in addition to the usual bands which appeared in the control (35‰). Glycine betaine, which has been considered a novel organic osmolyte in a number of organisms, has also been observed in C. vagabunda in response to salinity stress. The synthesis of the compatible solute glycine betaine and the amino acid proline with increasing salinity illustrates the contention that marine algae establish an osmotic equilibrium primarily by the synthesis of organic compounds. Presented at the 6th Meeting of the Asian Pacific Society of Applied Phycology, Manila, Philippines.     

The initial binding of Cu(II) to some amino acids and dipeptides: a 13C nuclear-magnetic-resonance study.

The initial binding of Cu2+ ot L-lysine, L-histidine, glycyl-histidine and histidyl-glycine in aqueous solutions was examined by 13C nuclear magnetic resonance spectroscopy. The measurements were carried out in a substantially improved way employing the pulse Fourier transform technique. Spectra of both high quality and resolution were obtained. Cu2+ complex formation with L-lysine occurred with the alpha-amino and carboxyl group attributable to the well expressed broadening effect of the 13C signals of the alpha-carbon atom and the carboxyl atom. The epsilon-amino group was not involved. Measurements of the Cu chelates using L-histidine and glycyl-histidine and histidyl-glycine confirmed the ambidentate nature of the histidine residue. It was concluded that an equilibrium exists between two Cu-complex species designated as histamine-like and histamine-like/glycine-like species. In the homogeneous histamine-like Cu complex, the Cu2+ is exclusively bound with 4 nitrogens, while in the other species one oxygen of the glycyl carboxyl group is involved in the Cu2+ binding. Blocking of this carboxyl groups by peptide bonding as found in histidyl-glycine favoured the formation of a Cu complex where the imidazole carbons of the histidyl residue were the most influenced species.     

Helix morphology changes in B-DNA induced by spontaneous B(I)<==>B(II) substrate interconversion

Investigations of spontaneous, i.e. not forced, B-DNA's B(I)<==>B(II) substate transitions are carried out on the d(CGCGAATTCGCG)2 EcoRI dodecamer sequence using Molecular Dynamics Simulations. Analysis of the resulting transition processes with respect to the backbone angles reveals concerted changes not only for backbone angles epsilon, zeta, and beta, but also for the 5'-delta and 5'-chi angles. For alpha and delta inside the interconverting base step, a change is seen in short lived B(II) conformers. With respect to base morphology distinct changes are observed for buckle, propeller twist, shift, roll and twist, as well as x-displacement and tip. The base mainly involved in the changes is identified as the base preceding the interconverting phosphate. Altogether single B(I)<==>B(II) interconversions result only in local distortions represented by the larger spread of most parameters. Comparison of the atomic positional fluctuations derived from the simulation with those obtained from the static X-ray structure results in striking similarities.     

Binding of mercury(II) to protein thiol groups: a study of proteinase K and carboxypeptidase Y.

Chemically modified enzymes have been prepared by incorporating an -Hg-L group into proteinase K and carboxypeptidase Y at the thiol groups of Cys-73 and Cys-341, respectively (L = CN- or I-). The -S-Hg-13CN group has been applied as a spectroscopic label for carbon-13 NMR spectroscopy.     

Vanadocene complexes of amino acids containing secondary amino group: The first evidence of O,O-bonded carboxylic group to vanadocene(IV) moiety

Reaction of vanadocene dichlorides (Cp₂VCl₂ and (η⁵-C₅H₄Me)₂VCl₂) with amino acids containing secondary amino groups gives three types of complexes: a) compounds with N,O-bonded amino acid, b) O-bonded amino acids and c) O,O-bonded amino acid. The complexes with N,O-bonded amino acid and O-bonded amino acids were observed in the case of l-proline and N-methylglycine (NMG). Reactions with N-phenylglycine (NPG) give O,O-chelates as the sole products. All three types of the complexes were characterized by spectroscopic methods. Structures of [(η⁵-C₅H₄Me)₂V(O-Pro)][BPh₄], [Cp₂V(O-Pro)₂][PF₆]₂, [Cp₂V(N,O-NMG)][BPh₄]·MeOH, [(η⁵-C₅H₄Me)₂V(N,O-NMG)][BPh₄]·MeOH, [Cp₂V(O-NMG)₂][Cl]₂·2H₂O, [(η⁵-C₅H₄Me)₂V(O-NMG)₂][Cl]₂·H₂O and [(η⁵-C₅H₄Me)₂V(O,O-NPG)][BPh₄] were determined by X-ray crystallography.     

The complexation of aqueous metal ions relevant to biological applications. 2. Reactions of copper(II) citrate and copper(II) succinate with selected amino acids

Abstract

Addition of amino acids, glycine, alanine, and serine, to poorly soluble copper(II) salts [copper(II) citrate and copper(II) succinate] all increase solubility of the copper(II) salts. Relative increases in solubility follow the polarity trend in the selected amino acids, with serine creating the greatest increase in solubility. Simultaneous equilibria calculations indicate the formation of mixed-ligand complexes in the copper(II) succinate–amino acid systems, the first time such mixed-ligand complexes have been observed. In contrast, mixed-ligand complexes are not predicted in the copper(II) citrate–amino acid systems. Potential bioavailability of copper(II) appears to be increased by the inclusion of amino acids in solution, roughly in parallel with the increase in solubility of the copper(II) salt. Therefore, measurement of the change in solubility caused by addition of amino acids to aqueous solution gives qualitative insight to the potential increase in bioavailability of the metal ion.     

Inhibition of beta-amyloid(40) fibrillogenesis and disassembly of beta-amyloid(40) fibrils by short beta-amyloid congeners containing N-methyl amino acids at alternate residues.

A potential goal in the prevention or therapy of Alzheimer's disease is to decrease or eliminate neuritic plaques composed of fibrillar beta-amyloid (Abeta). In this paper we describe N-methyl amino acid containing congeners of the hydrophobic "core domain" of Abeta that inhibit the fibrillogenesis of full-length Abeta. These peptides also disassemble preformed fibrils of full-length Abeta. A key feature of the inhibitor peptides is that they contain N-methyl amino acids in alternating positions of the sequence. The most potent of these inhibitors, termed Abeta16-22m, has the sequence NH(2)-K(Me-L)V(Me-F)F(Me-A)E-CONH(2). In contrast, a peptide, NH(2)-KL(Me-V)(Me-F)(Me-F)(Me-A)-E-CONH(2), with N-methyl amino acids in consecutive order, is not a fibrillogenesis inhibitor. Another peptide containing alternating N-methyl amino acids but based on the sequence of a different fibril-forming protein, the human prion protein, is also not an inhibitor of Abeta40 fibrillogenesis. The nonmethylated version of the inhibitor peptide, NH(2)-KLVFFAE-CONH(2) (Abeta16-22), is a weak fibrillogenesis inhibitor. Perhaps contrary to expectations, the Abeta16-22m peptide is highly soluble in aqueous media, and concentrations in excess of 40 mg/mL can be obtained in buffers of physiological pH and ionic strength, compared to only 2 mg/mL for Abeta16-22. Analytical ultracentrifugation demonstrates that Abeta16-22m is monomeric in buffer solution. Whereas Abeta16-22 is susceptible to cleavage by chymotrypsin, the methylated inhibitor peptide Abeta16-22m is completely resistant to this protease. Circular dichroic spectroscopy of Abeta16-22m indicates that this peptide is a beta-strand, albeit with an unusual minimum at 226 nm. In summary, the inhibitor motif is that of alternating N-methyl and nonmethylated amino acids in a sequence critical for Abeta40 fibrillogenesis. These inhibitors appear to act by binding to growth sites of Abeta nuclei and/or fibrils and preventing the propagation of the network of hydrogen bonds that is essential for the formation of an extended beta-sheet fibril.     

Differential responses in cyclic GMP formation induced by excitatory amino acids (EAA) and sodium nitroprusside (SNP) in various regions of the brain and of rats of varied age

• 1.1. Sodium nitroprusside (SNP, 100 μM) caused a rapid and great increase of formation of cGMP in rat cerebellar slices. This effect was not blocked by l-nmma (a NO synthetase inhibitor) or antagonists of the NMDA receptor complex (e.g. AP₅ or MK 801).
• 2.2. Similarly, NMDA (100 μM) and glutamate (I mM) caused a rapid but less significant increase of cGMP formation. This increase was blocked by NMDA receptor complex blockers (e.g. AP₅, MK801 and kynurenate), and l-NMMA and l-nitroarginine.
• 3.3. In rats aged 12 days, both NMDA and kainate (at 100 μM) caused significantly increased levels of cGMP in the cerebellum, pons and medulla areas, whereas no significant alterations were found in the cerebral cortex, hippocampus or midbrain areas.
• 4.4. NMDA (100 μM) and SNP (300μM) induced greater increases of cGMP in cerebellar slices in young (aged 13 days) animals than older ones of either sex. This effect decreased greatly after 35 days of age. In adult (2 months) animals the effect of NMDA had virtually disappeared whereas SNP was barely significantly present.
• 5.5. Our results suggest that brain region and age, but not sex, affected formation of cGMP induced by excitatory amino acids (EAA) and SNP. Furthermore, endogenous NO production is required by EAA, but not by SNP, in the formation of cGMP.

     

Copper(II) complexes of peptide fragments of the prion protein. Conformation changes induced by copper(II) and the binding motif in C-terminal protein region

In this paper, we report the characterization of copper(II) complexes with two prion (PrP) protein peptide fragment analogues (VNITKQHTVTTTT), one with the N-terminus acetylated and the C-terminus amidated (PrP Ac180-193NH2) and the other with both the C- and N-termini free (PrP 180-193). Such peptide sequence almost entirely encompasses the PrPC's helix 2 in the C-terminal region. The stoichiometry, the binding modes and the conformational features of the copper(II) complexes with the above mentioned two peptides were investigated by electrospray ionization-mass spectrometry (ESI-MS), UV-visible (UV-Vis) spectrometry and electron paramagnetic resonance (EPR) spectrometry as well as by circular dichroism (CD) measurements. The binding site location of copper(II) in the structured region of the protein can be here suggested on the basis of our findings that show the involvement of His 187 residue. The similarity of the EPR parameters suggests that the anchoring imidazole residue drives the copper(II) coordination environment towards a common binding motif in different regions of the prion protein.