Characterization of a putative sensory [FeFe]-hydrogenase provides new insight into the role of the active site architecture

[FeFe]-hydrogenases are known for their high rates of hydrogen turnover, and are intensively studied in the context of biotechnological applications. Evolution has generated a plethora of different subclasses with widely different characteristics. The M2e subclass is phylogenetically distinct from previously characterized members of this enzyme family and its biological role is unknown. It features significant differences in domain- and active site architecture, and is most closely related to the putative sensory [FeFe]-hydrogenases. Here we report the first comprehensive biochemical and spectroscopical characterization of an M2e enzyme, derived from Thermoanaerobacter mathranii. As compared to other [FeFe]-hydrogenases characterized to-date, this enzyme displays an increased H₂ affinity, higher activation enthalpies for H⁺/H₂ interconversion, and unusual reactivity towards known hydrogenase inhibitors. These properties are related to differences in active site architecture between the M2e [FeFe]-hydrogenase and “prototypical” [FeFe]-hydrogenases. Thus, this study provides new insight into the role of this subclass in hydrogen metabolism and the influence of the active site pocket on the chemistry of the H-cluster.

Characterization of a group D putative sensory [FeFe]-hydrogenase reveals how the active site can be tuned to decrease CO inhibition and increase stability of a reduced H-cluster while retaining the ability to catalyze H⁺/H₂ interconversion.     

A Levi–Civita functional equation on semigroups

Aequationes mathematicae - Let S be a semigroup. We describe the solutions $$f,g:S \rightarrow \mathbb {C}$$ of the functional equation $$\begin{aligned} f(xy) = f(x)g(y) + g(x)f(y) - g(x)g(y), \...     

Wilson's functional equations on groups

We study properties of solutionsf, g, h C(G) of the functional equation

Measuring the similarity between trajectories using clustering techniques

A clustering method has been developed to group signals that display similar dynamic behavior. The procedure involves using the method of time delay embedding to construct a trajectory in state space from a time series. Certain features that characterize the geometry of the trajectory have been defined. These features were subjected to a series of statistical tests to determine their usefulness in a hierarchical clustering analysis. The latter is aimed at finding groups of similar trajectories. The trajectory-based clustering algorithm has been applied to simulated data, which included both stochastic data generated by a linear AR model, and nonlinear data generated by a Duffing oscillator. The results show that the algorithm works reliably in both cases.     

Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution

Molecular dynamics simulations of hexapeptides TFDWMK and LFPWMR; the highly conserved regions of Hox proteins Hox B1 and Hox B8, respectively, are carried out starting from extended structures to investigate their conformational space in water solution. In addition, we have studied TADWMK and TADAMK, where the aromatic residues Phenylalanine and Tryptophan were successively substituted for Alanine to investigate effects from the presence/absence of aromatic amino acids and interactions between them to folding behavior. The backbone of the hexapeptides in all simulations folds to a similar conformation found in experimental studies in solution. Intramolecular, hydrophobically driven interactions between the aromatic residues and internal hydrogen bonds are found to stabilize the conformations.     

Detection of the hydrogen-bond stretching mode in the low-frequency Raman spectrum of catechol and catechol-D2

Low-frequency Raman spectra of catechol (1,2-dihydroxybenzene) and catechol-d₂ have been measured at 130 K. The stretching mode of the intermolecular hydrogen bond, ν_σ, has been assigned at 187 and 184 cm^?1, respectively. A short discussion of this assignment and its implications with respect to the previously reported guaiacol (2-methoxyphenol) spectra is presented.     

Identification of novel macrocyclic peptidase substrates via on-bead enzymatic cyclization

Peptidase-catalyzed formation of macrocyclic lactams on solid phase identifies ring systems that are favorably bound in the enzyme active site. We evaluated several cyclic peptide motifs linked by ester bonds between the P2 and P1' or the P1 and P2' side chains. The depsipeptide represented by structure 5 was readily generated by a variety of peptidases from precursor omega-amino acids or omega-amino esters. This strategy for identifying ring systems for potential macrocyclic transition state analogues was demonstrated with the serine peptidases trypsin and chymotrypsin, with the aspartic peptidase pepsin, and with the zinc peptidase thermolysin.     

Nonadiabatic alignment of asymmetric top molecules: rotational revivals

The rotational revival structure of asymmetric top molecules, following irradiation by an intense picosecond laser pulse, is explored theoretically and experimentally. Numerically we solve nonperturbatively for the rotational dynamics of a general asymmetric top subject to a linearly polarized intense pulse, and analyze the dependence of the dynamical alignment on the field and system parameters. Experimentally we use time-resolved photofragment imaging to measure the alignment of two molecules with different asymmetry, iodobenzene, and iodopentafluorobenzene. Our numerical results explain the experimental observations and generalize them to other molecules. The rotational revival structure of asymmetric tops differs qualitatively from the intensively studied linear top case. Potentially it provides valuable structural information about molecules.     

Animal models for treatment of unresectable liver tumours: a histopathologic and ultra-structural study of cellular toxic changes after electrochemical treatment in rat and dog liver

INTRODUCTION: Electrochemical treatment (EChT) has been taken under serious consideration as being one of several techniques for local treatment of malignancies. The advantage of EChT is the minimal invasive approach and the absence of serious side effects. Macroscopic, histopathological and ultra-structural findings in liver following a four-electrode configuration (dog) and a two-electrode EChT design (dog and rat) were studied. MATERIALS AND METHODS: 30 female Sprague-Dawley rats and four female beagle dogs were studied with EChT using Platinum:Iridium electrodes and the delivered dose was 5, 10 or 90 C (As). After EChT, the animals were euthanized. RESULTS: The distribution of the lesions was predictable, irrespective of dose and electrode configuration. Destruction volumes were found to fit into a logarithmic curve (dose-response). Histopathological examination confirmed a spherical (rat) and cylindrical/ellipsoidal (dog) lesion. The type of necrosis differed due to electrode polarity. Ultra-structural analysis showed distinct features of cell damage depending on the distance from the electrode. Histopathological and ultra-structural examination demonstrated that the liver tissue close to the border of the lesion displayed a normal morphology. CONCLUSIONS: The in vivo dose-planning model is reliable, even in species with larger tissue mass such as dogs. A multi-electrode EChT-design could obtain predictable lesions. The cellular toxicity following EChT is clearly identified and varies with the distance from the electrode and polarity. The distinct border between the lesion and normal tissue suggests that EChT in a clinical setting for the treatment of liver tumours can give a reliable destruction margin.     

Amino acid catalyzed neogenesis of carbohydrates: a plausible ancient transformation

Hexose sugars play a fundamental role in vital biochemical processes and their biosynthesis is achieved through enzyme-catalyzed pathways. Herein we disclose the ability of amino acids to catalyze the asymmetric neogenesis of carbohydrates by sequential cross-aldol reactions. The amino acids mediate the asymmetric de novo synthesis of natural L- and D-hexoses and their analogues with excellent stereoselectivity in organic solvents. In some cases, the four new stereocenters are assembled with almost absolute stereocontrol. The unique feature of these results is that, when an amino acid is employed as the catalyst, a single reaction sequence can convert a protected glycol aldehyde into a hexose in one step. For example, proline and its derivatives catalyze the asymmetric neogenesis of allose with >99 % ee in one chemical manipulation. Furthermore, all amino acids tested catalyzed the asymmetric formation of natural sugars under prebiotic conditions, with alanine being the smallest catalyst. The inherent simplicity of this catalytic process suggests that a catalytic prebiotic "gluconeogenesis" may occur, in which amino acids transfer their stereochemical information to sugars. In addition, the amino acid catalyzed stereoselective sequential cross-aldol reactions were performed as a two-step procedure with different aldehydes as acceptors and nucleophiles. The employment of two different amino acids as catalysts for the iterative direct aldol reactions enabled the asymmetric synthesis of deoxysugars with >99 % ee. In addition, the direct amino acid catalyzed C(2)+C(2)+C(2) methodology is a new entry for the short, highly enantioselective de novo synthesis of carbohydrate derivatives, isotope-labeled sugars, and polyketide natural products. The one-pot asymmetric de novo syntheses of deoxy and polyketide carbohydrates involved a novel dynamic kinetic asymmetric transformation (DYKAT) mediated by an amino acid.