274 research outputs found
Kinetic Modeling of the Mitochondrial Energy Metabolism of Neuronal Cells: The Impact of Reduced α
Reduced activity of brain α-ketoglutarate dehydrogenase complex (KGDHC) occurs in a number of neurodegenerative diseases like Parkinson's disease and Alzheimer's disease. In order to quantify the relation between diminished KGDHC activity and the mitochondrial ATP generation, redox state, transmembrane potential, and generation of reactive oxygen species (ROS) by the respiratory chain (RC), we developed a detailed kinetic model. Model simulations revealed a threshold-like decline of the ATP production rate at about 60% inhibition of KGDHC accompanied by a significant increase of the mitochondrial membrane potential. By contrast, progressive inhibition of the enzyme aconitase had only little impact on these mitochondrial parameters. As KGDHC is susceptible to ROS-dependent inactivation, we also investigated the reduction state of those sites of the RC proposed to be involved in ROS production. The reduction state of all sites except one decreased with increasing degree of KGDHC inhibition suggesting an ROS-reducing effect of KGDHC inhibition. Our model underpins the important role of reduced KGDHC activity in the energetic breakdown of neuronal cells during development of neurodegenerative diseases
structured representation of scientific evidence in the biomedical domain using Semantic Web techniques
Background Accounts of evidence are vital to evaluate and reproduce scientific
findings and integrate data on an informed basis. Currently, such accounts are
often inadequate, unstandardized and inaccessible for computational knowledge
engineering even though computational technologies, among them those of the
semantic web, are ever more employed to represent, disseminate and integrate
biomedical data and knowledge. Results We present SEE (Semantic EvidencE), an
RDF/OWL based approach for detailed representation of evidence in terms of the
argumentative structure of the supporting background for claims even in
complex settings. We derive design principles and identify minimal components
for the representation of evidence. We specify the Reasoning and Discourse
Ontology (RDO), an OWL representation of the model of scientific claims, their
subjects, their provenance and their argumentative relations underlying the
SEE approach. We demonstrate the application of SEE and illustrate its design
patterns in a case study by providing an expressive account of the evidence
for certain claims regarding the isolation of the enzyme glutamine synthetase.
Conclusions SEE is suited to provide coherent and computationally accessible
representations of evidence-related information such as the materials,
methods, assumptions, reasoning and information sources used to establish a
scientific finding by adopting a consistently claim-based perspective on
scientific results and their evidence. SEE allows for extensible evidence
representations, in which the level of detail can be adjusted and which can be
extended as needed. It supports representation of arbitrary many consecutive
layers of interpretation and attribution and different evaluations of the same
data. SEE and its underlying model could be a valuable component in a variety
of use cases that require careful representation or examination of evidence
for data presented on the semantic web or in other formats
Computer Simulations Suggest a Key Role of Membranous Nanodomains in Biliary Lipid Secretion
The bile fluid contains various lipids that are secreted at the canalicular
membrane of hepatocytes. As the secretion mechanism is still a matter of
debate and a direct experimental observation of the secretion process is not
possible so far, we used a mathematical model to simulate the extraction of
the major bile lipids cholesterol, phosphatidylcholine and sphingomyelin from
the outer leaflet of the canalicular membrane. Lipid diffusion was modeled as
random movement on a triangular lattice governed by next-neighbor interaction
energies. Phase separation in liquid-ordered and liquid-disordered domains was
modeled by assigning two alternative ordering states to each lipid species and
minimization of next-neighbor ordering energies. Parameterization of the model
was performed such that experimentally determined diffusion rates and phases
in ternary lipid mixtures of model membranes were correctly recapitulated. The
model describes the spontaneous formation of nanodomains in the external
leaflet of the canalicular membrane in a time window between 0.1 ms to 10 ms
at varying lipid proportions. The extraction of lipid patches from the bile
salt soluble nanodomain into the bile reproduced observed biliary phospholipid
compositions for a physiologi-cal membrane composition. Comparing the outcome
of model simulations with available experi-mental observations clearly favors
the extraction of tiny membrane patches composed of about 100–400 lipids as
the likely mechanism of biliary lipid secretion
Sequential Metabolic Phases as a Means to Optimize Cellular Output in a Constant Environment
Temporal changes of gene expression are a well-known regulatory feature of all
cells, which is commonly perceived as a strategy to adapt the proteome to
varying external conditions. However, temporal (rhythmic and non-rhythmic)
changes of gene expression are also observed under virtually constant external
conditions. Here we hypothesize that such changes are a means to render the
synthesis of the metabolic output more efficient than under conditions of
constant gene activities. In order to substantiate this hypothesis, we used a
flux-balance model of the cellular metabolism. The total time span spent on
the production of a given set of target metabolites was split into a series of
shorter time intervals (metabolic phases) during which only selected groups of
metabolic genes are active. The related flux distributions were calculated
under the constraint that genes can be either active or inactive whereby the
amount of protein related to an active gene is only controlled by the number
of active genes: the lower the number of active genes the more protein can be
allocated to the enzymes carrying non-zero fluxes. This concept of a
predominantly protein-limited efficiency of gene expression clearly differs
from other concepts resting on the assumption of an optimal gene regulation
capable of allocating to all enzymes and transporters just that fraction of
protein necessary to prevent rate limitation. Applying this concept to a
simplified metabolic network of the central carbon metabolism with glucose or
lactate as alternative substrates, we demonstrate that switching between
optimally chosen stationary flux modes comprising different sets of active
genes allows producing a demanded amount of target metabolites in a
significantly shorter time than by a single optimal flux mode at fixed gene
activities. Our model-based findings suggest that temporal expression of
metabolic genes can be advantageous even under conditions of constant external
substrate supply
A Conceptual Mathematical Model of the Dynamic Self-Organisation of Distinct Cellular Organelles
Formation, degradation and renewal of cellular organelles is a dynamic process based on permanent budding, fusion and inter-organelle traffic of vesicles. These processes include many regulatory proteins such as SNAREs, Rabs and coats. Given this complex machinery, a controversially debated issue is the definition of a minimal set of generic mechanisms necessary to enable the self-organization of organelles differing in number, size and chemical composition. We present a conceptual mathematical model of dynamic organelle formation based on interacting vesicles which carry different types of fusogenic proteins (FP) playing the role of characteristic marker proteins. Our simulations (ODEs) show that a de novo formation of non-identical organelles, each accumulating a different type of FP, requires a certain degree of disproportionation of FPs during budding. More importantly however, the fusion kinetics must indispensably exhibit positive cooperativity among these FPs, particularly for the formation of larger organelles. We compared different types of cooperativity: sequential alignment of corresponding FPs on opposite vesicle/organelles during fusion and pre-formation of FP-aggregates (equivalent, e.g., to SNARE clusters) prior to fusion described by Hill kinetics. This showed that the average organelle size in the system is much more sensitive to the disproportionation strength of FPs during budding if the vesicular transport system gets along with a fusion mechanism based on sequential alignments of FPs. Therefore, pre-formation of FP aggregates within the membranes prior to fusion introduce robustness with respect to organelle size. Our findings provide a plausible explanation for the evolution of a relatively large number of molecules to confer specificity on the fusion machinery compared to the relatively small number involved in the budding process. Moreover, we could speculate that a specific cooperativity which may be described by Hill kinetics (aggregates or Rab/SNARE complex formation) is suitable if maturation/identity switching of organelles play a role (bistability)
The speciation of the proteome
<p>Abstract</p> <p>Introduction</p> <p>In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the protein expression concept disclaims post-translational modifications by connecting protein names directly with function.</p> <p>Discussion</p> <p>Optimal proteome coverage is today reached by bottom-up liquid chromatography/mass spectrometry. But quantification at the peptide level in shotgun or bottom-up approaches by liquid chromatography and mass spectrometry is completely ignoring that a special peptide may exist in an unmodified form and in several-fold modified forms. The acceptance of the protein species concept is a basic prerequisite for meaningful quantitative analyses in functional proteomics. In discovery approaches only top-down analyses, separating the protein species before digestion, identification and quantification by two-dimensional gel electrophoresis or protein liquid chromatography, allow the correlation between changes of a biological situation and function.</p> <p>Conclusion</p> <p>To obtain biological relevant information kinetics and systems biology have to be performed at the protein species level, which is the major challenge in proteomics today.</p
Towards quantitative prediction of proteasomal digestion patterns of proteins
We discuss the problem of proteasomal degradation of proteins. Though
proteasomes are important for all aspects of the cellular metabolism, some
details of the physical mechanism of the process remain unknown. We introduce a
stochastic model of the proteasomal degradation of proteins, which accounts for
the protein translocation and the topology of the positioning of cleavage
centers of a proteasome from first principles. For this model we develop the
mathematical description based on a master-equation and techniques for
reconstruction of the cleavage specificity inherent to proteins and the
proteasomal translocation rates, which are a property of the proteasome specie,
from mass spectroscopy data on digestion patterns. With these properties
determined, one can quantitatively predict digestion patterns for new
experimental set-ups. Additionally we design an experimental set-up for a
synthetic polypeptide with a periodic sequence of amino acids, which enables
especially reliable determination of translocation rates.Comment: 14 pages, 4 figures, submitted to J. Stat. Mech. (Special issue for
proceedings of 5th Intl. Conf. on Unsolved Problems on Noise and Fluctuations
in Physics, Biology & High Technology, Lyon (France), June 2-6, 2008
The proteasome inhibitor PI31 competes with PA28 for binding to 20S proteasomes
AbstractPI31 is a previously described inhibitor of 20S proteasomes. Using recombinant PI31 we have analyzed its effect on proteasomal hydrolyzing activity of short fluorogenic substrates and of a synthetic 40-mer polypeptide. In addition, we investigated its influence on the activation of 20S proteasome by the proteasome activator PA28. PI31 inhibits polypeptide degradation already at concentrations which only partially inhibit fluorogenic substrate turnover and immunosubunits do not influence the PI31 binding affinity. Furthermore our data demonstrate that PI31 is a potent competitor of PA28-mediated activation
The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks
The dynamic behavior of metabolic networks is governed by numerous regulatory mechanisms, such as reversible phosphorylation, binding of allosteric effectors or temporal gene expression, by which the activity of the participating enzymes can be adjusted to the functional requirements of the cell. For most of the cellular enzymes, such regulatory mechanisms are at best qualitatively known, whereas detailed enzyme-kinetic models are lacking. To explore the possible dynamic behavior of metabolic networks in cases of lacking or incomplete enzyme-kinetic information, we present a computational approach based on structural kinetic modeling. We derive statistical measures for the relative impact of enzyme-kinetic parameters on dynamic properties (such as local stability) and apply our approach to the metabolism of human erythrocytes. Our findings show that allosteric enzyme regulation significantly enhances the stability of the network and extends its potential dynamic behavior. Moreover, our approach allows to differentiate quantitatively between metabolic states related to senescence and metabolic collapse of the human erythrocyte. We think that the proposed method represents an important intermediate step on the long way from topological network analysis to detailed kinetic modeling of complex metabolic networks
Interpretation of non-invasive breath tests using 13C-labeled substrates - a preliminary report with 13C-methacetin
Non-invasive breath tests can serve as valuable diagnostic tools in medicine as they can determine particular enzymatic and metabolic functions in vivo. However, methodological pitfalls have limited the actual clinical application of those tests till today. A major challenge of non-invasive breath tests has remained the provision of individually reliable test results. To overcome these limitations, a better understanding of breath kinetics during non-invasive breaths tests is essential. This analysis compares the breath recovery of a 13C-methacetin breath test with the actual serum kinetics of the substrate. It is shown, that breath and serum kinetics of the same test are significantly different over a period of 60 minutes. The recovery of the tracer 13CO2 in breath seems to be significantly delayed due to intermediate storage in the bicarbonate pool. This has to be taken into account for the application of non-invasive breath test protocols. Otherwise, breath tests might display bicarbonate kinetics despite the metabolic capacity of the particular target enzyme
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