A phosphoramidite of the perylene bisimide dye was synthesized as a DNA building block that allows incorporation of this chromophore as an artificial nucleoside surrogate either at the 5'-terminus or at internal positions of duplex DNA. The internally incorporated perylene bisimide chromophore shows strong interactions with the DNA base stack; the 5'-terminally attached perylene bisimide is able to induce dimerization of two whole DNA duplexes.

A new DNA assay has been designed, prepared and applied for the chemical investigation of reductive electron transfer through the DNA. It consists of 5-(10-methyl-phenothiazin-3-yl)-2'-deoxyuridine (Ptz-dU, 1) as the photoexcitable electron injector and 5-bromo-2'-deoxyuridine (Br-dU) as the electron trap. The Ptz-dU-modified oligonucleotides were synthesised by means of a Suzuki-Miyaura cross-coupling protocol and subsequent automated phosphoramidite chemistry. Br-dU represents a kinetic electron trap, since it undergoes a chemical modification after its one-electron reduction that can be analysed by piperidine-induced strand cleavage. The quantification of the strand cleavage yields from irradiation experiments reveals important information about the electron-transfer efficiency. The performed DNA studies focused on the base sequence dependence of the electron-transfer efficiency with respect to the proposal that C*- and T*- act as intermediate electron carriers during electron hopping. From our observations it became evident that excess-electron transfer is highly sequence dependent and occurs more efficiently over T-A base pairs than over C-G base pairs.

Mathematically, the calculation of elementary fluxes amounts to characterizing the space of solutions to a mixed system of linear equalities, given by the stoichiometry matrix, and linear inequalities, arising from the irreversibility of some or all of the reactions in the network. Previous approaches to this problem have iteratively solved for the equalities while satisfying the inequalities throughout the process. In an extension of previous work, here we consider the complementary approach and derive an algorithm which satisfies the inequalities one by one while staying in the space of solution of the equality constraints. Benchmarks on different subnetworks of the central carbon metabolism of Escherichia coli show that this new approach yields a significant reduction in the execution time of the calculation. This reduction arises since the odds that an intermediate elementary flux already fulfills an additional inequality are larger than when having to satisfy an additional equality constraint.

Hence, we propose to instead focus on the conversion cone, a projection of the flux cone, which describes the interaction of the metabolism with its external chemical environment. We present a direct method for calculating the elementary vectors of this cone and, by studying the metabolism of Saccharomyces cerevisiae, we demonstrate that such an analysis is computationally feasible even for genome scale networks.

The effect of intermediates on the rate of protein folding is explored by applying Kramers' theory of diffusive barrier crossing in the high friction limit. Intermediates are represented as local minima in the transition barrier. We observe that very large or very small additional barriers created by the intermediates slow down the folding process. The rate of folding markedly increases, however, when the additional barriers become >1 k B T but leave the overall barrier height unchanged. This rate-enhancing effect is caused by a favorable entropic contribution to the free energy of activation, and it increases with the number of intermediates up to a limiting value. From these calculations, we conclude that optimized transition barriers should contain partially folded high energy intermediates.Various models have been proposed to describe the mechanism of protein folding. The experimental observation of transiently populated, partially folded intermediates in many proteins gave rise to the framework model, which assumes that the native structure is formed in a hierarchical way on a linear pathway involving several consecutive transition states (1, 2). In this model, partially folded intermediates are essential for protein folding by directing the chain to the native state. In theoretical approaches, the folding process is conceived as a movement of molecules on a rough, funnel-like energy landscape starting from the ensemble of unfolded conformations and leading to the native state (3-5). In these models, transiently populated intermediates often represent misfolded structures trapped in local energy minima.Based on these opposing views, the study of the role of protein folding intermediates has been of major interest in theoretical and experimental work. Recent experimental results provided evidence for the presence of metastable, high energy states located in the transition barrier between the native state and the ensemble of unfolded molecules. Native state hydrogen exchange studies revealed partially unfolded states in cytochrome c (6) and RNase H (7), which are higher in energy than the native protein. Although these intermediates were identified as fluctuations from the native structure under equilibrium conditions, it was postulated that they might represent intermediates on linear folding pathways (6). Local energy minima in the transition barrier also were observed in unfolding reactions of fast-folding proteins that reach the native state without transient population of partially folded intermediates. For the dimeric arc repressor (8) and staphylococcal nuclease (9), a nonlinearity in the denaturant dependence of the free energy of activation for the unfolding reaction (⌬G u 0 ‡ ) was interpreted as evidence for two distinct transition states on a sequential pathway. A similar observation was made for the formation of a helical intermediate in lysozyme folding, which proceeds through a reactive high energy intermediate (10). For chymotrypsin inhibitor 2, a pronounced curvatures in the denaturan...

The analysis of metabolic networks has become a major topic in biotechnology in recent years. Applications range from the enhanced production of selected outputs to the prediction of genotype-phenotype relationships. The concepts used are based on the assumption of a pseudo steady-state of the network, so that for each metabolite inputs and outputs are balanced. The stoichiometric network analysis expands the steady state into a combination of nonredundant subnetworks with positive coefficients called extremal currents. Based on the unidirectional representation of the system these subnetworks form a convex cone in the flux-space. A modification of this approach allowing for reversible reactions led to the definition of elementary modes. Extreme pathways are obtained with the same method but splitting up internal reactions into forward and backward rates. In this study, we explore the relationship between these concepts. Due to the combinatorial explosion of the number of elementary modes in large networks, we promote a further set of metabolic routes, which we call the minimal generating set. It is the smallest subset of elementary modes required to describe all steady states of the system. For large-scale networks, the size of this set is of several magnitudes smaller than that of elementary modes and of extreme pathways.

Lysozyme folds through two competing pathways. A fast pathway leads directly from a collapsed state to the native protein, whereas folding on a slow pathway proceeds through a partially folded intermediate (I(1)). At NaCl concentrations above 100 mM, a second transient intermediate (I(2)) is induced as judged by the appearance of an additional apparent rate constant in the refolding kinetics. Monitoring the time course of native molecules and of both intermediates shows that the NaCl-induced state (I(2)) is located on neither of the two folding pathways observed at low-salt concentrations. These results suggest that I(2) is a metastable high-energy intermediate at low-ionic strength and is located on a third folding pathway. The folding landscape of lysozyme seems to be complex with several high-energy intermediates located on parallel folding routes. However, the experiments show no evidence for partially folded states on the fast direct pathway.

Growth hormone (GH) induces growth in animals and humans and also has important metabolic functions. The GH neuroendocrine axis consists of a signaling cascade from the hypothalamus to the pituitary, the liver, and peripheral tissues, including two major feedback mechanisms. GH is secreted from the pituitary into the circulating blood according to the effect on the somatotrophs of two hypothalamic peptides, GH-releasing hormone (GHRH) and its antagonist, somatostatin (SRIF). The typical GH profile in the male rat shows secretory episodes every 3.3 h, which are subdivided into two peaks. Focusing on the mechanisms for generation of this ultradian GH rhythm, we simulated the time course of GH secretion under a variety of conditions. The model that we propose is based on feedback of GH on its own release mediated both by GH receptors on SRIF neurons in the brain and by a delayed SRIF release into both the brain and portal blood. SRIF, with a resultant periodicity of 3.3 h, affects both the somatotroph cells in the pituitary and the GHRH neurons in the hypothalamus. The secretion of GHRH is postulated to occur in an ∼1-h rhythm modulated by the level of SRIF in the hypothalamus. The model predicts a possible mechanism for the feminization of the male GH rhythm by sex steroids and vice versa, and suggests experiments that might reveal the proposed intrinsic 1-h GHRH rhythm.