13,690 research outputs found
Detailed simulations of cell biology with Smoldyn 2.1.
Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program. Compared to the popular MCell and ChemCell simulators, we found that Smoldyn was in many cases more accurate, more computationally efficient, and easier to use. Using Smoldyn, we modeled pheromone response system signaling among yeast cells of opposite mating type. This model showed that secreted Bar1 protease might help a cell identify the fittest mating partner by sharpening the pheromone concentration gradient. This model involved about 200,000 protein molecules, about 7000 cubic microns of volume, and about 75 minutes of simulated time; it took about 10 hours to run. Over the next several years, as faster computers become available, Smoldyn will allow researchers to model and explore systems the size of entire bacterial and smaller eukaryotic cells
Integrating Cell-level Kinetic Modeling into the Optimization of Cancer Therapeutics
Cancer therapy benefits today from the availability of new promising classes of drugs such as
therapeutic proteins. Due to their ability to specifically bind targets in the body they allow to
modulate specific chemical reactions and ultimately to modify the functional response of the
cell, such as cell growth or cell division. Targeting receptor systems by competitive inhibition
is the objective of various protein drugs in development and on the market. Many targeted
receptor systems also constitute a degradation mechanism for the drug via endocytosis and a
thorough understanding of the complex interplay between the drug's pharmacokinetics and
its effect, is largely missing.
For complex diseases such as cancer, systems biology models of therapeutically relevant
cellular processes have proven valuable for identifying potent drug targets. So far, such
information about the dynamics of the targeted system is neglected in later stages of the drug
development process when pharmacokinetic modeling is used to guide dose finding and analyze
preclinical or clinical in vivo data. This is especially critical for therapeutic proteins where,
due to the degradation mediated by the targeted receptor, drug effect and pharmacokinetics
are inherently interdependent.
This thesis combines the points of view of systems biology and pharmacokinetics. We
present a detailed mechanistic model of the targeted cellular system that explicitly takes into
account receptor binding and trafficking inside the cell and that is used to derive reduced
models of drug degradation which retain a mechanistic interpretation. By integrating cell-level
models with established pharmacokinetic models, we translate biophysical properties
of protein drugs into a transient drug effect in vivo. We illustrate the approach for antibodies
against the epidermal growth factor receptor used in cancer therapy. The cell-level
pharmacokinetic/pharmacodynamic model identifies options and limits for future therapeutic
antibodies and links their inhibitory effect with genomic alteration of tumor cells
Defining the organizational structure of dopamine and muscarninic acetylcholine receptors
No abstract available
Anomalous transport in the crowded world of biological cells
A ubiquitous observation in cell biology is that diffusion of macromolecules
and organelles is anomalous, and a description simply based on the conventional
diffusion equation with diffusion constants measured in dilute solution fails.
This is commonly attributed to macromolecular crowding in the interior of cells
and in cellular membranes, summarising their densely packed and heterogeneous
structures. The most familiar phenomenon is a power-law increase of the MSD,
but there are other manifestations like strongly reduced and time-dependent
diffusion coefficients, persistent correlations, non-gaussian distributions of
the displacements, heterogeneous diffusion, and immobile particles. After a
general introduction to the statistical description of slow, anomalous
transport, we summarise some widely used theoretical models: gaussian models
like FBM and Langevin equations for visco-elastic media, the CTRW model, and
the Lorentz model describing obstructed transport in a heterogeneous
environment. Emphasis is put on the spatio-temporal properties of the transport
in terms of 2-point correlation functions, dynamic scaling behaviour, and how
the models are distinguished by their propagators even for identical MSDs.
Then, we review the theory underlying common experimental techniques in the
presence of anomalous transport: single-particle tracking, FCS, and FRAP. We
report on the large body of recent experimental evidence for anomalous
transport in crowded biological media: in cyto- and nucleoplasm as well as in
cellular membranes, complemented by in vitro experiments where model systems
mimic physiological crowding conditions. Finally, computer simulations play an
important role in testing the theoretical models and corroborating the
experimental findings. The review is completed by a synthesis of the
theoretical and experimental progress identifying open questions for future
investigation.Comment: review article, to appear in Rep. Prog. Phy
Signaling pathways for transduction of the initial message of the glycocode into cellular responses
The sugar units of glycan structures store information and establish an alphabet of life. The language of the oligosaccharide coding units is deciphered by receptors such as lectins and the decoded message can be transduced by multiple signaling pathways. Similar to glycoconjugates, these receptors can exhibit pronounced changes in quantitative and qualitative aspects of expression, as attested by a wealth of lectin and immunohistochemical studies. Since histochemistry provides a static picture, it is essential to shed light on the mechanisms of how a recognitive protein-carbohydrate interplay can be transduced into cellular responses. Their consequences for example for cell morphology will then be visible to the histochemist. Therefore, basic signaling routes will be graphically outlined and their trigger potential will be explained by selected examples from the realm of glycosciences
ATM in focus:a damage sensor and cancer target
The ability of a cell to conserve and maintain its native DNA sequence is fundamental for the survival and normal functioning of the whole organism and protection from cancer development. Here we review recently obtained results and current topics concerning the role of the ataxia-telangiectasia mutated (ATM) protein kinase as a damage sensor and its potential as therapeutic target for treating cancer. This monograph discusses DNA repair mechanisms activated after DNA double-strand breaks (DSBs), i.e. non-homologous end joining, homologous recombination and single strand annealing and the role of ATM in the above types of repair. In addition to DNA repair, ATM participates in a diverse set of physiological processes involving metabolic regulation, oxidative stress, transcriptional modulation, protein degradation and cell proliferation. Full understanding of the complexity of ATM functions and the design of therapeutics that modulate its activity to combat diseases such as cancer necessitates parallel theoretical and experimental efforts. This could be best addressed by employing a systems biology approach, involving mathematical modelling of cell signalling pathways
Spatial intensity distribution analysis: studies of G Protein-coupled receptor oligomerization
Spatial intensity distribution analysis (SpIDA) is a recently developed approach for determining quaternary structure information on fluorophore-labelled proteins of interest in situ. It can be applied to live or fixed cells and native tissue. Using confocal images, SpIDA generates fluorescence intensity histograms that are analysed by super-Poissonian distribution functions to obtain density and quantal brightness values of the fluorophore-labelled protein of interest. This allows both expression level and oligomerisation state of the protein to be determined. We describe the application of SpIDA to investigate the oligomeric state of G protein-coupled receptors (GPCRs) at steady state and following cellular challenge, and consider how SpIDA may be used to explore GPCR quaternary organisation in pathophysiology and to stratify medicines
Coupling biochemistry and mechanics in cell adhesion: a model for inhomogeneous stress fiber contraction
Biochemistry and mechanics are closely coupled in cell adhesion. At sites of
cell-matrix adhesion, mechanical force triggers signaling through the
Rho-pathway, which leads to structural reinforcement and increased
contractility in the actin cytoskeleton. The resulting force acts back to the
sites of adhesion, resulting in a positive feedback loop for mature adhesion.
Here we model this biochemical-mechanical feedback loop for the special case
when the actin cytoskeleton is organized in stress fibers, which are
contractile bundles of actin filaments. Activation of myosin II molecular
motors through the Rho-pathway is described by a system of reaction-diffusion
equations, which are coupled into a viscoelastic model for a contractile actin
bundle. We find strong spatial gradients in the activation of contractility and
in the corresponding deformation pattern of the stress fiber, in good agreement
with experimental findings.Comment: Revtex, 35 pages, 13 Postscript figures included, in press with New
Journal of Physics, Special Issue on The Physics of the Cytoskeleto
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