Biomedical subjects

Bernd Binder

Publications and source records attributed to Bernd Binder.

6 recordsLinked to original sources

PubMed2005

Control of MAPK signalling: from complexity to what really matters.

Oncogenesis results from changes in kinetics or in abundance of proteins in signal transduction networks. Recently, it was shown that control of signalling cannot reside in a single gene product, and might well be dispersed over many components. Which of the reactions in these complex networks are most important, and how can the existing molecular information be used to understand why particular genes are oncogenes whereas others are not? We implement a new method to help address such questions. We apply control analysis to a detailed kinetic model of the epidermal growth factor-induced mitogen-activated protein kinase network. We determine the control of each reaction with respect to three biologically relevant characteristics of the output of this network: the amplitude, duration and integrated output of the transient phosphorylation of extracellular signal-regulated kinase (ERK). We confirm that control is distributed, but far from randomly: a small proportion of reactions substantially control signalling. In particular, the activity of Raf is in control of all characteristics of the transient profile of ERK phosphorylation, which may clarify why Raf is an oncogene. Most reactions that really matter for one signalling characteristic are also important for the other characteristics. Our analysis also predicts the effects of mutations and changes in gene expression.

Computer Simulation↗

PubMed2005

Principles behind the multifarious control of signal transduction. ERK phosphorylation and kinase/phosphatase control.

General and simple principles are identified that govern signal transduction. The effects of kinase and phosphatase inhibition on a MAP kinase pathway are first examined in silico. Quantitative measures for the control of signal amplitude, duration and integral strength are introduced. We then identify and prove new principles, such that total control on signal amplitude and on final signal strength must amount to zero, and total control on signal duration and on integral signal intensity must equal -1. Collectively, kinases control amplitudes more than duration, whereas phosphatases tend to control both. We illustrate and validate these principles experimentally: (a) a kinase inhibitor affects the amplitude of EGF-induced ERK phosphorylation much more than its duration and (b) a phosphatase inhibitor influences both signal duration and signal amplitude, in particular long after EGF administration. Implications for the cellular decision between growth and differentiation are discussed.

Blotting, Western↗

PubMed2005

Structural and dynamical analyses of the kinase network derived from the transpath database.

We analyze the structural design and the dynamical properties of a protein kinase network derived from the Transpath database. We consider structural properties, such as feedback cycles, pathway lengths, fraction of shortest pathways and crosstalk. Dynamic characteristics of the network are analyzed by using nonlinear differential equations with a special focus on kinase amplitudes and signal propagation times. Comparison with random networks shows that the cellular kinase network exhibits special features which might be a result of natural selection. In particular, the Transpath network contains no cycles, and input kinases and output kinases are generally connected by shortest signalling routes. Moreover, it displays a characteristic spectrum of cross-talk between different pathways.

Algorithms↗

PubMed2004

Interrelations between dynamical properties and structural characteristics of signal transduction networks.

We present a theoretical approach for understanding the interrelations between dynamics and structure of signal transduction pathways. We consider large sets of networks with a specific number of kinases and phosphatases. Our methods are based on nonlinear differential equations and pathway dynamics is characterised in terms of signal amplification and signal duration. We show that networks with a high number of kinases, high connectivities and low phosphatase activities tend to be unstable and run, therefore, the risk to display autoactivation. Analysis of signal transduction pathways retrieved from databases reveals that several structural characteristics required for pathway stability are fulfilled for networks of very large size.

Animals↗

PubMed2003

Urokinase type plasminogen activator receptor is involved in insulin-like growth factor-induced migration of rhabdomyosarcoma cells in vitro.

Urokinase-type plasminogen activator (uPA) binds to its receptor, uPAR, on the surface of cancer cells, leading to the formation of plasmin. Rhabdomyosarcoma (RMS) cell lines secrete high levels of insulin-like growth factor II (IGF-II), suggesting autocrine IGFs play a major role in the unregulated growth and metastasis of RMS. In vitro, IGF-II and IGF-I increased migration of RD cells to 124+/-9% (P<0.01) and 131+/-8% (P<0.05) of control, respectively. IGF-II-induced migration was abolished by insulin-like growth factor binding protein-6 (IGFBP-6) (P<0.01), a relatively specific inhibitor of IGF-II, and by plasminogen activator inhibitor type 1 (PAI-1) (P<0.05). Aprotinin, a plasmin inhibitor, and mannosamine, which inhibits the synthesis of glycosylphosphatidylinositol (GPI), thereby preventing anchorage of GPI-linked proteins such as uPAR to the cell membrane, also decreased IGF-II- (P<0.05 for both) but not IGF-I-induced migration. [Arg54,Arg55]IGF-II and [Leu27]IGF-II, which preferentially bind to the IGF-I and IGF-II/mannose-6-phosphate receptors (IGF-II/M6PR), respectively, both induced RD cell migration to 146+/-8% (P<0.01) and 120+/-7% (P<0.05) of control, respectively. An anti-uPAR anti-serum reduced IGF-II- and IGF-I-induced migration (P<0.05 for both). An anti-low density lipoprotein-related protein (LRP) anti-serum reduced IGF-I-induced migration (P<0.05). IGF-I and -II both increased specific 125I-single chain uPA (scuPA) binding to RD cells in a dose-dependent manner (P<0.01). These results suggest involvement of the PA/plasmin system in IGF-induced migration and indicate important roles these systems may have in RMS metastasis.

Aprotinin↗

PubMed2002

Dynamic stability of signal transduction networks depending on downstream and upstream specificity of protein kinases.

Mathematical methods are used for explaining the structural design of signal transduction networks, e.g. MAP kinase cascades, which control cell proliferation, differentiation or apoptosis. Taking into account protein kinases and phosphatases the interrelation between the topology of signaling networks and the stability of their ground state are analysed. It is shown that the stability is closely related to the system's dimension and to the number of cycles within the network. Systems with a higher number of kinases and/or cycles tend to be more unstable. In contrast to that increasing phosphatase activity stabilises the ground state.

Animals↗