This paper presents an extension of stoichiometric analysis in systems where the catalytic compounds (enzymes) are also intermediates of the metabolic network (dual property), so they are produced and degraded by the reaction network itself. To take this property into account, we introduce the definition of enzyme-maintaining mode, a set of reactions that produces its own catalyst and can opera...

The functional repertoire of a network is determined by its topology. Ma et al. (2009) analyze enzyme networks with three nodes and take a reverse-engineering approach to ask how many core network topologies can establish perfect adaptation, the ability to reset after perturbation. Surprisingly, the answer is just two.

A novel approach to reveal intramolecular signal transduction network is proposed in this work. To this end, a new algorithm of network construction is developed, which is based on a new protein dynamics model of energy dissipation. A key feature of this approach is that direction information is specified after inferring protein residue-residue interaction network involved in the process of sig...

MOTIVATION Misannotation in sequence databases is an important obstacle for automated tools for gene function annotation, which rely extensively on comparison with sequences with known function. To improve current annotations and prevent future propagation of errors, sequence-independent tools are, therefore, needed to assist in the identification of misannotated gene products. In the case of e...

Understanding global change impacts on the globally important carbon storage in alpine, Arctic and sub-Arctic soils requires knowledge of the mechanisms underlying the balance between plant primary productivity and decomposition. Given that nitrogen availability limits both processes, understanding the response of the soil nitrogen cycle to shifts in temperature and other global change factors ...

One of the most intriguing questions in modern enzymology is whether enzyme dynamics evolved to enhance the catalyzed chemical transformation. In this study, dihydrofolate reductase, a small monomeric protein that catalyzes a single C-H-C transfer, is used as a model system to address this question. Experimental and computational studies have proposed a dynamic network that includes two residue...

Mitochondrial cytochrome c oxidase plays an essential role in aerobic cellular respiration, reducing dioxygen to water in a process coupled with the pumping of protons across the mitochondrial inner membrane. An aspartate residue, Asp-51, located near the enzyme surface, undergoes a redox-coupled x-ray structural change, which is suggestive of a role for this residue in redox-driven proton pump...

background: we aimed at evaluating the toxicity effects of low (subtoxic) concentrations of silver nanoparticles (agnp, 5-10 nm) in human hepatoblastoma (hepg2) cell line after and during a period of about one month. methods: xtt and mtt assays were used to draw a dose-response curve ic50 (half maximal inhibitory concentration) value of the agnp on hepg2 cells was calculated to be 2.75-3.0 mg/l...

The set of chemicals producible and usable by metabolic pathways must have evolved in parallel with the enzymes that catalyze them. One implication of this common historical path should be a correspondence between the innovation steps that gradually added new metabolic reactions to the biosphere-level biochemical toolkit, and the gradual sequence changes that must have slowly shaped the corresp...

background and aims: cytomegalovirus (cmv) is a member of herpesviruses. it is one of the most common cause of congenital and prenatal infections. cmv infection of pregnant women, especially in the first trimester may lead to congenital abnormalities in the newborns. the prevalence of cmv infection in developed countries is about 40% and in developing countries may be 100%. because there is no ...