Extraribosomal cyclic tetradepsipeptides beauverolides: profiling and modeling the fragmentation pathways

Profiling of cyclic tetradepsipeptides beauverolides was tested as a chemotaxonomic tool for fungal strain identification/discrimination. Two new tetradepsipeptides, beauverolides Q and R, were characterized by tandem mass spectrometry. Specific elimination of 113 atomic mass units from both protonated and sodiated molecules of beauverolides is ubiquitous for all 12 most dominant congeners evaluated in this profiling study. Reconstruction of the total ion chromatogram, according to this neutral fragment release, was used for data filtering and selectivity enhancement. Selective ring opening and fragment ion formation of beauverolide I are discussed in detail utilizing high-level theoretical modeling of the fragmentation pathways.     

PHOTOCHEMICAL BEHAVIOR OF BACTERIORHODOPSIN IMMOBILIZED IN NaCl PELLETS

Abstract— Some photochemical reactions of bacteriorhodopsin (BR) embedded in NaCl pellets (BR-NaCI) in the visible region are described here. BR in these preparations is a mixture of two classes of species: a drastically blue-shifted form and the unchanged purple pigment. Depending on the illumination history of the BR before being immobilized, both kinds of BR could be demonstrated in light-adapted (LA) and dark-adapted (DA) forms, but light adaptation was not possible once the pellets were made. Analogously to BR suspensions, the light-adapted blue-shifted BRexhibited an a/l-trans type photocycle, but the thermal steps were greatly slowed down (time constants 1 to 5 min). The parent species absorb at 506 nm. The DA blue-shifted BR exhibited absorption changes resolved into two photoreactions, one all-(rans- like (as in LA-BR) and another, 13-cw like, whose decay rate is also greatly slowed down (recovery time several hours). The parent species of the 13-cis like cycle absorb at 480 nm. That pigment fraction in the pellets whose absorption was not blue-shifted, also exhibited similar photoreactions to BR in suspension, but with an overall turnover rate only one order of magnitude slower. From a previous report (Lazarev and Terpugov, Biochim. Biophys. Acta 590 ,324–338,1980) and this one, it appears that the very slow photocycles in NaCl-BR of low moisture content originate from blue-shifted chromophores rather than from unchanged BR.     

Site‐Specific Iron Substitution in STA‐28, a Large Pore Aluminophosphate Zeotype Prepared by Using 1,10‐Phenanthrolines as Framework‐Bound Templates

An AlPO₄ zeotype has been prepared using the aromatic diamine 1,10‐phenanthroline and some of its methylated analogues as templates. In each case the two template N atoms bind to a specific framework Al site to expand its coordination to the unusual octahedral AlO₄N₂ environment. Furthermore, using this framework‐bound template, Fe atoms can be included selectively at this site in the framework by direct synthesis, as confirmed by annular dark field scanning transmission electron microscopy and Rietveld refinement. Calcination removes the organic molecules to give large pore framework solids, with BET surface areas up to 540 m² g^?1 and two perpendicular sets of channels that intersect to give pore space connected by 12‐ring openings along all crystallographic directions.     

Site-Specific Iron Substitution in STA-28, a Large Pore Aluminophosphate Zeotype Prepared by Using 1,10-Phenanthrolines as Framework-Bound Templates

An AlPO₄ zeotype has been prepared using the aromatic diamine 1,10-phenanthroline and some of its methylated analogues as templates. In each case the two template N atoms bind to a specific framework Al site to expand its coordination to the unusual octahedral AlO₄N₂ environment. Furthermore, using this framework-bound template, Fe atoms can be included selectively at this site in the framework by direct synthesis, as confirmed by annular dark field scanning transmission electron microscopy and Rietveld refinement. Calcination removes the organic molecules to give large pore framework solids, with BET surface areas up to 540 m² g⁻¹ and two perpendicular sets of channels that intersect to give pore space connected by 12-ring openings along all crystallographic directions.     

Different effects of redundant feedback loops on a bistable switch

Bistable switches have important roles in cellular decision-making processes. Bistability can be the consequence of positive or double-negative feedback loops. Although necessary, such feedback is not sufficient for bistability, which also requires nonlinearity. Nonlinearity can be provided by synergy of multiple feedback loops or by an ultrasensitive response within a single feedback loop. However, these two possibilities are not mutually exclusive; a combination of them is also possible. Here we analyze a biochemical regulatory network that controls a crucial cell cycle transition in all eukaryotic cells and contains multiple redundant feedback loops and nonlinearity. We show in this realistic biological example that two redundant feedback loops have different effects on the position of one of the saddle-node bifurcations of the system, which determines where the system switches. This illustrates that even though the roles of positive and double-negative feedbacks have been regarded as equivalent, the difference in their architectures can lead to differences in their effects on the system. We speculate that this conclusion could be general for other bistable systems with redundant feedback loops.     

Thermodynamic functions of conformational changes: conformational network of glycine diamide folding, entropy lowering, and informational accumulation

A refined grid of a conformational potential energy surface (PES) and a conformational entropy surface for glycine diamide was generated by ab initio molecular computations. The possible network of reaction paths was recognized in terms of the linear combinations of internal coordinates corresponding to conrotatory and disrotatory modes of motions. Such a Woodward-Hoffmann-like path selection principle was detected for the folding of this peptide from extended to some virtually cyclic structure. It seemed reasonable to assume that this principle (or its generalized form) might be applicable to protein folding. A reaction path network was projected on the potential energy, and a continuous entropy surface was constructed under the condition of reduced dimensionality. The low entropy of the folded conformation indicated an information accumulation between 326% and 1414% with respect to the fully extended or unfolded structure. It is found that the location of existing and 'latent' critical points on the surface is revealed by the extrema and inflection points of the entropy curve.     

Thermodynamic functions of conformational changes. 2. Conformational entropy as a measure of information accumulation

Various folded molecular structures contain different amount of information. The relative amount of information may be related to relative entropy or entropy change. The conformational entropy change for n-butane has been computed as the function of rotation around the central C-C bond. It appears that the g+ or g- conformers contain about 16% more information than the anti-structure. Furthermore, the syn conformation with the two groups eclipsed contained about 42% more information than the fully staggered anti orientation. The conformational entropy function calculated from 3N - 7 internal degrees of freedom was found to be a continuous function.