Oleg Demin

Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor

During the past decade, our knowledge of molecular mechanisms involved in growth factor signaling has proliferated almost explosively. However, the kinetics and control of information transfer through signaling networks remain poorly understood. This paper combines experimental kinetic analysis and computational modeling of the short term pattern of cellular responses to epidermal growth factor (EGF) in isolated hepatocytes. The experimental data show transient tyrosine phosphorylation of the EGF receptor (EGFR) and transient or sustained response patterns in multiple signaling proteins targeted by EGFR. Transient responses exhibit pronounced maxima, reached within 15–30 s of EGF stimulation and followed by a decline to relatively low (quasi-steady-state) levels. In contrast to earlier suggestions, we demonstrate that the experimentally observed transients can be accounted for without requiring receptor-mediated activation of specific tyrosine phosphatases, following EGF stimulation. The kinetic model predicts how the cellular response is controlled by the relative levels and activity states of signaling proteins and under what conditions activation patterns are transient or sustained. EGFR signaling patterns appear to be robust with respect to variations in many elemental rate constants within the range of experimentally measured values. On the other hand, we specify which changes in the kinetic scheme, rate constants, and total amounts of molecular factors involved are incompatible with the experimentally observed kinetics of signal transfer. Quantitation of signaling network responses to growth factors allows us to assess how cells process information controlling their growth and differentiation.

The Edinburgh human metabolic network reconstruction and its functional analysis

A better understanding of human metabolism and its relationship with diseases is an important task in human systems biology studies. In this paper, we present a high‐quality human metabolic network manually reconstructed by integrating genome annotation information from different databases and metabolic reaction information from literature. The network contains nearly 3000 metabolic reactions, which were reorganized into about 70 human‐specific metabolic pathways according to their functional relationships. By analysis of the functional connectivity of the metabolites in the network, the bow‐tie structure, which was found previously by structure analysis, is reconfirmed. Furthermore, the distribution of the disease related genes in the network suggests that the IN (substrates) subset of the bow‐tie structure has more flexibility than other parts.

Modeling of ATP–ADP steady‐state exchange rate mediated by the adenine nucleotide translocase in isolated mitochondria

A computational model for the ATP–ADP steady‐state exchange rate mediated by adenine nucleotide translocase (ANT) versus mitochondrial membrane potential dependence in isolated rat liver mitochondria is presented. The model represents the system of three ordinary differential equations, and the basic components included are ANT, F0/F1‐ATPase, and the phosphate carrier. The model reproduces quantitatively the relationship between mitochondrial membrane potential and the ATP–ADP steady‐state exchange rate mediated by the ANT operating in the forward mode, with the assumption that the phosphate carrier functions under rapid equilibrium. Furthermore, the model can simulate the kinetics of experimentally measured data on mitochondrial membrane potential titrated by an uncoupler. Verified predictions imply that the ADP influx rate is highly dependent on the mitochondrial membrane potential, and in the 0–100 mV range it is close to zero, owing to extremely low matrix ATP values. In addition to providing theoretical values of free matrix ATP and ADP, the model explains the diminished ADP–ATP exchange rate in the presence of nigericin, a condition in which there is hyperpolarization of the inner mitochondrial membrane at the expense of the mitochondrial ΔpH gradient; the latter parameter influences matrix inorganic phosphate and ATP concentrations in a manner also described.

Kinetic modelling of central carbon metabolism in Escherichia coli

In the present study, we developed a detailed kinetic model of Escherichia coli central carbon metabolism. The main model assumptions were based on the results of metabolic and regulatory reconstruction of the system and thorough model verification with experimental data. The development and verification of the model included several stages, which allowed us to take into account both in vitro and in vivo experimental data and avoid the ambiguity that frequently occurs in detailed models of biochemical pathways. The choice of the level of detail for the mathematical description of enzymatic reaction rates and the evaluation of parameter values were based on available published data. Validation of the complete model of the metabolic pathway describing specific physiological states was based on fluxomics and metabolomics data. In particular, we developed a model that describes aerobic growth of E. coli in continuous culture with a limiting concentration of glucose. Such modification of the model was used to integrate experimental metabolomics data obtained in steady‐state conditions for wild‐type E. coli and genetically modified strains, e.g. knockout of the pyruvate kinase gene (pykA). Following analysis of the model behaviour, and comparison of the coincidence between predicted and experimental data, it was possible to investigate the functional and regulatory properties of E. coli central carbon metabolism. For example, a novel metabolic regulatory mechanism for 6‐phosphogluconate dehydrogenase inhibition by phosphoenolpyruvate was hypothesized, and the flux ratios between the reactions catalysed by enzyme isoforms were predicted.

Kinetic model of mitochondrial Krebs cycle: unraveling the mechanism of salicylate hepatotoxic effects

This paper studies the effect of salicylate on the energy metabolism of mitochondria using in silico simulations. A kinetic model of the mitochondrial Krebs cycle is constructed using information on the individual enzymes. Model parameters for the rate equations are estimated using in vitro experimental data from the literature. Enzyme concentrations are determined from data on respiration in mitochondrial suspensions containing glutamate and malate. It is shown that inhibition in succinate dehydrogenase and α-ketoglutarate dehydrogenase by salicylate contributes substantially to the cumulative inhibition of the Krebs cycle by salicylates. Uncoupling of oxidative phosphorylation has little effect and coenzyme A consumption in salicylates transformation processes has an insignificant effect on the rate of substrate oxidation in the Krebs cycle. It is found that the salicylate-inhibited Krebs cycle flux can be increased by flux redirection through addition of external glutamate and malate, and depletion in external α-ketoglutarate and glycine concentrations.

The pathway editor: a tool for managing complex biological networks

Biological networks are systems of biochemical processes inside a cell that involve cellular constituents such as DNA, RNA, proteins, and various small molecules. Pathway maps are often used to represent the structure of such networks with associated biological information. Several pathway editors exist, and they vary according to specific domains of knowledge. This paper presents a review of existing pathway editors, along with an introduction to the Edinburgh Pathway Editor (EPE). EPE was designed for the annotation, visualization, and presentation of a wide variety of biological networks that include metabolic, genetic, and signal transduction pathways. EPE is based on a metadata-driven architecture. The editor supports the presentation and annotation of maps, in addition to the storage and retrieval of reaction kinetics information in relational databases that are either local or remote. EPE also has facilities for linking graphical objects to external databases and Web resources, and is capable of reproducing most existing graphical notations and visual representations of pathway maps. In summary, EPE provides a highly flexible tool for combining visualization, editing, and database manipulation of information relating to biological networks. EPE is open-source software, distributed under the Eclipse open-source application platform license.

'Channelled' pathways can be more sensitive to specific regulatory signals.

In ‘simple’ metabolic pathways the response to an external signal is readily described in terms of the effect of the signal on its receptor enzyme and the control exerted by that enzyme. We show here that in the response of ‘channelled’ pathways to such a signal, additional terms appear that reflect the direct enzyme‐enzyme interactions. They tend to enhance the responsiveness of the pathway. The normalized value of the response is called the signal transduction coefficient. We show that in channelled pathways these coefficients are usually larger than in corresponding non‐channelled (simple) pathways.

Kinetic mechanisms of biological regulation in photosynthetic organisms.

Principles of regulation on different levels of photosynthetic apparatus are discussed. Mathematical models of isolated photosynthetic reaction centers and general system of energy transduction in chloroplast are developed. A general approach to model these complex metabolic systems is suggested. Regulatory mechanisms in plant cell are correlated with the different patterns of fluorescence induction curve at different internal physiological states of the cells and external (environmental) conditions. Light regulation inside photosynthetic reaction centers, diffusion processes in thylakoid membrane, generation of transmembrane electrochemical potential, coupling with processes of CO2 fixation in Calvin Cycle are considered as stages of control of energy transformation in chloroplasts in their connection with kinetic patterns of fluorescence induction curves and other spectrophotometric data.

Kinetic modeling of energy metabolism and superoxide generation in hepatocyte mitochondria

AbstractDirect nonenzymatic oxidation of semiquinone by oxygen is one of the main sources of superoxide radicals