Studies on interaction of oligopeptides with sodium dodecyl sulfate: Stopped-flow kinetics of chemical modification of tryptophan residues withN-bromosuccinimide

The stopped-flow kinetics of the reaction between oligopeptides containing tryptophan residues andN-bromosuccinimide (NBS) were studied in 50 mM sodium phosphate buffer (pH 7.0) containing sodium dodecyl sulfate (SDS). Decreases in the reaction rates attributable to the interaction between oligopeptides and SDS were observed, and oligopeptides studied were classified into types I and II on the basis of the interaction modes. Type I oligopeptides were dissolved in SDS micelles; type II oligopeptides interacted cooperatively with SDS monomers. The manner of interaction between SDS and oligopeptides of type II could be interpreted by a simple equilibrium relation: oligopeptide+n·(SDS)=oligopeptide·(SDS) _n .     

Interaction of mithramycin with isolated GC and CG sites

We have studied the interaction of the GC-specific, minor groove-binding ligand, mithramycin, with cloned DNA inserts containing isolated GC and CG sites flanked by regions of (AT)_n and A_n · T_n using DNase I and hydroxyl radical footprinting. We find that mithramycin binds to GC better than CG and that AGCT is a better site than TGCA. Sites flanked by (AT)_n appear to be bound better than those surrounded by A_n · T_n. Although no footprints are produced at T₉GCA₉ and T₁₅CGA₁₅, DNase I cleavage is enhanced with the GC sites suggesting that there is some interaction with the ligand. Mithramycin also alters the DNase I cleavage of (GA)_n · (CT)_n.     

Co-oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. VI. Circular dichroism studies of Co-oligopeptides of l-phenylalanine, L-tryptophan, and glycine.

The circular dichroic properties of H-Gly-Phe-(Gly)_n-Trp-Gly-OH (II, n = 0,1,2) and of related simpler peptides, such as H-Phe-Gly-OH, H-Gly-Phe-OH, H-Gly-Phe-Gly-OH, H-Phe-Trp-OH, H-Phe-Trp-Gly-OH, and H-Gly-Phe-Trp-OH in water and trifluoroethanol solutions are investigated. Peptides containing only one phenylalanyl residue show markedly different near-uv dichroic signals depending on whether this residue is in the N-terminal position or not. The possible origin of this feature is discussed. The study of the oligopeptides II (n = 0,1,2) shows that no strong intramolecular interaction between the two aromatic rings is present. However, the dichroic properties of II (n = 0) are clearly anomalous, and the analysis of H-Gly-Phe-Trp-OH, H-Phe-Trp-Gly-OH, and of H-Phe-Trp-OH at different pH's, confirms that the presence of two adjacent aromatic residues may bring about chiroptical properties which indicate a restriction in the conformational equilibrium of the molecule. The limits, and the possible generalization of this finding, are discussed.     

Increased enzymatic activity of the neutral ribonuclease II-inhibitor system of liver and muscle after the administration of polyinosinylyl-polycytidylyl complex to mice

Administration of the synthetic, double-stranded polynucleotide, (I)_n·(C)_n, to mice in the range from 10–100 μg per g body weight results 24 hr later in increases approaching 2-fold in total RNase II (EC 3.1.4.22) activity levels in liver and skeletal muscle. Free RNase inhibitor levels fall so that free RNase II activities approach 5-fold increases. This response of RNase II may be part of the general defensive response against infectious agents exhibited by mammalian and avian cells and could also account for accompanying effects on inhibition of cellular protein synthesis which are caused by agents such as viruses and (I)_n·(C)_n.     

Synthesis,structure and a fourier transform infrared study of Pt(II), Cu(II), and Mg(II) Complexes with xanthosine-5′-monophosphate

The reaction of xanthosine-5′'-monophosphate disodium salt (5′-XMPNa₂) with Pt(II), Cu(II) and Mg(II) ions produced compounds of the type cis- and trans-Pt(NH₃)₂(XMPNa₂)_nCl₂·xH₂O, where n = 1 or 2; Pt(XMPNa₂)_nCl₂·xH₂O, where n = 1-4, x = 1,4 & 6; Cu(XMP)·6H₂O and Mg(XMP)·xH₂O, where x = 9 or 4. In the complexes synthesized here at neutral pH values, the nucleotide binds through the N_7-atom of the purine ring system, whereas for Cu(II) and Mg(II) compounds obtained at pH = 4 a direct metal-phosphate interaction as well as N_τ bonding is proposed.     

Protein sequences and redox titrations indicate that the electron acceptors in reaction centers from heliobacteria are similar to Photosystem I

Photosynthetic reaction centers isolated from Heliobacillus mobilis exhibit a single major protein on SDS-PAGE of 47 000 M_r. Attempts to sequence the reaction center polypeptide indicated that the N-terminus is blocked. After enzymatic and chemical cleavage, four peptide fragments were sequenced from the Heliobacillus mobilis apoprotein. Only one of these sequences showed significant specific similarity to any of the protein and deduced protein sequences in the GenBank data base. This fragment is identical with 56% of the residues, including both cysteines, found in the highly conserved region that is proposed to bind iron-sulfur center F_X in the Photosystem I reaction center peptide that is the psaB gene product. The similarity to the psaA gene product in this region is 48%.Redox titrations of laser-flash-induced photobleaching with millisecond decay kinetics on isolated reaction centers from Heliobacterium gestii indicate a midpoint potential of –414 mV with n=2 titration behavior. In membranes, the behavior is intermediate between n=1 and n=2, and the apparent midpoint potential is –444 mV. This is compared to the behavior in Photosystem I, where the intermediate electron acceptor A₁, thought to be a phylloquinone molecule, has been proposed to undergo a double reduction at low redox potentials in the presence of viologen redox mediators.These results strongly suggest that the acceptor side electron transfer system in reaction centers from heliobacteria is indeed analogous to that found in Photosystem I. The sequence similarities indicate that the divergence of the heliobacteria from the Photosystem I line occurred before the gene duplication and subsequent divergence that lead to the heterodimeric protein core of the Photosystem I reaction center.Abbreviations BChl bacteriochlorophyll - %C percent bisacrylamide as a percentage of total acrylamide - DTT dithiothreitol - EPR electron paramagnetic resonance - Fe-S iron-sulfur center - H. Heliobacterium - Hb. Heliobacillus - k one thousand - M_r molecular retention - PS I Photosystem I - PS II Photosystem II - RCs reaction centers - SDS sodium dodecyl sulfate - SDS-PAGE sodium dodecyl sulfate polyacrylamide electrophoresis - %T percent total acrylamide - Tris tris(hydroxymethyl)aminomethane     

Sequential extraction of chlorophyll from chlorophyll-protein complexes in lyophilized pea thylakoids with solvents of different polarity

Lyophilized chloroplasts of Pisum sativum (pea) have been extracted with petroleum ether of different polarity (obtained by adding varying amounts of ethanol to the petroleum ether). Extracted thylakoids have then been solubilized by sodium dodecyl sulphate (SDS) and chlorophyll-protein complexes have been isolated by polyacrylamide gel electrophoresis (PAGE). Absorption- and low temperature fluorescence emission spectro-scopy have been used to characterize thylakoids and purified chlorophyll-protein complexes. Weakly polar solvents extracted mainly chlorophyll a. SDS-PAGE scan profiles of similarly extracted thylakoids contained no photosystem II chlorophyll a reaction center antennae (CP-a_n) and the amount of photosystem I chlorophyll a reaction center antennae (CP-a₁) was reduced as compared with an unextracted control. This was due partly to the extraction of chlorophyll a prior to SDS-PAGE, and partly to the increased solubilization of chlorophyll a by SDS as a result of β-carotene extraction. By increasing the polarity of the solvent CP-a₁ also disappeared in the scan profile, leaving only the light-harvesting chlorophyll a/b-protein complex (CP-a/b) and SDS complexed chlorophyll. From these results we conclude that the chlorophyll molecules in the reaction center antennae are relatively more hydrophobically associated than the molecules in the light-harvesting CP-a/b complex. The chlorophyll a of CP-a_u and the far red absorbing chlorophyll a fraction of CP-a₁ appear to be the most hydrophobically associated chlorophyll molecules.     

Left-handed Z-DNA Helices in Polymers,Restriction Fragments,and Recombinant Plasmids

Abstract

Studies on DNA polymers, restriction fragments, and recombinant plasmids have revealed the following: A) A family of left-handed DNA conformations exists for (dC-dG)_n·(dC-dG)_n. The observation of a particular conformation is dependent on the salt, the salt concentration and dehydrating agent. B) In sodium acetate solutions, (dC-dG)_n·(dC-dG)_n forms left-handed, ψ(+)-condensed structures as detected by Raman spectroscopy and circular dichroism. C) (dT-dG)_n·(dC-dA)_n undergoes a right-to-left-handed transition only when reacted with AAF and at high salt concentrations. D) Transitions observed for polymer DNAs also are observed for restriction fragments containing both (dC-dG)·(dC-dG) and (dT-dG)·(dC-dA) sequences, but the transitions in the fragments generally require higher salt concentrations than observed for the polymers. E) Studies with recombinant plasmids containing (dC-dG) sequences from 10 to 58 bp in length demonstrate that left-handed Z-DNA segments can exist contiguous to B-DNA segments. F) Negative supercoil density (σ≤ ?0.072) is sufficient to convert the (dC-dG) regions in those plasmids into left-handed structures under physiological ionic conditions (200 mM NaCl). G) The favorable free energy contribution of methyla- tion in stabilizing the Z form in fragments and plasmids is approximately offset by the unfavorable free energy contributions of the B/Z junctions. H) S₁ and BAL 31 nucleases recognize aberrant structural features at the confluence of the B and Z regions. I) Detailed mapping of S₁ nuclease cleavage on supercoiled plasmids shows that the nuclease sensitive regions extend over at least five to ten bp. J) Even though the (dT-dG)_n·(dC-dA)_n polymer requires base modification and high salt conditions to undergo the R?L transition, supercoiling (σ ?0.07) can supply enough energy to allow a plasmid containing the intervening sequence of a human fetal globin gene with (dT-dG)·(dC-dA) sequences to undergo a R?L transition.     

Characterization of β-bend ribbon spiral forming peptides using electronic and vibrational CD

Terminally blocked (L-Pro-Aib)_n and Aib-(L-Pro-Aib)_n sequential oligopeptides are known to form right-handed β-bend ribbon spirals under a variety of experimental conditions. Here we describe the results of a complete CD and ir characterization of this subtype of 3₁₀-helical structure. The electronic CD spectra were obtained in solvents of different polarity in the 260-180 nm region. The vibrational CD and Fourier transform ir (FTIR) spectra were measured in deuterochloroform solution in the amide I and amide II (1750-1500 cm^?1) regions. The critical chain length for full development of the β-bend ribbon spiral structure is found to be five to six residues. Spectral effects related to concentration-induced stabilization of the structures of the longer peptides were seen in the resolution-enhanced FTIR spectra. Comparison to previous studies of (Aib)_n and (Pro)_n oligomers indicate that the low frequency of the amide I mode is due to the interaction of secondary and tertiary amide bonds and not to a strong difference in conformation from a regular 3₁₀-helix. © 1995 John Wiley & Sons, Inc.     

The unrestricted local properties: application in nanoelectronics and for predicting radicals reactivity

I have performed quantum chemical calculations for the CF₃X (X = Cl, Br) ???Au_n (n?=?2, 3, and 4) complexes at M05-2X/aug-cc-pVDZ(PP) level. Two types of optimized structures were obtained. Type I complexes are stabilized by the coordination force between the negative electrostatic potential of halogen atom and the gold atom, and type II complexes contain halogen bonds formed between the σ-hole of the halogen atoms and the negative electrostatic potential of Au_n. Results of the interaction energy indicate that type I complexes are more stable than type II complexes. AIM analysis reveals that type II complexes are a closed shell interaction and there is a partially covalent nature for type I complexes.     

Catalytic effect of (H2O)n (n = 1–3) clusters on the reaction of HNO2 + HO → H2O + NO2 under tropospheric conditions

ABSTRACT

The effect of (H₂O)_n (n?=?1–3) on the HNO₂?+?HO → H₂O?+?NO₂ reaction has been investigated theoretically at the CCSD(T)/CBS//B3LYP/6-311?+?G(3df,2pd) level of theory, coupled with rate constant calculations by using variational transition state theory. Our results show that, when (H₂O)_n (n?=?1–3) was introduced into HNO₂?+?HO → H₂O?+?NO₂ reaction, the product of the reaction did not change, but the potential energy surface became quite complex, yielding two kinds of reactions, namely HNO₂···(H₂O)_n (n?=?1–3)?+?HO and HO···(H₂O)_n (n?=?1–3)?+?HNO₂. In all catalysed reactions with (H₂O)_n (n?=?1–3), the former reaction type is favourable than the latter one with its effective rate constant respectively larger by 6–1 orders of magnitude than that of latter one. Within the temperature range of 240–320?K, the relative impacts on water monomer are much more obvious than dimer and trimer. However, the effective rate constant with water is larger by 658%–17% times of magnitude, showing that the positive water effect is obvious under atmospheric conditions.     

Microsolvation of aminoethanol: a study using DFT combined with QTAIM

The microsolvation of aminoethanol (AE) with one, two, three or four water molecules was investigated using a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen-bonding characteristics of AE–(H₂O) _n (n = 1–4) complexes. The results showed that AE tends to break its intramolecular OH^AE···N^AE hydrogen bond (H-bond) upon microsolvation and form intermolecular H-bonds with water molecules, while complexes that retain the intramolecular OH^AE···N^AE H-bond show reduced stabilities. The intermolecular H-bond that forms between the nitrogen atom of AE and the hydroxyl of a water molecule is the strongest one for the most stable AE–(H₂O) _n (n = 1–4) complexes, and as n increases from 1 to 4 they grow stronger. The partial covalent character of this H-bond was confirmed by QTAIM analyses. Many-body interaction analysis showed that the relaxation energies and two- and three-body energies make significant contributions to the binding energies of the complexes.     

Block oligopeptides (L-lysyl)m-(L-alanyl) L-tyrosyl-(L-alanyl)n- (L-lysyl)m. I. Synthesis through fragment condensation and characterization

Model peptides containing one aromatic residue were synthesized and characterized in order to investigate their interactions with polynucleotides. Chromatographically pure block oligopeptides (L -alysyl)_m-(L -alanyl)_n- L -tyrosyl- (L -alanyl)_n, with n = 3 and m=3 or 6, were prepared by fragments condensation using the mixed anhydride method. The protected fragments were prepared by stepwise addition of amino acid residues through the dicyclohexylcarbodiimide method. The purity of the intermediate coupling product was analyzed by gradient elution chromotography on carboxylmethylcellulose. Both block oligopeptides were isolated by preparative chromatography on carboxymethylcellulose. The different features of these syntheses are discussed.     

Co-oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. II. Ultraviolet absorption and circular dichroism properties of co-oligopeptides of tryptophan and glycine

The uv absorption and circular dichroism (CD) properties in water (pH 5.9) and trifluoroethanol of several co-oligopeptides of glycine and tryptophan have been investigated. These compounds contain one tryptophyl residue, such as H-Gly-Trp-OH, H-Trp-Gly-OH, and H-Gly-Trp-Gly-OH; or two, such as H-Trp-Trp-OH, H-Gly-Trp-Trp-OH, H-Trp-Trp-Gly-OH, and H-Gly-Trp-(Gly)_n-Trp-Gly-OH (I, n = 0,1,2). Furthermore, the case of some protected derivatives, such as Z-Trp-Gly-OMe, Z-Gly-Trp-Gly-OMe, and Z-Trp-Trp-OMe, Z-Trp-Trp-Gly-OMe, Z-Gly-Trp-Trp-Ome were investigated. The extinction coefficients in H₂O in the region of the L bands, referred to one mole of tryptophyl residue, are essentially the same for all compounds within the limit of experimental error, thus indicating that no strong chromophoric interaction takes place in the oligopeptides containing two aromatic residues. However, in the far uv region, anomalies in the absorption properties cannot be excluded. The investigated compounds show marked differences in their CD properties. Whereas in the case of lower molecular-weight peptides (e.g., H-Trp-Gly-OH and H-Gly-Trp-OH), these differences can be ascribed, at least in part, to the influence of the charge end groups on the indole chromophore, in the case of the compounds containing two tryptophyl residues, the differences in CD properties are assumed to reflect the different structures and conformations of the oligopeptides. In particular, we observed a negative dichroic band at ～225 nm in H-Gly-Trp-Trp-OH and I(n = 0) in water. In trifluoroethanol, this band has a much larger intensity, and it is present also in Z-Gly-Trp-Trp-OMe, Z-Trp-Trp-Gly-OMe, and Z-Trp-Trp-OMe. It is argued that such a negative band is characteristic of the sequence -CO-Trp-Trp-, and the possibility that it derives from intramolecular chromophoric interaction is discussed. It is also pointed out, particularly in view of the high ellipticity values found in some cases (up to 100,000 deg cm² dmol^?1), that this feature may reflect a high degree of conformational rigidity connected with the sequence -CO-Trp-Trp-.     

Derivatives of the red-violet cluster of copper and penicillamine prepared by mixed ligand formation reactions or direct additions

Mixed ligand clusters of the type Cu(I)₈Cu(II)₆L'_(n)L_(12?n)Cl are easily distinguished by zone electrophoresis if ligands L and L' differ in formal charge. Approximately random species distributions were observed when L was penicillamine and L' a related ligand lacking the negative charge of a carboxylate group, provided the L'/L molar ratio was less than $\text{1}\text{9}$ in the reaction mixture. Depending on the choice of L or L', it should be possible to prepare clusters with a variety of pendant groups. The cluster containing only penicillamine apparently forms addition products with carbodiimides and aziridines based on reactions involving the cluster's peripheral carboxylate groups.     

Study on the interaction of a copper(II) complex containing the artificial sweetener aspartame with human serum albumin

A copper(II) complex containing aspartame (APM) as ligand, Cu(APM)₂Cl₂·2H₂O, was synthesized and characterized. In vitro binding interaction of this complex with human serum albumin (HSA) was studied at physiological pH. Binding studies of this complex with HSA are useful for understanding the Cu(APM)₂Cl₂·2H₂O–HSA interaction mechanism and providing guidance for the application and design of new and more efficient artificial sweeteners drive. The interaction was investigated by spectrophotometric, spectrofluorometric, competition experiment and circular dichroism. Hyperchromicity observed in UV absorption band of Cu(APM)₂Cl₂·2H₂O. A strong fluorescence quenching reaction of HSA to Cu(APM)₂Cl₂·2H₂O was observed and the binding constant (K_f) and corresponding numbers of binding sites (n) were calculated at different temperatures. Thermodynamic parameters, enthalpy change (?H) and entropy change (?S) were calculated to be ?458.67 kJ mol^?1 and ?1,339 J mol^?1 K^?1 respectively. According to the van’t Hoff equation, the reaction is predominantly enthalpically driven. In conformity with experimental results, we suggest that Cu(APM)₂Cl₂·2H₂O interacts with HSA. In comparison with previous study, it is found that the Cu(II) complex binds stronger than aspartame.     

Prolonged high light treatment of plant cells results in changes of the amount,the localization and the electrophoretic behavior of several thylakoid membrane proteins

The effect of a 30 h high light treatment on the amount and the localization of thylakoid proteins was analysed in low light grown photoautotrophic cells of Marchantia polymorpha and Chenopodium rubrum. High light treatment resulted in a net loss of D1 protein which was accompanied by comparable losses of other proteins of the PS II core (reaction center with inner antenna). LHC II proteins were not reduced correspondingly, indicating that these complexes are less affected by prolonged high light. High light influenced the distribution of PS II components between the grana and the stroma region of the thylakoid membrane, probably by translocation of the respective PS II proteins. Additionally, modifications of several thylakoid proteins were detected in high light treated cells of C. rubrum. These effects are discussed in relation to photoinhibitory damage and repair processes.Abbreviations BCA bioinchonic acid - chl chlorophyll - CF₁ coupling factor - CYC cycloheximide - GT grana thylakoids - HL high light - LL low light - PAGE polyacrylamide gel electrophoresis - PFD photon flux density - PS I Photosystem I - PS II Photosystem II - RC reaction center - SDS sodium dodecylsulfate - ST stroma thylakoids - Thyl unfractionated thylakoids     

The presequence of the precursor to the nucleus-encoded 30 kDa protein of photosystem II in Euglena gracilis Z includes two hydrophobic domains

A cDNA clone for the extrinsic 30 kDa protein (OEC30) of photosystem II in Euglena gracilis Z was isolated and characterized. The open reading frame of the cDNA encoded a polypeptide of 338 amino acids, which consisted of a long presequence of 93 amino acids and a mature polypeptide of 245 amino acids. Two hydrophobic domains were identified in the presequence, in contrast to the presence of a single hydrophobic domain in the presequence of the corresponding proteins from higher plants. At the N- and C-terminal regions, respectively, of the presequence, a signal-peptide-like sequence and a thylakoid-transfer domain were identified. The presence of a long and unique presequence in the precursor to OEC30 is probably related to the complexity of the intracellular processes required for the synthesis and/or transport of the protein in Euglena.Abbreviations ER endoplasmic reticulum - cDNA complementary DNA - SSU small subunit; Rubisco, ribulose 1,5-bisphosphate carboxylase/oxygenase - Rubico, ribulose 1,5 bisphosphate carboxylase/oxygenase - LHC II light-harvesting chlorophyll protein of photosystem II - PS II photosystem II - OEC30 the extrinsic 30 kDa protein of photosystem II in Euglena - PCR polymerase chain reaction - SDS sodium dodecyl sulfate - TE a solution containing 10 mM Tris-HCl and 1 mM EDTA pH 8.0 - SSPE a solution containing 0.15 M NaCl, 10 mM NaH₂PO₄ and 1 mM EDTA pH 7.4 - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis - PVDF poly(vinylidene difluoride)     

Solvent coordination in changing dimensionality of lead benzoate coordination polymers

The reaction of lead (II) nitrate with sodium benzoate at low temperature gives one dimensional coordination polymer with composition [Pb(Ben)₂(MeOH)₂]_n (where Ben = benzoate, MeOH = methanol). This one dimensional polymer on heating in aqueous solution results in the formation of a two dimensional polymer having composition [Pb(Ben)₂(H₂O)]_n. Similar reaction of lead (II) nitrate with 2-methylbenzoic acid in the presence of sodium hydroxide in methanol at low temperature gives a coordination polymer having composition [Pb(o-TOL)₂(MeOH)₂]_n (where o-TOL = 2-methylbenzoate); which on re-dissolution in aqueous methanol or keeping in water, at room temperature leads to another coordination polymer having a composition of [Pb(o-TOL)₂(H₂O)]_n.     

Proton-NMR study of the interaction of trans-dichloro-diamine-platinum(II) with poly(I) and poly(I).poly(C)

The fixation of trans-(NH₃)₂Cl₂ Pt(II) to poly(I)·poly(C) at low r_b (< 0.05) leads to the formation of two complexed species. The major species (ca. 82% of bound platinum) involves coordination of platinum to a single hypoxanthine base, while the other species involves coordination of two hypoxanthine bases, which are either far apart on the same strand or on separate poly(I) strands, to the platinum. These same two species are found after reaction with poly(I), as are two other species throughout the entire r_b range studied (r_b = 0–0.30). The latter two species are assigned to trans-Pt bound to two bases on a poly(I) strand with (a) one or (b) two free bases between the two bound bases. These two species, (a) and (b), account for ca. 35% of the bound platinum, although the 1:1 species remains dominant (ca. 55%). These two additional species are observed at high r_b (>0.075) after reaction with poly(I)·poly(C) but as very minor species. They are formed by reaction with melted poly(I) loops. Also at high r_b, we have observed a shifted cytidine H⁵ resonance arising from interaction of trans-Pt with a melted loop of poly(C). Most probably, this arises from an intramolecular poly(I) to poly(C) crosslink. Results from the reaction of trans-Pt with poly(C) are presented for comparison.