H. V. Westerhoff

SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation (2009)

Albers, S.V., Birkeland, N.K., Driessen, A.J.M., Gertig, S., Haferkamp, P., Klenk, H.P., ...

SulfoSYS (Sulfolobus Systems Biology) focuses on the study of the CCM (central carbohydrate metabolism) of Sulfolobus solfataricus and its regulation under temperature variation at the systems level....

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology (2008)

Herrgård, M.J., Swainston, N., Dobson, P., Dunn, W.B., Arga, K.Y., Arvas, M., ...

Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several...

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology (2008)

Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, Mikko, ...

Nature Biotechnology Vol.26 Nr.10, 1155 - 1160

Networks: A New Summation Law (2007)

M. A. Peletier, H. V. Westerhoff, B. N. Kholodenko, Mark A. Peletier, Hans V. Westerhoff, Boris N. Kholodenko

Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law

en Informatica REPORTRAPPORT Modelling, Analysis and Simulation Modelling, Analysis and Simulation (2007)

C. Francke, P. W. Postma, H. V. Westerhoff, J. G. Blom, M. A. Peletier, Christof Francke, ...

Why the phosphotransferase system of Escherichia coli escapes the diffusion limitation of signal transduction, transport and metabolism that confronts mammalian cells

Systems biology and food science. (2007)

Brul, S., Westerhoff, H.V.

Standardization and 'in vivo'-like enzyme activity measurements in yeast. (2007)

Bouwman, J., Van Eunen, K., Tuzun, I., Postmus, J., Canelas, A., ...

The fluxes through glycolytic enzymes in S. cerevisiae are predominantly regulated at posttranscriptional levels (2007)

Daran-Lapujade, P., Rossell, S., Gulik, W.M. Van, Slijper, M., ...

Metabolic fluxes may be regulated ‘‘hierarchically,’’ e.g., by changes of gene expression that adjust enzyme capacities (Vmax) and/or ‘‘metabolically’’ by interactions of enzymes with...

Standardization and 'in vivo'-like enzyme activity measurements in yeast. (2007)

Bouwman, J., Van Eunen, K., Tuzun, I., Postmus, J., Canelas, A., ...

Systems biology and food science. (2007)

Brul, S., Westerhoff, H.V.

Frequency-dependent incidence in models of sexually transmitted diseases: portrayal of pair-based transmission and effects of illness on contact behaviour (2004)

Lloyd-Smith, J O, Getz, W M, Westerhoff, H V

We explore the transmission process for sexually transmitted diseases (STDs). We derive the classical frequency-dependent incidence mechanistically from a pair-formation model, using an approximation...

Control analysis of trophic chains (2003)

Getz, Wayne M, Westerhoff, H V, Hofmeyr, JHS, Snoep, J L

Inspired by the application of metabolic control analysis (MCA) to biochemical networks, we conduct a generalized sensitivity analysis of the equilibrium of a set of differential equations used to...

From cell to molecule and back; mechanistic modelling in the prediction of microbial food stability. (2003)

Brul, S., Mensonides, F.I.C., Teixeira De Mattos, M.J., Resende, C., Boeree, P.T., Smits, G.J., ...

Why the phosphotransferase system of Escherichia coli escapes diffusion limitation. (2003)

Francke, C., Postma, P.W., Westerhoff, H.V., Blom, J.G., Peletier, M.A.

Redirecting the main pathway flux in branched systems : a metabolic control analysis perspective (2002)

Snoep, J.L., Hoefnagel, M.H.N., Westerhoff, H.V.

DNA supercoiling by gyrase is linked to nucleoid compaction. (2002)

Stuger, R., Woldringh, C.L., Vischer, N.O.E., Bakker, B.M., ...

The distribution of the glucose specific PTS proteins in the Escherichia coli cell (2001)

Francke, C., Blom, J.G., Peletier, M.A., Hink, M.A., ...

Cytochromes c550, c552, c1 in the electron transport network of Paracoccus denitrificans: redundant or subtly different in function? (2001)

Otten, M.F., Reijnders, W.N.M., Westerhoff, H.V., Ludwig, B.

Paracoccus denitrificans strains with mutations in the genes encoding the cytochrome c550, c552, or c1 and in combinations of these genes were constructed, and their growth characteristics were...

Autoamplificationof a two-component regulatory system results in "learning" behavior. (2001)

Hoffer, S.M., Westerhoff, H.V., Hellingwerf, K.J., Postma, P.W., Tomassen, J.

Pumping capacity of bacterial reaction centers and backpressure regulation of energy transduction. (2001)

Rotterdam, B.J. Van, Westerhoff, H.V., Visschers, R.W., Bloch, D.A., Hellingwerf, K.J., Jones, M.R., ...

A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. (2001)

Raamsdonk, L.M., Teusink, B., Broadhurst, D., Zhang, N., Hayes, A., Walsh, M.C., ...

Efficient redirecting of metabolic fluxes in L.lactis using metabolic control analysis (2000)

Hoefnagel, M.H.N., Martens, D.E., Hugenholtz, J., Westerhoff, H.V., Snoep, J.L.

Modeling pyruvate distribution in L. lactis: A kinetic model to support metabolic engineering strategies (2000)

Hoefnagel, M.H.N., Hugenholtz, J., Westerhoff, H.V., Snoep, J.L.

Steady state cyclic electron transfer through solubilized Rhodobacter sphaeroides reaction centres. (2000)

Rotterdam, B.J. Van, Westerhoff, H.V., Visschers, R.W., Jones, M.R., Hellingwerf, K.J., Crielaard, W.

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. (2000)

Teusink, B., Passarge, J., Reijenga, C.A., Esgalhado, E., Schepper, M.G.J., ...

'Slave' metabolites and enzymes. A rapid way of delineating metabolic control. (2000)

Teusink, B., Westerhoff, H.V.

Cellular information transfer regarded from a stoichiometry and control analysis perspective. (2000)

Schuster, S., Kholodenko, B.N., Westerhoff, H.V.

Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations. (2000)

Wolf, J., Passarge, J., Somsen, O.J.G., Snoep, J.L., Heinrich, R., Westerhoff, H.V.

Macromolecular intelligence in microorganisms (2000)

Bruggeman, F.J., Heeswijk, W.C. Van, Boogerd, F.C., Westerhoff, H.V.

Metabolic control from the back benches: Biochemistry towards biocomplexity (2000)

Westerhoff, H.V., Teusink, B., Mensonides, F.I.C., Reijenga, K.A., Esgalhado, E., Kholodenko, B.N., ...

Understanding glucose transport by the bacterial phosphoenolpyruvate: Glucose phosphotransferase system on the basisi of kinetic measurements in vitro. (2000)

Rohwer, J.M., Meadowi, N.D., Rosemani, S., Westerhoff, H.V.

Engineering a living cell to desired metabolite concentrations and fluxes: Pathways with multifunctional enzymes. (2000)

Kholodenko, B.N., Westerhoff, H.V., Schwaber, J., Cascante, M.

Compartmentation protects trypasonomes from the dangerous design of glycolysis. (2000)

Bakker, B.M., Mensonides, F.I.C., Teusink, B., Hoek, P. Van, Michels, P.A.M., Westerhoff, H.V.

Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs (2000)

Bakker, B.M., Westerhoff, H.V., Opperdoes, F.R., Michels, P.A.M.

Relating multidrug resistance phenotypes to the kinetic properties of their drug-efflux pumps (2000)

Westerhoff, H.V., Riethorst, A., Jongsma, A.P.M.

Evaluating limited specificity of drug pumps. Reduced relative resisance in human MDR phenotypes (2000)

Jongsma, A.P.M., Riethorst, A., Lankelma, J., Dekker, A., Westerhoff, H.V.

Modelling metabolism: experimental and theoretical approaches to modelling metabolism. Live control of the living cell. (1999)

Heeswijk, W.C. Van, Bakker, B.M., Teusink, B., Kholodenko, B.N., Somsen, O.J.G., Snoep, J.L., ...

Teaching metabolic control analysis and kinetic modelling. (1999)

Snoep, J.L., Mendes, P., Westerhoff, H.V.

Modular control analysis of slipping enzymes. (1999)

Schuster, S., Westerhoff, H.V.

The reduction state of the Q-pool regulates the electron flux through the branched respiratory network of Paracoccus denitrificans (1999)

Otten, M.F., Reijnders, W.N.M., Bedaux, J.J.M., Westerhoff, H.V., Krab, K.

Non-equilibrium thermodynamics of light absorption. (1999)

Meszena, G., Westerhoff, H.V.

Control analysis of metabolic systems involving quasi-equilibrium reactions. (1999)

Kholodenko, B.N., Garcia, J., Westerhoff, H.V., Cascante, M.

What controls glycolysis in bloodstream form Trypanosoma brucei (1999)

Bakker, B.M., Michels, P.A.M., Opperdoes, F.R., Westerhoff, H.V.

Metabolic control analysis reveals that glucose transport incompletely controls the glycolytic flux in Trypanosoma brucei (1998)

Bakker, B.M., Mensonides, F.I.C., Kuile, F.O. Ter, Michels, P.A.M., Westerhoff, H.V., Walsh, M.C.

Correlation of glucose catabolism and the frequency of glycolytic oscillations in Saccharomyces cerevisiae (1998)

Reijenga, C.A., Teusink, B., Verseveld, H.W., Snoep, J.L., Westerhoff, H.V.

Thermodynamics of complexity. The live cell (1998)

Westerhoff, H.V., Jensen, P.R., Snoep, J.L., Kholodenko, B.N.

Intracellular glucose concentration in derepressed yeast cells consuming glucose in high enough to reduce the glucose transport rate by 50% (1998)

Teusink, B., Diderich, J.A., Westerhoff, H.V., Dam, K. Van, Walsh, M.C.

The danger of metabolic pathways with turbo design (1998)

Teusink, B., Walsh, M.C., Dam, K. Van, Westerhoff, H.V.

Limits to inducer exclusiom: inhibition of the bacterial phosphotransferase system by glycerol kinase (1998)

Rohwer, J.M., Bader, R., Westerhoff, H.V., Postma, P.W.

Inplications of macromolecular crowding for signal transduction and metabolite channeling (1998)

Rohwer, J.M., Postma, P.W., Kholodenko, B.N., Westerhoff, H.V.

Hierarchical control of electron-transfer (1998)

Westerhoff, H.V., Jensen, P.R., Egger, L., Heeswijk, W.C. Van, Kholodenko, B.N., ...

BTK traditions and perspectives: Complex biothermokinetics and control analysis (1998)

Westerhoff, H.V., Rotterdam, B.J. Van, Heeswijk, W.C. Van, Kholodenko, B.N.

Metabolic control analysis as a tool in the elucidation of the function of novel genes (1998)

Teusink, B., Baganz, F., Westerhoff, H.V., Oliver, S.G.

Regulation through moiety conservation: the rolle of product sensitivity in glycolysis of yeast and trypanosomes (1998)

Teusink, B., Mensonides, F.I.C., Bakker, B.M., Walsh, M.C., Snoep, J.L., Dam, K. Van, ...

Control of the F1F0ATP synthase on cell metabolism and growth in Saccharmyces cerevisiae (1998)

Raamsdonk, L.M., Berden, J.A., Westerhoff, H.V., Dam, K. Van

Mathematical modelling of superoxide generation with bc1 complex of mitochondria (1998)

Demin, O.V., Westerhoff, H.V., Kholodenko, B.N.

FnrP and NNR of Paracoccus denitrificans are both members of the FNR family of transcr. activators but have distinct contr. on resp. adaptation in response to oxygen limitation. (1997)

Reijnders, W.N.M., Westerhoff, H.V., Stouthamer, A.H.

Interaction of Nitrogen fixation and phosphorus limitation in alphanizomenon flos-aquae (cyanophyceae)1 (1997)

Nobel, W.T. De, Snoep, J.L., Westerhoff, H.V., Mur, L.R.

Thermodynamics of complexity. The live cell (1997)

Westerhoff, H.V., Jensen, P.R., Snoep, J.L., Kholodenko, B.N.

Global bioenergetics (1997)

Westerhoff, H.V., Crielaard, W., Hellingwerf, K.J.

Internal regulation of a modular system; the different faces of internal control (1997)

Westerhoff, H.V.

Internal glucose concentration is a major determinant of the rate of glucose influx in Saccharomyces cerevisiae (1997)

Teusink, B., Westerhoff, H.V., Dam, K. Van, Walsh, M.C.

The bug in the machine. Control analysis at constant input flux rather that at constant substrate concentration (1997)

Snoep, J.L., Kholodenko, B.N., Westerhoff, H.V.

Simulation of the distribution of parental strains genomes in RC strains of mice (1997)

Moen, C.J., Stoffers, H.J., Hart, A.A.M., Westerhoff, H.V., Demant, P.

Quantification of information transfer via cellular signal transduction pathways (1997)

Kholodenko, B.N., Hoek, J.B., Westerhoff, H.V., Brown, G.C.

Control analysis of periodic phenomena in biological systems (1997)

Kholodenko, B.N., Demin, O.V., Westerhoff, H.V.

Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes (1997)

Bakker, B.M., Michels, P.A.M., Opperdoes, F.R., Westerhoff, H.V.

An alternative model for heme ligation in nitrate reductase and analogous respiratory cytochrome b complexes. (1996)

Nederkoorn, P.H.J., Stouthamer, A.H., Westerhoff, H.V.

Does the bacteriorhodopsin MNET model describe electron-motive-force generation in reconstituted mutant bacterial reaction centers (1996)

Rotterdam, B.J. Van, Westerhoff, H.V., Bloch, D.A., Hellingwerf, K.J., Jones, R., Crielaard, W.

Direct transfer of control and multidrug resistance (1996)

Westerhoff, H.V., Rohwer, J.M., Heijn, M., Mulder, S., Ghauharali, R.I., Wielinga, P., ...

Control of dynamics and steady state: applications to multidrug resistance (1996)

Westerhoff, H.V., Bier, M., Molenaar, D., Spoelstra, E.C., Lankelma, J., Jongsma, A.P.M., ...

Global bioenergetics (1996)

Westerhoff, H.V., Crielaard, W., Hellingwerf, K.J.

Nonlinear control and self-organization (1996)

Westerhoff, H.V., Jensen, P.R., Kahn, D., Kholodenko, B.N., Richard, P.

Regulation and control seen through the eyes of a physicist (1996)

Westerhoff, H.V.

What biotechnologists knew all along....? (1996)

Westerhoff, H.V., Kell, D.B.

DNA supercoiling depends on the phosphorylation potential in Escherichia coli (1996)

Workum, M. Van, Oldenburg, N., Molenaar, D., Jensen, P.R., Snoep, J.L., ...

An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli (1996)

Heeswijk, W.C. Van, Hoving, S., Molenaar, D., Stegeman, B., Kahn, D., Westerhoff, H.V.

Ntr: a signal transduction system with neural network characteristics? (1996)

West, W.S. Van, Heeswijk, W.C. Van, Westerhoff, H.V., Postma, P.W.

Control of frequency and amplitudes is shared by all enzymes in three models for yeast glycolytic oscillations (1996)

Teusink, B., Bakker, B.M., Westerhoff, H.V.

The extent to which the glycolytic flux in Saccharomyces cerevisiae is controlled by the glucose transport system varies with the extracellular glucose concentration (1996)

Teusink, B., Walsh, M.C., Dam, K. Van, Gustafsson, L., Westerhoff, H.V.

Synchronised heat-flux oscillations in yeast-cell populations (1996)

Teusink, B., Larsson, C., Diderich, J.A., Richard, P., Dam, K. Van, Gustafsson, L., ...

Control of glycolytic flux in Zymomonas mobilis by glucose 6-phosphate dehydrogenase activity (1996)

Snoep, J.L., Arfman, N., Yomano, L.P., Westerhoff, H.V., Conway, Y., Ingram, L.O.N.

Changes in the cellular energy state affect the activity of the bacterial phosphotransferase system (1996)

Rohwer, J.M., Jensen, P.R., Shinohara, Y., Postma, P.W., Westerhoff, H.V.

How to recognize monofunctional units in a metabolic system (1996)

Rohwer, J.M., Schuster, S., Westerhoff, H.V.

Protein-protein interactions, metabolite channelling, and the control flux (1996)

Rohwer, J.M., Westerhoff, H.V., Kholodenko, B.N., Postma, P.W.

Acetaldehyde mediates the synchronization of sustained glycolytic oscillations in populations of yeast cells (1996)

Richard, P., Bakker, B.M., Teusink, B., Dam, K. Van, Westerhoff, H.V.

Sustained oscillations in free-energy state and hexose phosphates in yeast (1996)

Richard, P., Teusink, B., Hemker, M.B., Dam, K. Van, Westerhoff, H.V.

Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel (1996)

Mendes, P., Kell, D.B., Westerhoff, H.V.

Effect of channelling on the concentration of bulk-phase intermediates as cytosolic proteins become more concentrated (1996)

Kholodenko, B.N., Westerhoff, H.V., Cascante, M.

The metabolic control theory of biochemical ocsillating systems. 1. Definitions of the quantitative character (1996)

Kholodenko, B.N., Demin, O.V., Westerhoff, H.V.

Control and regulation of channelled versus ideal pathways (1996)

Kholodenko, B.N., Cascante, M., Westerhoff, H.V., Kushmerick, M.J.

Strong control on the transit time in metabolic channelling (1996)

Kholodenko, B.N., Sakamoto, N., Puigjaner, J., Westerhoff, H.V., Cascante, M.

The signal transduction function for oxidative phosphorylation is at least second order in ADP (1996)

Jeneson, J.A.L., Wiseman, R.W., Westerhoff, H.V., Kushmerick, M.J.

Saturable P-glycoprotein kinetics assayed by fluorescence studies of drug efflux from suspended human KB8-5 cells (1996)

Ghauharali, R.I., Westerhoff, H.V., Dekker, H., Lankelma, J.

Metabolic control theory of biochemical oscillating systems. 2. Calculation of the periodic control coefficients (1996)

Demin, O.V., Kholodenko, B.N., Westerhoff, H.V.

Control and absence thereof in steady periodic phenomena (1996)

Demin, O.V., Westerhoff, H.V., Kholodenko, B.N.

The possible control of chaos in chronic inflammation (1996)

Daams, J.H., Westerhoff, H.V.

Molecular control analysis: Control within proteins and molecular processes. (1996)

Brown, G.C., Westerhoff, H.V., Kholodenko, B.N.

Control analysis of glycolytic oscillations. (1996)

Bier, M., Teusink, B., Kholodenko, B.N., Westerhoff, H.V.

Control of the glycolytic flux in Trypanosoma brucei: why control can shift suddenly (1996)

Bakker, B.M., Michels, P.A.M., Westerhoff, H.V.

Cellular daunorubicin transport in human cancer (1996)

Lankelma, J., Westerhoff, H.V., Heijn, M., Broxterman, H.J., Pinedo, H.M.

Structure and partitioning of bacterial DNA: determined by a balance of compaction and expansion forces? (1995)

Woldringh, C.L., Jensen, P.R., Westerhoff, H.V.

Experimental determination of control by the HE+-ATPase in Escherichia coli (1995)

Jensen, P.R., Michelsen, O., Westerhoff, H.V.

Control over electron flow through the Rhodobacter sphaeroides reaction centre. (1995)

Rotterdam, B.J. Van, Crielaard, W., Westerhoff, H.V., Hellingwerf, K.J.

Calcium indirectly increases the control exerted by the adenine nucleotide translocator over 2-oxoglutarate oxidation in rat heart mitochondria. (1995)

Mildaziene, V., Baniene, R., Nauciene, Z., Bakker, B.M., Brown, G.C., Westerhoff, H.V., ...

Henrik Kacser 1918-1995: Metabolism of control. (1995)

Westerhoff, H.V.

Structure and partitioning of bacterial DNA: Determined by a balance of compaction and expansion forces? (1995)

Woldringh, C.L., Jensen, P.R., Westerhoff, H.V.

Elusive control (1995)

Westerhoff, H.V., Kholodenko, B.N., Cascante, M., Dam, K. Van

Regulation of oxidative phosphorylation: the flexible respiratory network of Paracoccus denitrificansEI. (1995)

Reijnders, W.N.M., Delorme, C.O., Stouthamer, A.H., ...

An additional PC1C1 in Escherichia coli: a new regulatory protein in the glutamine synthetase cascade. (1995)

Heeswijk, W.C. Van, Stegeman, B., Hoving, S., Molenaar, D., Kahn, D., Westerhoff, H.V.

Protein burden in Zymomonas mobilis: negative flux and growth control due to overproduction of glycolytic enzymes. (1995)

Snoep, J.L., Yomana, L.P., Westerhoff, H.V., Ingram, L.O.

Regulation and control of compartmentalized glycolysis in bloodstream form Trypanosoma brucei. (1995)

Bakker, B.M., Westerhoff, H.V., Michels, P.A.M.

Hypothesis. Composite control of cell function: metabolic pathways behaving as single control units. (1995)

Kholodenko, B.N., Schuster, S., Rohwer, J.M., Cascante, M., Westerhoff, H.V.

Molecular biology for flux control (1995)

Jensen, P.R., Snoep, J.L., Molenaar, D., Heeswijk, W.C. Van, Kholodenko, B.N., ...

Quasi-linear relationship between Gibbs free energy of ATP hydrolysis and power output in human forearm muscle. (1995)

Jeneson, J.A.L., Westerhoff, H.V., Brown, T.R., Berger, R.

Energy buffering of DNA structure fails when Escherichia coli runs out of substrate. (1995)

Jensen, P.R., Loman, L., Petra, B., Weijden, C. Van Der, Westerhoff, H.V.

Subtlety in control-metabolic pathway engineering. (1995)

Westerhoff, H.V.

Coenzyme cycles and metabolic control analysis: the determination of the elasticity coefficients from the generalised connectivity theorem. (1995)

Kholodenko, B.N., Sauro, H.M., Westerhoff, H.V., Cascante, M.

Control theory of group transfer pathways. (1995)

Kholodenko, B.N., Westerhoff, H.V.

How to reveal various aspects of regulation in grouptransfer pathways. (1995)

Kholodenko, B.N., Westerhoff, H.V.

Dynamic aspects of cascade-type metabolic regulation (1995)

Molenaar, D., Kholodenko, B.N., Heeswijk, W.C. Van, Westerhoff, H.V.

Signal transduction in bacteria: phospho-neural network(s) in Escherichia coli? (1995)

Hellingwerf, K.J., Postma, P.W., Tommassen, J., Westerhoff, H.V.

Control analysis of metabolic systems consisting of uni- and/or multifunctional units. Application to modular systems and slipping enzymes. (1995)

Schuster, S., Kahn, D., Westerhoff, H.V.

Nitrite and nitric oxide reduction in Paracoccus denitrificans is under the control of NNR, a regulatory protein that belongs to the FNR family of transcriptional activators. (1995)

Reijnders, W.N.M., Spiro, S., Westerhoff, H.V., Stouthamer, A.H., ...

The macroworld versus the microworld of biochemical regulation and control. (1995)

Kholodenko, B.N., Westerhoff, H.V.

Control in channelled pathways. A matrix method calculating the enzyme control coefficients (1995)

Kholodenko, B.N., Westerhoff, H.V., Puigjaner, J., Cascante, M.

Energy, control and DNA structure in the living cell. (1995)

Wijker, J.E., Jensen, P.R., Vaz Gomes, A., Waal, A. De, Workum, M. Van, Heeswijk, W.C. Van, ...

Functional synergism of magainins PGLa and magainin-2 in Escherichia coli, tumor cells and liposomes (1995)

Westerhoff, H.V., Zasloff, M., Rosner, J.L., Hendler, R.W., Waal, A. De, Vaz Gomes, A., ...

On the expected relationship between Gibbs energy of ATP hydrolysis and muscle performance. (1995)

Westerhoff, H.V., Jeneson, J.A.L.

Control theory of cell metabolism: towards more realistic "non-ideal" systems. (1995)

Kholodenko, B.N., Cascante, M., Molenaar, D., Demin, O.V., Westerhoff, H.V.

Hierarchies in control (1995)

Jensen, P.R., Bier, M., Heeswijk, W.C. Van, Rohwer, J.M., Molenaar, D., ...

Defining control coefficients in non-ideal metabolic pathways (1995)

Kholodenko, B.N., Molenaar, D., Schuster, S., Heinrich, R., Westerhoff, H.V.

Control theory of metabolic channelling (1995)

Kholodenko, B.N., Cascante, M., Westerhoff, H.V.

Comparison of retinal-based and chlorophyll-based photosynthesis: A biothermokinetic description of fotochemical reaction centers. (1994)

Hellingwerf, K.J., Crielaard, W., Westerhoff, H.V.

Multiplicity of control. (1994)

Westerhoff, H.V., Jensen, P.R., Kahn, D., Kholodenko, B.N., Schuster, S., ...

Getting to the inside of cells using metabolic control analysis. (1994)

Westerhoff, H.V., Hofmeyr, J.H.S., Kholodenko, B.N.

Biothermokinetics. (1994)

Westerhoff, H.V.

Structure-function relationship of magainins. Studies in liposomal model system. (1994)

Vaz Gomes, A., Waal, A. De, Berden, J.A., Westerhoff, H.V.

Cascade control of ammonia assimilation. (1994)

Heeswijk, W.C. Van, Westerhoff, H.V., Kahn, D.

The C.E=I=E.C square matrix method illustrated for a simple case of a complex pathway. (1994)

Westerhoff, H.V.

Object oriented simulation of metabolic processes. (1994)

Stoffers, H.J., Stigt, B. Van, Richard, P., Westerhoff, H.V., Blommestijn, G.J.F.

Simulating cell metabolism in C**. (1994)

Stoffers, H.J., Blommestijn, G.J.F., Sonnhammer, E.L.L., Raat, N.J.H., Westerhoff, H.V.

The multidrug-resistance-reverser verapamil with cellular P-glycoprotein-mediated pumping of daunorubicin as a non-competing substrate (1994)

Spoelstra, E.C., Westerhoff, H.V., Pinedo, H.M., Dekker, H., Lankelma, J.

How to determine control of growth rate in a chemostat. Using metabolic control analysis to resolve the paradox. (1994)

Snoep, J.L., Jensen, P.R., Groeneveld, P., Molenaar, D., Kholodenko, B.N., Westerhoff, H.V.

a modular approach to the description of the control of connected metabolic systems. (1994)

Schuster, S., Kahn, D., Westerhoff, H.V.

Synchronization of glycolytic oscillations in intact yeast cells. (1994)

Richard, P., Teusink, B., Westerhoff, H.V., Dam, K. Van

Yeast cells with a specific cellular make-up and an environment that removes acetaldehyde are prone to sustained glycolytic oscillations. (1994)

Richard, P., Diderich, J.A., Bakker, B.M., Teusink, B., Dam, K. Van, Westerhoff, H.V.

Photovoltage measurements as a probe of light distribution and ion movements around photosynthetic apparatus. (1994)

Meszena, G., Westerhoff, H.V.

Light intensity distribution in thylakoids and the polarity of the photovoltage effect. (1994)

Meszena, G., Westerhoff, H.V.

Rate limitation within a single enzyme is directly related to enzyme intermediate levels. (1994)

Kholodenko, B.N., Westerhoff, H.V., Brown, G.C.

Sum of the flux control coefficients: What is it equal to in different systems? (1994)

Kholodenko, B.N., Westerhoff, H.V.

Control theory of one enzyme. (1994)

Kholodenko, B.N., Westerhoff, H.V.

Control by enzymes, coenzymes and conserved moieties. (1994)

Kholodenko, B.N., Sauro, H.M., Westerhoff, H.V.

Regulation and homeostasis in metabolic control theory: Interplay between fluctuations of variables and paraeter changes. (1994)

Kahn, D., Westerhoff, H.V.

Control analysis of modular metabolic networks. (1994)

Kahn, D., Westerhoff, H.V.

Magainin oligomers reversibly dissipate DeltamuH in cytochrome oxidase liposomes. (1994)

Juretic, D., Hendler, R.W., Kamp, F., Caughey, W.S., Zasloff, M., Westerhoff, H.V.

Modulation of cellular energy state and DNA supercoiling in E. coli. (1994)

Jensen, P.R., Oldenburg, N., Petra, B., Michelsen, O., Westerhoff, H.V.

Comparison of retinal-based and chlorophyll-based photosynthesis: A biothermokinetic description of photochemical reaction centers. (1994)

Hellingwerf, K.J., Crielaard, W., Westerhoff, H.V.

Cooperative P-glycoprotein mediated daunorubicin transport into DNA-loaded plasma membrane vesicles. (1994)

Guiral, M., Viratelle, O., Westerhoff, H.V., Lankelma, J.

Tumor progression and catastrophe theory. (1994)

Daams, H., Cortassa, S., Aon, M.A., Westerhoff, H.V.

Temporal self-organization and linear non equilibrium thermodynamics are not mutually exclusive in autocatalytic systems. (1994)

Cortassa, S., Aon, M.A., Westerhoff, H.V.

The multidrug resistance reverter verapamil interferes with cellular P-glycoprotein-mediated pumping of daunorubicin as a non-competing substrate (1994)

Spoelstra, E.C., Westerhoff, H.V., Pinedo, H.M., Dekker, H., Lankelma, J.

Verapamil as a substrate for P-glycoprotein; a model for competition between verapamil and daunorubicin for the active efflux pump (1994)

Spoelstra, E.C., Westerhoff, H.V., Pinedo, H.M., Dekker, H., Lankelma, J.

Redox interactions in cytochrome c oxidase: from the "neoclassical" toward "modern" models (1992)

Hendler, R.W., Westerhoff, H.V.

Linear nonequilibrium thermodynamics describes the dynamics of an autocatalytic system (1991)

Cortassa, S., Aon, M.A., Westerhoff, H.V.

Energetics of microbial growth: an analysis of the relationship between growth and its mechanistic basis by mosaic non-equilibrium thermodynamics (1982)

Hellingwerf, K.J., Lolkema, J.S., Otto, R., Neijssel, O.M., Stouthamer, A.H., Harder, W., ...

Control analysis of the dependence of Escherichia coli physiology on the H(+)-ATPase.

Jensen, P R, Michelsen, O, Westerhoff, H V

The H(+)-ATPase plays a central role in Escherichia coli free-energy transduction and hence in E. coli physiology. We here investigate the extent to which this enzyme also controls the growth rate,...

Energy buffering of DNA structure fails when Escherichia coli runs out of substrate.

Jensen, P R, Loman, L, Petra, B, Westerhoff, H V

To study how changes in the [ATP]/[ADP] ratio affect the level of DNA supercoiling in Escherichia coli, the cellular content of H(+)-ATPase was modulated around the wild-type level. A relatively...

Coupling of vectorial proton flow to a biochemical reaction by local electric interactions.

Kamp, F, Astumian, R D, Westerhoff, H V

For a transmembrane redox enzyme and a (passive) protonophore, the complete set of rate equations is given. Turnover causes cyclic variation of their electric polarization. This is responsible not...

Magainins and the disruption of membrane-linked free-energy transduction.

Westerhoff, H V, Juretić, D, Hendler, R W, Zasloff, M

Magainins, a family of positively charged peptides, are partly if not wholly responsible for antimicrobial activity in skin extracts of Xenopus laevis. We report here that members of the magainin...

Can free energy be transduced from electric noise?

Astumian, R D, Chock, P B, Tsong, T Y, Chen, Y D, Westerhoff, H V

Recently, it was shown that free energy can be transduced from a regularly oscillating electric field to do chemical or transport work when coupled through an enzyme with appropriate electrical...

Mosaic nonequilibrium thermodynamics describes biological energy transduction.

Westerhoff, H V, Hellingwerf, K J, Arents, J C, Scholte, B J, Van Dam, K

A procedure, called "mosaic nonequilibrium thermodynamics," for describing ion movement and energy transduction in biological membranes is tested in a model system: bacteriorhodopsin liposomes. The...

How enzymes can capture and transmit free energy from an oscillating electric field.

Westerhoff, H V, Tsong, T Y, Chock, P B, Chen, Y D, Astumian, R D

Recently, it has been demonstrated that free energy from an alternating electric field can drive the active transport of Rb+ by way of the Na+, K+-ATPase. In the present work, it is shown why many...

Stochastic free energy transduction.

Westerhoff, H V, Chen, Y

Theoretical free-energy coupling systems in which the free energy coupling intermediate (e.g., the proton) occurs only in small numbers of molecules per coupling unit are shown to exhibit a number of...

Excess capacity of H(+)-ATPase and inverse respiratory control in Escherichia coli.

Jensen, P R, Westerhoff, H V, Michelsen, O

With succinate as free-energy source, Escherichia coli generating virtually all ATP by oxidative phosphorylation might be expected heavily to tax its ATP generating capacity. To examine this the...

A model system for delocalized chemiosmotic coupling exhibited the features thought diagnostic of localized coupling.

Westerhoff, H V, Van Der Bend, R L, Van Dam, K, Berden, J, Peterson, J

A critical appraisal of evidence for localized energy coupling. Kinetic studies on liposomes containing bacteriorhodopsin and ATP synthase.

Van Der Bend, R L, Petersen, J, Berden, J A, Van Dam, K, Westerhoff, H V

In intact systems (chloroplasts, mitochondria and bacteria) many experiments have been reported which are indicative of localized coupling between ATP synthase and electron transfer complexes. We...

THe proton-per-electron stoicheiometry of 'site 1' of oxidative phosphorylation at high protonmotive force is close to 1.5.

De Jonge, P C, Westerhoff, H V

The maximum redox potential difference between the NAD+/NADH couple and the succinate/fumarate couple generated during ATP-energized reduction of NAD+ by succinate in submitochondrial particles was...

The hypothesis of localized chemiosmosis is unsatisfactory.

Westerhoff, H V, Simonetti, A L, Van Dam, K

The hypothesis of 'localized' chemiosmosis have been put to an experimental test in the system of oxidative phosphorylation by rat liver mitochondria. We find that the variation of the ratio of...

The two opposing activities of adenylyl transferase reside in distinct homologous domains, with intramolecular signal transduction.

Jaggi, R, Van Heeswijk, W C, Westerhoff, H V, Ollis, D L, Vasudevan, S G

Adenylyl transferase (ATase) is the bifunctional effector enzyme in the nitrogen assimilation cascade that controls the activity of glutamine synthetase (GS) in Escherichia coli. This study addresses...

Effect of channelling on the concentration of bulk-phase intermediates as cytosolic proteins become more concentrated.

Kholodenko, B N, Westerhoff, H V, Cascante, M

This paper shows that metabolic channelling can provide a mechanism for decreasing the concentration of metabolites in the cytoplasm when cytosolic proteins become more concentrated. A dynamic...

Glucose and the ATP paradox in yeast.

Somsen, O J, Hoeben, M A, Esgalhado, E, Snoep, J L, Visser, D, Van Der Heijden, R T, ...

A sustained decrease in the intracellular ATP concentration has been observed when extra glucose was added to yeast cells growing aerobically under glucose limitation. Because glucose degradation is...

Linear nonequilibrium thermodynamics describes the dynamics of an autocatalytic system.

Cortassa, S, Aon, M A, Westerhoff, H V

A model simulating oscillations in glycolysis was formulated in terms of nonequilibrium thermodynamics. In the kinetic rate equations every metabolite concentration was replaced with an exponential...

Redox interactions in cytochrome c oxidase: from the "neoclassical" toward "modern" models.

Hendler, R W, Westerhoff, H V

Because of recent experimental data on the redox characteristics of cytochrome c oxidase and renewed interest in the role of cooperativity in energy coupling, the question of redox cooperativity in...

How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment.

Bier, M, Bakker, B M, Westerhoff, H V

Of all the lifeforms that obtain their energy from glycolysis, yeast cells are among the most basic. Under certain conditions the concentrations of the glycolytic intermediates in yeast cells can...

Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations.

Wolf, J, Passarge, J, Somsen, O J, Snoep, J L, Heinrich, R, Westerhoff, H V

Under certain well-defined conditions, a population of yeast cells exhibits glycolytic oscillations that synchronize through intercellular acetaldehyde. This implies that the dynamic phenomenon of...

Control of glycolytic dynamics by hexose transport in Saccharomyces cerevisiae.

Reijenga, K A, Snoep, J L, Diderich, J A, Van Verseveld, H W, Westerhoff, H V, Teusink, B

It is becoming accepted that steady-state fluxes are not necessarily controlled by single rate-limiting steps. This leaves open the issue whether cellular dynamics are controlled by single pacemaker...

Control analysis of the dependence of Escherichia coli physiology on the H(+)-ATPase.

Jensen, P R, Michelsen, O, Westerhoff, H V

The H(+)-ATPase plays a central role in Escherichia coli free-energy transduction and hence in E. coli physiology. We here investigate the extent to which this enzyme also controls the growth rate,...

Energy buffering of DNA structure fails when Escherichia coli runs out of substrate.

Jensen, P R, Loman, L, Petra, B, Westerhoff, H V

To study how changes in the [ATP]/[ADP] ratio affect the level of DNA supercoiling in Escherichia coli, the cellular content of H(+)-ATPase was modulated around the wild-type level. A relatively...

Coupling of vectorial proton flow to a biochemical reaction by local electric interactions.

Kamp, F, Astumian, R D, Westerhoff, H V

For a transmembrane redox enzyme and a (passive) protonophore, the complete set of rate equations is given. Turnover causes cyclic variation of their electric polarization. This is responsible not...

Magainins and the disruption of membrane-linked free-energy transduction.

Westerhoff, H V, Juretić, D, Hendler, R W, Zasloff, M

Magainins, a family of positively charged peptides, are partly if not wholly responsible for antimicrobial activity in skin extracts of Xenopus laevis. We report here that members of the magainin...

Can free energy be transduced from electric noise?

Astumian, R D, Chock, P B, Tsong, T Y, Chen, Y D, Westerhoff, H V

Recently, it was shown that free energy can be transduced from a regularly oscillating electric field to do chemical or transport work when coupled through an enzyme with appropriate electrical...

Mosaic nonequilibrium thermodynamics describes biological energy transduction.

Westerhoff, H V, Hellingwerf, K J, Arents, J C, Scholte, B J, Van Dam, K

A procedure, called "mosaic nonequilibrium thermodynamics," for describing ion movement and energy transduction in biological membranes is tested in a model system: bacteriorhodopsin liposomes. The...

How enzymes can capture and transmit free energy from an oscillating electric field.

Westerhoff, H V, Tsong, T Y, Chock, P B, Chen, Y D, Astumian, R D

Recently, it has been demonstrated that free energy from an alternating electric field can drive the active transport of Rb+ by way of the Na+, K+-ATPase. In the present work, it is shown why many...

Stochastic free energy transduction.

Westerhoff, H V, Chen, Y

Theoretical free-energy coupling systems in which the free energy coupling intermediate (e.g., the proton) occurs only in small numbers of molecules per coupling unit are shown to exhibit a number of...

Excess capacity of H(+)-ATPase and inverse respiratory control in Escherichia coli.

Jensen, P R, Westerhoff, H V, Michelsen, O

With succinate as free-energy source, Escherichia coli generating virtually all ATP by oxidative phosphorylation might be expected heavily to tax its ATP generating capacity. To examine this the...

A model system for delocalized chemiosmotic coupling exhibited the features thought diagnostic of localized coupling.

Westerhoff, H V, Van Der Bend, R L, Van Dam, K, Berden, J, Peterson, J

A critical appraisal of evidence for localized energy coupling. Kinetic studies on liposomes containing bacteriorhodopsin and ATP synthase.

Van Der Bend, R L, Petersen, J, Berden, J A, Van Dam, K, Westerhoff, H V

In intact systems (chloroplasts, mitochondria and bacteria) many experiments have been reported which are indicative of localized coupling between ATP synthase and electron transfer complexes. We...

THe proton-per-electron stoicheiometry of 'site 1' of oxidative phosphorylation at high protonmotive force is close to 1.5.

De Jonge, P C, Westerhoff, H V

The maximum redox potential difference between the NAD+/NADH couple and the succinate/fumarate couple generated during ATP-energized reduction of NAD+ by succinate in submitochondrial particles was...

The hypothesis of localized chemiosmosis is unsatisfactory.

Westerhoff, H V, Simonetti, A L, Van Dam, K

The hypothesis of 'localized' chemiosmosis have been put to an experimental test in the system of oxidative phosphorylation by rat liver mitochondria. We find that the variation of the ratio of...

The two opposing activities of adenylyl transferase reside in distinct homologous domains, with intramolecular signal transduction.

Jaggi, R, Van Heeswijk, W C, Westerhoff, H V, Ollis, D L, Vasudevan, S G

Adenylyl transferase (ATase) is the bifunctional effector enzyme in the nitrogen assimilation cascade that controls the activity of glutamine synthetase (GS) in Escherichia coli. This study addresses...

Effect of channelling on the concentration of bulk-phase intermediates as cytosolic proteins become more concentrated.

Kholodenko, B N, Westerhoff, H V, Cascante, M

This paper shows that metabolic channelling can provide a mechanism for decreasing the concentration of metabolites in the cytoplasm when cytosolic proteins become more concentrated. A dynamic...

Glucose and the ATP paradox in yeast.

Somsen, O J, Hoeben, M A, Esgalhado, E, Snoep, J L, Visser, D, Van Der Heijden, R T, ...

A sustained decrease in the intracellular ATP concentration has been observed when extra glucose was added to yeast cells growing aerobically under glucose limitation. Because glucose degradation is...

Linear nonequilibrium thermodynamics describes the dynamics of an autocatalytic system.

Cortassa, S, Aon, M A, Westerhoff, H V

A model simulating oscillations in glycolysis was formulated in terms of nonequilibrium thermodynamics. In the kinetic rate equations every metabolite concentration was replaced with an exponential...

Redox interactions in cytochrome c oxidase: from the "neoclassical" toward "modern" models.

Hendler, R W, Westerhoff, H V

Because of recent experimental data on the redox characteristics of cytochrome c oxidase and renewed interest in the role of cooperativity in energy coupling, the question of redox cooperativity in...

How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment.

Bier, M, Bakker, B M, Westerhoff, H V

Of all the lifeforms that obtain their energy from glycolysis, yeast cells are among the most basic. Under certain conditions the concentrations of the glycolytic intermediates in yeast cells can...

Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations.

Wolf, J, Passarge, J, Somsen, O J, Snoep, J L, Heinrich, R, Westerhoff, H V

Under certain well-defined conditions, a population of yeast cells exhibits glycolytic oscillations that synchronize through intercellular acetaldehyde. This implies that the dynamic phenomenon of...

Control of glycolytic dynamics by hexose transport in Saccharomyces cerevisiae.

Reijenga, K A, Snoep, J L, Diderich, J A, Van Verseveld, H W, Westerhoff, H V, Teusink, B

It is becoming accepted that steady-state fluxes are not necessarily controlled by single rate-limiting steps. This leaves open the issue whether cellular dynamics are controlled by single pacemaker...

Approaches to Biosimulation of Cellular Processes

Bruggeman, F. J., Westerhoff, H. V.

Modelling and simulation are at the heart of the rapidly developing field of systems biology. This paper reviews various types of models, simulation methods, and theoretical approaches that are...