Oligomers Of Various Sizes Research Articles

ChemInform Abstract: Two‐Dimensional Infrared and Near‐Infrared Correlation Spectroscopy: Applications to Studies of Temperature‐Dependent Spectral Variations of Self‐Associated Molecules

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Two-Dimensional Infrared and Near-Infrared Correlation Spectroscopy: Applications to Studies of Temperature-Dependent Spectral Variations of Self-Associated Molecules

This paper demonstrates the potential of generalized two-dimensional (2D) Fourier transform (FT) infrared (IR) and near-infrared (NIR) correlation spectroscopy in the studies of temperature-dependent spectral variations of self-associated molecules. Three examples of the 2D correlation analysis are discussed in this paper. The first two are concerned with the temperature-dependent IR and NIR spectral changes of N-methylacetamide (NMA) in the pure liquid state. The 2D IR correlation approach revealed that almost all the peaks of NMA in the 3400–1100-cm−1 region consist of two to four separate bands. For example, the amide I band contains contributions from at least four distinct bands at 1685, 1665, 1650, and 1635 cm−1. The analysis of the asynchronous 2D IR spectrum in the amide I region showed that the sequence of spectral intensity change in the ascending order of temperature was given by 1635<1650<1665<1685 cm−1. These bands at 1635, 1650, 1665, and 1685 cm−1 were assigned to the amide I modes of chain oligomers of various sizes and dimer of NMA; the longer the chain, the lower the frequency. The closeup view of 2D NIR correlation spectra of NMA obtained at narrow spectral and temperature windows enabled us to propose not only band assignments in the 6800–6050-cm−1 region but also a detailed mechanistic picture of the thermally induced dissociation of NMA for each temperature range. We also applied the generalized 2D correlation approach to the analysis of a set of FT NIR spectra of oleyl alcohol under temperature variations. The 2D NIR analysis enhanced the spectral resolution and simplified the spectra with overlapped bands. For example, it was found that a band at 7090 cm−1 arising from the first overtone of an OH stretching mode of the monomeric alcohol consists of two bands due to the rotational isomerism of the free OH group. An intriguing possibility of correlating various overtone and fundamental bands to establish unambiguous assignments was also suggested from the 2D NIR study on oleyl alcohol.

Two-Dimensional Correlation Spectroscopy Study of Temperature-Dependent Spectral Variations of N-Methylacetamide in the Pure Liquid State. 1. Two-Dimensional Infrared Analysis

This paper reports two-dimensional Fourier-transform infrared (2D FT IR) correlation spectroscopy study of temperature-dependent spectral variations of N-methylacetamide (NMA) in the pure liquid. The 2D correlation spectroscopic analysis has demonstrated that the amide I band of NMA consists of at least four distinct bands at 1685, 1665, 1650, and 1635 cm-1. The signs of asynchronous cross peaks corresponding to these four bands have shown that the sequence of spectral intensity change in the ascending order of temperature is given by 1635 cm-1 < 1650 cm-1 < 1665 cm-1 < 1685 cm-1. These bands at 1635, 1650, 1665, and 1685 cm-1 may be due to the amide I modes of chain oligomers of various sizes and dimer of NMA. The longer the chain, the lower the frequency. Similarly, it has been found that the amide A, II, and III bands consist of at least two bands. For example, the amide II is split into two bands at 1570 and 1545 cm-1. The 2D correlation analysis between different spectral regions has enabled to make ...

Triplet states in reaction center, light-harvesting complex B875 and its spectral form B840 from Rubrivivax gelatinosus investigated by absorbance-detected electron spin resonance in zero magnetic field (ADMR)

Absorbance-detected magnetic resonance (ADMR) spectroscopy was used for characterization of the triplet states in several pigment-protein complexes from Rubrivivax gelatinosus, namely the isolated reaction center, the core light-harvesting complex B875, and the B875 subunit form that absorbs in the infrared at 820 nm (B820), and, in the presence of glycerol, at about 840 nm (B840). The zero-field splitting parameters of the triplet states were determined and T - S spectra were recorded at 1.2 K. The absorbance and T - S spectra of the reaction center resemble closely those of Rhodobacter sphaeroides, except for slight shifts in the band positions. For the isolated B875 complex, only the triplet state of carotenoid was observed, indicating that triplet-triplet transfer from bacteriochlorophyll a to the carotenoid proceeds as in the native system. The near-infrared absorption spectrum of B840 at 1.2 K revealed several overlapping bands, which were deconvoluted in five Gaussian components corresponding to free BChl a (795 nm), B820 (826 nm), small population of B875 (888 nm) and two new spectral forms B846 and B868. The origin of these two latter spectral forms is proposed to reflect inaccurate reassociation of B820. Probably, oligomers of various sizes are formed, with different strengths of pigment-pigment and pigment-protein interactions. The T - S spectrum of B840 is consistent with that of a BChl a dimer containing a localized triplet state.

Chitinase isoenzymes induced in carrot cell culture by treatment with ethylene

In cultured carrot cells, treatment with exogenously supplied ethylene or 1-aminocyclopropane-1-carboxylic acid induced chitinase activity. Most of the induced enzymes were secreted into the culture medium. The extracellular chitinases induced by ethylene were resolved by gel-filtration chromatography into four isoenzymes with different molecular sizes. Two of them were exo-hydrolases which liberated chitobiose as a sole product from insoluble chitin. Another two isomers were thought to be endo-chitinase because they yielded chitin oligomers of various sizes. As major molecular species of chitinase found in ethylene-treated carrot cell cultures were different from those induced by fungal walls, it was suggested that ethylene and fungal components act as independent signals in chitinase induction.

Degradation of poly(3-hydroxybutyrate) by poly(3-hydroxybutyrate) depolymerase from Alcaligenes faecalis T 1

The extracellular poly(3-hydroxybutyrate) depolymerase purified from Alcaligenes faecalis T 1 has two disulfide bonds, one of which appears to be necessary for the full enzyme activity. This depolymerase hydrolyzed not only hydrophobic poly(3-hydroxybutyrate) but also water-soluble trimer and larger oligomers of D-(−)-3-hydroxybutyrate, regardless of their solubilities in water. Kinetic analyses with oligomers of various sizes indicated that the substrate cleaving site of the enzyme consisted of four subsites with individual affinities for monomer units of the substrate. Analyses of the hydrolytic products of oligomers, which had labeled D-(−)-3-hydroxybutyrate at the hydroxy terminus, showed that the enzyme cleaved only the second ester linkage from the hydroxy terminus of the trimer and tetramer, and acted as an endo-type hydrolase toward the pentamer and higher oligomers. The enzyme appeared to have a hydrophobic site which interacted with poly(3-hydroxybutyrate) and determined the affinity of the enzyme toward the hydrophobic substrate.

Histone H5 promotes the association of condensed chromatin fragments to give pseudo-higher-order structures.

We describe two distinct situations in which chicken erythrocyte chromatin fragments associate in solution. The erythrocyte-specific histone H5 is implicated since chromatins that do not contain H5 do not show this behaviour. Well-defined oligomers of between approximately 6 and approximately 18 nucleosomes prepared at low ionic strength condense and associate when the ionic strength is raised to 75 mM, forming pseudo-higher-order structures. The associated forms, probably predominantly dimers, are stabilized by migration of about 10% of the H5, and of the minor lysine-rich histone H1, from the non-associated forms, probably reflecting the preference of H5 for higher-order structures observed previously [Thomas, J. O. and Rees, C. (1983) Eur. J. Biochem. 134, 109-115]. Since the final (H1 + H5) content of the aggregate at 75 mM is never higher than that of the fragment prepared at low ionic strength, migration is probably to a small proportion of sites that have inevitably become vacant due to handling losses at the higher (but not at low) ionic strength. H5 thus maximizes its interactions in the condensed state of chromatin and even maintains the association of two or more fragments without continuity of the DNA. Aggregates of oligomers larger than about 18 nucleosomes may be too long to withstand hydrodynamic shear forces in the absence of such continuity. During nuclease digestion of nuclear chromatin, H5 and, to a lesser extent, H1, are released from the ends of very short fragments and bind to larger oligomers of various sizes leading to heterogeneous aggregates that survive exposure to low ionic strength. These aggregates, in contrast to those described above, have up to 60% more H5 and 20% more H1 than chromatin prepared at low ionic strength. Whether the excess H5 and H1 bind non-specifically or to a second low-affinity binding site on each nucleosome is not known. The associated forms described above (1) are well defined and potentially useful for structural studies, whereas the other aggregates (2) seem less likely to be directly relevant to the native structure of chromatin.

Sphere-Rod Morphogenesis in Arthrobacter crystallopoietes II. Peptides of the Cell Wall Peptidoglycan

Cell walls of Arthrobacter crystallopoietes grown as spheres and as rods were solubilized by treatment with the B enzyme from Chalaropsis, an N-acetylmuramidase. The neutral glycopeptides were then isolated by chromatography on ECTEOLA cellulose. The glycopeptides, consisting of disaccharide-peptide units interlinked by peptide cross-bridges, were fractionated by gel filtration on Sephadex columns into oligomers of various sizes. The size distribution ranged from monomers with no cross-bridges to polymers with a high degree of polymerization, but did not differ significantly between cell walls from cells grown as spheres or rods. Some small differences in the distribution of C- and N-terminal amino acids were found. Analyses revealed that all the peptide bridges in the glycopeptide fractions from rod cell walls were formed by one l-alanine residue. In sphere cell walls, l-alanine was also found, but, in addition, higher oligomers of the glycopeptide contained glycine in their cross-bridges. These results were confirmed by determinations of C- and N-terminal amino acids released after lysostaphin and AL-1 enzyme digestions and by Edman degradations. Models representing the structures of the sphere and rod cell walls are presented. These structures indicate that the sphere cell wall is probably a more loosely knit macromolecule than is the rod cell wall.