Kinetics of cooperative conformational transitions of lineal biopolymers

Cooperative conformational transitions of proteins and nucleic acids are of decisive importance to many processes of molecular biology, and particularly to their regulation. They proceed via numerous interdependent elementary processes, and their kinetics are therefore often complicated. They are frequently also very fast. However, kinetic analyses can be carried out by chemical relaxation methods. The theoretical interpretation is comparatively simple in the case of linear biopolymers. When the linear Ising model extended for kinetics was applied to model peptides and polynucleotides, it provided an insight into the fundamental principles of cooperative transformations.     

Synthesis and properties of 7,7-bis(heteroazulen-3-yl)-8,8-dicyano-1,4-quinodimethanes

The synthesis and properties of a novel type of 7,7-bis(heteroazulen-3-yl)-8,8-dicyano-1,4-quinodimethanes (9a-c) are studied. The synthetic method is based on a TFA-catalyzed electrophilic aromatic substitution on the heteroazulenes with 4-(dicyanomethyl)benzaldehyde to afford the corresponding methane derivatives, followed by oxidative hydrogen abstraction with DDQ. The polarization of 9a-c is evaluated by the inspection of their ¹³C NMR and IR spectra. Based on the investigation of the UV-Vis spectra of 9a-c and protonated cations 10a-c, conformational changes of the heteroazulene-moiety and (dicyanomethyl)phenyl group are suggested. In the CV measurements of 9a-c, two reversible reduction waves are observed, indicating the stabilizing ability of heteroazulenes toward the corresponding radical and anion species. Furthermore, 9a-c exhibit two irreversible oxidation waves, which suggest a conformational change in the radical cation during the redox process. The conformational change is rationalized on the basis of the MO calculations.     

Volume and compressibility changes of complex formation between 18-Crown-6 and NaCl,KCl, and CsCl in water

The apparent molal volumes and compressibilities of NaCl, KCl, and CsCl in mixtures of 18-Crown-6 and water have been calculated from density and speed-of-sound measurements at 25°C. The partial molal volumes and compressibilities of the salts when all cations have formed complexes with 18-Crown-6 molecules have been evaluated. The sign and magnitude of the volume and compressibility changes of complex formation strongly suggest that the charge of the cation becomes very effectively screened by the crown ether.     

Model dipeptides incorporating the trans cyclohexane analogues of phenylalanine: further evidence of the relationship between side-chain orientation and β-turn type

In order to study the influence of the side-chain orientation on the peptide backbone conformation we have synthesised the model dipeptides t-BuCO-l-Pro-(1S,2R)-c₆Phe-NHMe and t-BuCO-l-Pro-(1R,2S)-c₆Phe-NHMe, incorporating each enantiomer of the trans cyclohexane analogue of phenylalanine (trans-1-amino-2-phenylcyclohexanecarboxylic acid). The orientation of the aromatic side-chain determines the β-turn type accommodated by these peptides to the point that the (1S,2R)-c₆Phe derivative retains the type I β-turn in the crystalline state, in contrast to the behaviour exhibited by the natural counterpart t-BuCO-l-Pro-l-Phe-NHMe.     

Interactions of D-Maltose and Sucrose with Some Amino Acids in Aqueous Solutions

Calorimetric titrations have been performed at 298.15 K in aqueous solutions to derive the stability constants and thermodynamic parameters of the interactions of D-maltose and sucrose with some amino acids (glycine, DL-alanine, DL-leucine, and L-serine). The apparent molal volumes of the disaccharides in dilute aqueous solutions of the amino acids have been determined from density measurements at 298.15 K. In contrast to D-maltose, sucrose was found to associate with the amino acids and these associated species are preferentially entropy stabilized. These results are interpreted in terms of the influence of the nature of the solutes, their specific conformations, and hydration, on the ability of the disaccharides to form associated complexes with the amino acids.     

Computer simulation of conformational movement based on interconversion phenomena

A computer method has been developed which is an alternative to molecular dynamics in the sense that it pictures conformational motion. It simulates propagation in conformational movement based on conformational interconversion phenomena. The method starts with the knowledge of the topology of the conformational potential energy hyper-surface, which is described by the minima and the transition states. The topology is obtained by the recently described software . The simulation of conformational motion is based on the Boltzmann statistics of movement between the minima and the transition states at a given temperature. The method is illustrated for methyl--glucopyranoside and - -galNAc(1-3)[- -Fuc(1-2)]Gal-O-Me molecules. Conformational transitions of hydroxyl groups as well as glycosidic linkages are discussed.     

Stability of the FID sensitivity during an analysis in capillary GC

The sensitivity of an FID may change when the carrier gas flow rate changes during a chromatographic run. Sample parts which are eluted at reduced FID sensitivity produce a reduced peak area, hence are discriminated as compared to other components. Sensitivity changes were studied for hydrogen as carrier gas. For the detector tested, differences in the carrier gas flow rates of 1 ml/min shifted the FID sensitivity by 1 to 5% (depending on the fuel gas supply). Thus the stability of the sensitivity is no longer ensured as soon as the carrier gas flow rate is changed manually or by an automatic programmer during an analysis. Sensitivity drifts may also occur during temperature programmed runs with a pressure regulated carrier gas supply since the gas flow through the capillary drops with increasing temperature. Such shifts in the response became noticeable as soon as relatively high carrier gas flow rates combined with long range temperature programmes were used. The typical patterns of such discriminations are shown, closing with a discussion on the possibilities for minimizing such undesired effects.     

Solvent and substituent effects on the conformational equilibria and intramolecular hydrogen bonding of 4-substituted-2-hydroxybenzaldehydes

By applying the B3LYP/6-31G(d) method with the SCIPCM model on seven 4X substituted 2-hydroxybenzaldehydes, some structural characteristics related with their conformational equilibria and intramolecular hydrogen bonds have been clarified. The compounds are almost completely under the planar conformation characterized by a strong intramolecular hydrogen bond, which decreases in those solvents that possess a higher hydrogen bond donating capability and polarity. The substituents exert a marked influence on the conformational equilibrium constants and the strength of the IHB. Moreover, the excellent Hammett-type equations obtained support the proposed conformational reactions to quantify the IHB in the o-hydroxybenzaldehydes studied.     

Small-angle X-ray scattering studies of the open and closed conformations of aspartate aminotransferase

Summary Aspartate aminotransferase was investigated by X-ray small-angle scattering. A small difference was found between the open (active) and the closed (liganded) conformation of the enzyme. The results were compared with X-ray crystallography data.

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Untersuchungen zur Röntgenkleinwinkelstreuung der offenen und geschlossenen Konformation von Aspartat-Aminotransferase

Zusammenfassung Aspartat-Aminotransferase wurde mittels Röntgenkleinwinkelstreuung untersucht. Ein kleiner Unterschied zwischen der offenen (aktiven) und der geschlossenen (ligandierten) Konformation wurde gefunden. Die Ergebnisse wurden mit Röntgenkristallstrukturdaten verglichen.

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Abbreviations AspAT aspartate aminotransferase     

Conformational and stereoelectronic investigation in 1,2-difluoropropane: The gauche effect

The effect of attaching an additional fluorine atom at C-2 in 1-fluoropropane (FP), giving 1,2-difluoropropane (DFP), on its conformational equilibrium, is theoretically evaluated. This substitution causes critical implications on the conformer stabilities of DFP (TG, GT and GG conformations) and the steric and electrostatic interactions should favor the conformer with fluorine atoms trans. However, the gauche effect plays a major role in describing the energies balance in DFP, shifting the equilibrium towards the conformation in which the two fluorine atoms are gauche. The origin of this effect is discussed through an NBO analysis, which allows the evaluation of both classical and non-classical (hyperconjugation and bent bonds) interactions as the prevailing factors governing the conformational equilibrium of molecules containing the 1,2-difluoroethane fragment.