Metal clips induce folding of a short unstructured peptide into an alpha-helix via turn conformations in water. Kinetic versus thermodynamic products

Short peptides corresponding to two to four alpha-helical turns of proteins are not thermodynamically stable helices in water. Unstructured octapeptide Ac-His1-Ala2-Ala3-His4-His5-Glu6-Leu7-His8-NH(2) (1) reacts with two [Pd((15)NH(2)(CH(2))(2)(15)NH(2))(NO(3))(2)] in water to form a kinetically stable intermediate, [[Pden](2)[(1,4)(5,8)-peptide]](2), in which two 19-membered metallocyclic rings stabilize two peptide turns. Slow subsequent folding to a thermodynamically more stable two-turn alpha-helix drives the equilibrium to [[Pden](2)[(1,5)(4,8)-peptide]] (3), featuring two 22-membered rings. This transformation from unstructured peptide via turns to an alpha-helix suggests that metal clips might be useful probes for investigating peptide folding.     

An improved method for the synthesis of cellulose membrane-bound peptides with free C termini is useful for PDZ domain binding studies

SPOT synthesis permits parallel synthesis and screening of thousands of cellulose membrane-bound peptides to study protein-protein interactions in a proteomic context. Recognition of C-terminal residues is one of the most common binding features of PDZ domains. Unfortunately, most solid support-bound peptide libraries lack a free C terminus due to C-terminal fixation on the solid support. To overcome this restriction, we developed a robust methodology based on our previous strategy for generating peptides with authentic C termini. To validate this improved method, we screened a human peptide library of 6223 C termini with the syntrophin PDZ domain. Furthermore, using the same library, new peptide ligands derived from membrane proteins and receptors were found for the ERBIN PDZ domain. Finally, we identified the protein kinase breakpoint cluster region, which is known as a negative regulator of cell proliferation and oncogenic transformation, as an ERBIN ligand.     

π‐Facial Selectivity in the Formation of Tricarbonylchromium(0) Complexes of Estra‐1, 3, 5(10), 6‐tetraenes

The preparation of two η⁶‐estra‐1, 3, 5(10), 6‐tetraene tricarbonylchromium complexes 4 and 6 are described. In both cases only one stereoisomer can be isolated, in contrast to other estrane‐tricarbonylchromium complexes, where complexations are non‐stereoselective. X‐ray crystal structural analysis of 4 discloses that only the more sterically hindered β‐facial isomer is formed. It is assumed that the 6, 7‐olefinic moiety exerts a directive influence on the complexation.     

Novel dye-attached macroporous films for cadmium, zinc and lead sorption: Alkali Blue 6B-attached macroporous poly(2-hydroxyethyl methacrylate)

Alkali Blue 6B-attached poly(2-hydroxyethyl methacrylate) (poly(HEMA)) microporous films were investigated as chelate forming sorbents for heavy metal removal. Poly(HEMA) microporous films were prepared by UV-initiated photo-polymerization of HEMA in the presence of an initiator (azobisisobutyronitrile (AIBN)). Alkali Blue 6B was attached covalently. These films with a swelling ratio of 58%, and carrying 14.8 mmol Alkali Blue 6B m(-2) which were then used in the removal of Cd(II), Zn(II) and Pb(II) from aqueous media. Adsorption rates were very high, equilibrium was achieved in about 30 min. The maximum adsorption of heavy metal ions onto the Alkali Blue 6B-attached films were 41.4 mmol m(-2) for Cd(II), 52.4 mmol m(-2) for Zn(II), and 64.5 mmol m(-2) for Pb(II). When the heavy metal ions competed during the adsorption from a mixture the adsorption values for Cd(II), Zn(II) and Pb(II) were quite close. Heavy metal ions were desorbed by using 0.1 M HNO(3). A significant amount of the adsorbed heavy metal ions (up to 95%) could be desorbed in 30 min. Repeated adsorption/desorption cycles showed the feasibility of these novel dye-attached microporous films for heavy metal removal.     

Observations on clear solution silicalite-1 growth by nanoslabs

Several research groups have reported the presence of nanometer-sized particles (nanoslabs) in clear solutions, which precipitate the crystalline MFI (ZSM-5) structure. Debate about the growth mechanism for Al-free ZSM-5 (silicalite-1) has revolved around growth by small silicate units (monomers, dimers, etc.) from solution vs growth by nanoslab addition. A model developed for precipitation of uniform sized colloids by addition of sub-colloidal precursor units has been adapted for this zeolite synthesis system. Parameter values were adjusted for the simulation results to match experimental observations from work reported previously, at least to the extent possible. The model involved the simultaneous solution of up to 6000 ordinary differential equations, and required computation times of up to 24 h. The results shed light on the crystal growth mechanism, but pose questions for further investigations of the nucleation mechanism.     

Genotoxic properties of 2-dodecylcyclobutanone, a compound formed on irradiation of food containing fat

When food containing fat is treated by ionizing radiation, a group of 2-alkylcyclobutanones is formed. These components contain the same number of carbon atoms as their precursor fatty acids and the alkyl group is located in ring position 2. Thus, from palmitic acid 2-dodecylcyclobutanone is derived. To date, there is no evidence that the cyclobutanones occur in unirradiated food. Therefore, these components cannot be considered inherent to food, and for questions pertaining to risk assessment of irradiated food it would be advisable to determine the genotoxic and toxic potentials of cyclobutanones. Measurements of DNA damage in cells exposed to 2-dodecylcyclobutanone, employing the single cell microgel electrophoresis technique, have been carried out. In vitro experiments using rat and human colon cells indicate that 2-docylcyclobutanone in the concentration range of about 0.30 – 1.25 mg/ml induces DNA strand breaks in the cells. Simultaneously, a concentration related cytotoxic effect is observed as was determined by trypan blue exclusion. To which extent these in vitro findings are of relevancy for the in vivo human exposure situation needs to be investigated in further studies. In vivo tests in rats are in progress.     

A many-body diagrammatic theory of rotation–vibration spectra

A many-body diagrammatic perturbation theory of rotation–vibration spectra is elaborated. The present approach is based on two many-body techniques, namely on the second quantization formalism (a rotating–vibrating molecule is formally treated here as a system of interacting vibrons, obeying the Bose–Einstein statistics) and the many-body diagrammatic theory of a model Hamiltonian, initially suggested in the microscopic theory of nuclei and in the last decade very frequently exploited in the accounting for the correlation effects in many electron systems. In the framework of this theory, the rotation–vibration energies are determined as the eigenvalues of a finite-dimensional model eigenproblem.     

Über die Wahl der Lösungsmittelsysteme bei der papierchromatographischen Trennung organischer Verbindungen

Zusammenfassung An praktischen Beispielen wurde gezeigt, in welcher Weise die Trennung organischer Verbindungen mittels Papierchromatographie erzielt werden kann. Man ist nicht auf einige bewährte Lösungsmittel systeme allein angewiesen, sondern kann von Fall zu Fall systematisch neue und geeignete Systeme benützen. Es hat sich bewährt, sich nach den elementaren Löslichkeitsregeln für organische Stoffe zu richten, unter der Voraussetzung, daß die zu chromatographierende Verbindung in der stationären Phase gut, in der mobilen Phase dagegen weniger löslich ist. Durch Änderung der stationären Phase (Wasser, nicht wäßriges, polares Lösungsmittel, nicht polares Lösungsmittel) oder der Polarität und Zusammensetzung der mobilen Phase kann man das Wandern der Flecke am Chromatogramm beeinflussen, beliebige R_fWerte erhalten und in vielen Fällen auch eine beliebige Reihenfolge der Verbindungen am Chromatogramm erzielen.Da die Löslichkeit organischer Verbindungen von intermolekularen Kräften abhängig ist, erscheint das Problem im Zusammenhang mit strukturellen Einflüssen sehr kompliziert und muß für jeden Fall auf eigene Weise gelöst werden. Die Löslichkeitseigenschaften können weiter durch Benutzung reaktiver Lösungsmittel beeinflußt werden, die z. B. die Verbindungen in wasserlösliche Salze überführen können. Dabei ist an die möglichen Komplikationen, die bei ionisierbaren Verbindungen durch Dissoziation und Hydrolyse entstehen können, zu achten.Von den Hauptfaktoren, die eine Trennung ermöglichen können, seien die folgenden erwähnt: funktionelle Gruppen, ihre Anzahl, Polarität, gegenseitige Stellung, bzw. ihre Basizität oder Azidität, C-Atomanzahl in homologen Verbindungen, inter- und intramolekulare Wasserstoffbindungen, sterische Faktoren u. a. Es ist dann von der Art des gewählten Lösungsmittelsystems abhängig, welche der genannten Faktoren im Vordergrund stehen und welche beseitigt werden.Wenn die Löslichkeitsunterschiede der zu trennenden Stoffe zu gering sind, um gute Trennungen zu ermöglichen, ist es zweckmäßig, die Verbindungen in solche Derivate zu überführen, deren Strukturunterschiede größer sind.

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Summary Practical examples are given to show how organic compounds can be separated by means of paper chromatography. The operator is not limited to tested solvent systems, but can use new suitable systems as the occasion demands. It has been found best to abide by the elementary rules of solubility of organic compounds, provided the compound to be chromatographed is quite soluble in the stationary phase but less soluble in the mobile phase. By altering the stationary phase (water, nonaqueous, polar solvent, non-polar solvent) or the polarity and composition of the mobile phase, the migration of the stains in the chromatogram can be influenced, selectedR _f -values can be obtained, and in many cases it is also possible to secure a desired succession of the compounds on the chromatogram.Since the solubility of organic compounds depends on intermolecular forces, the problem in connection with structural influences appears very complicated and must be solved individually for each case. Moreover, the solubility characteristics can be affected by using reactive solvents; for instance, the compounds can be converted into water soluble salts. Under such circumstances, sight must not be lost of the complications which may arise because of the dissociation and hydrolysis of ionizable compounds. The following are among the chief factors, which may make a separation possible: functional groups, their number, polarity, relative position, their basicity or acidity, C-atom number in homologous compounds, inter- and intramolecular hydrogen bonds, steric factors, etc. It then depends on the type of solvent system selected, which of these factors are predominant and which can be neglected or eliminated.If the solubility differences are too slight to permit good separations, the compounds to be separated should, if possible, be converted into derivatives whose structural differences are more pronounced.

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Résumé Des exemples pratiques montrent comment il est possible d'effectuer la séparation de combinaisons organiques par Chromatographie sur papier. Il n'est pas uniquement fait appel à des systèmes de solvants éprouvés mais, dans certains cas, de nouveaux systèmes appropriés sont systématiquement utilisés.Il s'est avéré satisfaisant de faire appel aux règles élémentaires de solubilité des substances organiques sous réserve que la combinaison à chromatographier soit suffisamment soluble dans la phase stationnaire et moins soluble dans la phase mobile. En faisant varier la phase stationnaire (eau, solvant non aqueux, solvant polaire, solvant non polaire) ou la polarité et la composition de la phase mobile, il est possible d'influencer la migration des taches du chromatogramme, d'obtenir des valeurs deR _f désirées et, dans de nombreux cas, d'obtenir les combinaisons dans un ordre déterminé sur le chromatogramme.La solubilité des combinaisons organiques étant fonction des forces intermoléculaires il en résulte que le problème se complique considérablement dans la mesure où l'on considère les influences structurelles et que chaque cas particulier doit recevoir une solution qui lui est propre. Les propriétés de solubilité peuvent en outre être influencées par l'emploi de solvants réactifs qui peuvent transformer, par exemple les combinaisons en sels solubles dans l'eau. Il faut alors tenir compte des possibilités de complications qui peuvent apparaître par dissociation et hydrolyse des combinaisons ionisables.Parmi les principaux facteurs qui permettent une séparation, il convient de mentionner les suivants: les groupes fonctionnels, leur nombre, leur polarité, leur position relative, ou encore leur acidité ou leur basicité, le nombre d'atomes de carbone de combinaisons homologues, les liaisons hydrogène inter- et intramoléculaires, les facteurs stériques, etc. Suivant la nature du système solvant choisi pourront alors varier les facteurs dont l'effet est prépondérant et ceux dont l'effet est nul. Lorsque les différences de solubilité des substances à séparer sont trop faibles pour permettre des séparations satisfaisantes, il est commode de transformer les combinaisons en dérivés dont les différences de structure soient plus importantes.

     

Anionic copper complex fragmentations from enkephalins under low-energy collision-induced dissociation in an ion trap mass spectrometer

Peptide metallation with Cu2+ was explored in the negative ESI mode using an ion trap mass spectrometer. Under these conditions, the [(M-3H) + CuII]- species formed were investigated under low-energy collision-induced dissociation conditions. MS2 experiments indicate a very different behavior of CuII metallated complexes compared with [M-H]- species. CuII induces an easy loss of CO2 and specific side-chain cleavages (by radical losses) at the C-terminal residue, as observed previously by prompt 'in source' dissociation experiments. The loss of CO2 yields an unstable carbylide that leads to further dissociations involving the migration of a proton or a hydrogen radical (through the reduction of CuII). Multistage MS3 experiments were carried out to rationalize this behavior. Fragmentation pathways are proposed in order to explain the product ions observed. The side-chain radical loss at the C-terminus was demonstrated to be a consecutive process. Finally, evidence is provided that the specific side-chain cleavages can be used for the differentiation of Leu/Ile and Gln/Lys residues when they are located at the C-terminus. The existence of a zwitterionic form in the case of the anionic YGGFK-CuII complex is proposed.     

Methyl cellulose-based edible films and coatings I. Effect of plasticizer content on water and 1-octen-3-ol sorption and transport

Edible films were prepared from methyl cellulose with various concentrations of poly(ethylene glycol) 400 (PEG400) used as a plasticizer. Water vapour and 1-octen-3-ol (an aroma compound) were selected as hydrophilic and hydrophobic volatile penetrants respectively. Their solubility and permeability through methyl cellulose-based edible films were studied using gas chromatography methods. Whatever penetrant was used, the flux increased with the PEG400 content. Transfer behaviour, i.e., the order of increased magnitude of the transfer rate, strongly depends on the nature of the volatile compound. However, water sorption only depends on the PEG400 content whereas the aroma compound sorption is affected by both the water and the PEG400 concentrations. Relationships between solubility and permeability can be partially explained by the plasticization phenomenon.