Hans V Westerhoff | Vrije Universiteit Amsterdam (original) (raw)

Papers by Hans V Westerhoff

International Journal of Molecular Sciences, 2017

Mathematical models are key to systems biology where they typically describe the topology and dyn... more Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase. In this study we formulate three hypotheses that could explain functionally why GAPN exists in these Archaea, and then construct and use mathematical models to test these three hypotheses. We used kinetic parameters of enzymes of Sulfolobus solfataricus (S. solfataricus) which is a thermo-acidophilic archaeon that grows optimally between 60 and 90 • C and between pH 2 and 4. For comparison, we used a model of Saccharomyces cerevisiae (S. cerevisiae), an organism that can live at moderate temperatures. We find that both the first hypothesis, i.e., that the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plus phosphoglycerate kinase (PGK) route (the alternative to GAPN) is thermodynamically too much uphill and the third hypothesis, i.e., that GAPDH plus PGK are required to carry the flux in the gluconeogenic direction, are correct. The second hypothesis, i.e., that the GAPDH plus PGK route delivers less than the 1 ATP per pyruvate that is delivered by the GAPN route, is only correct when GAPDH reaction has a high rate and 1,3-bis-phosphoglycerate (BPG) spontaneously degrades to 3PG at a high rate.

Biosimulation in Drug Development

Page 433. 403 15 Silicon Cell Models: Construction, Analysis, and Reduction Frank J. Bruggeman, H... more Page 433. 403 15 Silicon Cell Models: Construction, Analysis, and Reduction Frank J. Bruggeman, Hanna M. Hardin, Jan H. van Schuppen, and Hans V. Westerhoff Abstract Biosimulation has a dominant role to play in systems biology. ...

Trends in Microbiology, 2007

Challenges faced by systems biology The complete sequencing of the genome of an organism or the d... more Challenges faced by systems biology The complete sequencing of the genome of an organism or the determination of the crystal structures of all of its proteins might constitute the biology of that system, and Review

Philosophical Psychology, 2002

The biological sciences study (bio)complex living systems. Research directed at the mechanistic e... more The biological sciences study (bio)complex living systems. Research directed at the mechanistic explanation of the "live" state truly requires a pluralist research program, i.e. BioComplexity research. The program should apply multiple intra-level and inter-level theories and methodologies. We substantiate this thesis with analysis of BioComplexity: metabolic and modular control analysis of metabolic pathways, emergence of oscillations, and the analysis of the functioning of glycolysis.

Nature Communications, 2013

It is an accepted paradigm that extended stress predisposes an individual to pathophysiology. How... more It is an accepted paradigm that extended stress predisposes an individual to pathophysiology. However, the biological adaptations to minimize this risk are poorly understood. Using a computational model based upon realistic kinetic parameters we are able to reproduce the interaction of the stress hormone cortisol with its two nuclear receptors, the high affinity glucocorticoid receptor (GR) and the low affinity pregnane X-receptor (PXR). We demonstrate that regulatory signals between these two nuclear receptors are necessary to optimise the body's response to stress episodes, attenuating both the magnitude and duration of the biological response. In addition, we predict that the activation of PXR by multiple, low affinity endobiotic ligands is necessary for the significant PXR-mediated transcriptional response observed following stress episodes. This integration allows responses mediated through both the high and low affinity nuclear receptors, which we predict is an important strategy to minimise the risk of disease from chronic stress.

Journal of Mathematical Biology, 2008

Systems Biology is the science that aims to understand how biological function absent from macrom... more Systems Biology is the science that aims to understand how biological function absent from macromolecules in isolation, arises when they are components of their system. Dedicated to the memory of Reinhart Heinrich, this paper discusses the origin and evolution of the new part of systems biology that relates to met

Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1996

The three main existing models for glycolytic oscillations in yeast were reexamined to investigat... more The three main existing models for glycolytic oscillations in yeast were reexamined to investigate how these oscillations are controlled. We implemented the operational definitions provided by metabolic control analysis to quantify the control properties of enzymes with regard to glycolytic oscillations. In all three models, the control of the frequency and that of the amplitudes of the metabolites were distributed among the enzymes. There was no obvious correlation between the control of the average flax and the control of the frequency. Most importantly, the so-called 'oscillophore' of the system, traditionally the enzyme primarily held responsible for the generation of the oscillation, was not the only controlling step. We conclude that just like steady-state flux control is not necessarily limited to a rate-limiting step, oscillations are not dictated by a single 'oscillophore'.

Archives of Toxicology, 2012

An important goal of toxicology is to understand and predict the adverse effects of drugs and oth... more An important goal of toxicology is to understand and predict the adverse effects of drugs and other xenobiotics. For pharmaceuticals, such effects often emerge unexpectedly in man even when absent from trials in vitro and in animals. Although drugs and xenobiotics act on molecules, it is their perturbation of intracellular networks that matters. The tremendous complexity of these networks makes it difficult to understand the effects of xenobiotics on their ability to function. Because systems biology integrates data concerning molecules and their interactions into an understanding of network behaviour, it should be able to assist toxicology in this respect. This review identifies how in silico systems biology tools, such as kinetic modelling, and metabolic control, robustness and flux analyse, may indeed help understanding network-mediated toxicity. It also shows how these approaches function by implementing them vis-à-vis the glutathione network, which is important for the detoxification of reactive drug metabolites. The tools enable the appreciation of the steady state concept for the detoxification network and make it possible to simulate and then understand effects of perturbations of the macromolecules in the pathway that are counterintuitive. We review how a glutathione model has been used to explain the impact of perturbation of the pathway at various molecular sites, as would be the effect of single-nucleotide polymorphisms. We focus on how the mutations impact the levels of glutathione and of two candidate biomarkers of hepatic glutathione status. We conclude this review by sketching how the various systems biology tools may help in the various phases of drug development in the pharmaceutical industry.

Journal of Bacteriology, 1998

In Saccharomyces cerevisiae cells exhibiting high-affinity glucose transport, the glucose consump... more In Saccharomyces cerevisiae cells exhibiting high-affinity glucose transport, the glucose consumption rate at extracellular concentrations above 10 mM was only half of the zero trans -influx rate. To determine if this regulation of glucose transport might be a consequence of intracellular free glucose we developed a new method to measure intracellular glucose concentrations in cells metabolizing glucose, which compares glucose stereoisomers to correct for adhering glucose. The intracellular glucose concentration was 1.5 mM, much higher than in most earlier reports. We show that for the simplest model of a glucose carrier, this concentration is sufficient to reduce the glucose influx by 50%. We conclude that intracellular glucose is the most likely candidate for the observed regulation of glucose import and hence glycolysis. We discuss the possibility that intracellular glucose functions as a primary signal molecule in these cells.

Methods in Enzymology, Vol 500, 2011

Systems biology has come of age. In most scientifically active countries, significant research pr... more Systems biology has come of age. In most scientifically active countries, significant research programs are funded. Various scientific journals, standards, repositories, and Web sites are devoted to the topic. Systems biology has spun off new subdisciplines such as synthetic biology and systems medicine. There are training courses at the M.Sc. and Ph.D. level at various Universities. And various industries are engaging systems biology in their R&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;D. Systems biology has also developed numerous new methodologies. This chapter attempts to organize these methodologies from the perspectives of the unique aims of systems biology, and by comparing with one of its parents, molecular biology.

Springer Series in Biophysics, 2013

This chapter discusses how metabolic control analysis (MCA) and generalisations thereof such as h... more This chapter discusses how metabolic control analysis (MCA) and generalisations thereof such as hierarchical control analysis (HCA) may help to understand the control of cell function through signal transduction, as well as the control of signal transduction itself. It reviews the key concepts of MCA paying attention to their applicability to signal transduction. Control analysis has already led to major insights into signal transduction such as that control of signalling tends to be distributed over multiple components and that the phosphatases are as important as, or more important than, the kinases. Examples of applications of control analysis in the medical domain are discussed.

Proceedings of the National Academy of Sciences, 2000

Unlike in other organisms, in trypanosomes and other Kinetoplastida the larger part of glycolysis... more Unlike in other organisms, in trypanosomes and other Kinetoplastida the larger part of glycolysis takes place in a specialized organelle, called the glycosome. At present it is impossible to remove the glycosome without changing much of the rest of the cell. It would seem impossible, therefore, to assess the metabolic consequences of this compartmentation. Therefore, we here develop a computer experimentation approach, which we call computational cell biology. A validated molecular kinetic computer replica was built of glycolysis in the parasite Trypanosoma brucei. Removing the glycosome membrane in that replica had little effect on the steady-state flux, which argues against the prevalent speculation that glycosomes serve to increase flux by concentrating the enzymes. Removal of the membrane did cause ( i ) the sugar phosphates to rise to unphysiologically high levels, which must have pathological effects, and ( ii ) a failure to recover from glucose deprivation. We explain these e...

Proceedings of the National Academy of Sciences, 2007

Metabolic fluxes may be regulated “hierarchically,” e.g., by changes of gene expression that adju... more Metabolic fluxes may be regulated “hierarchically,” e.g., by changes of gene expression that adjust enzyme capacities ( V max ) and/or “metabolically” by interactions of enzymes with substrates, products, or allosteric effectors. In the present study, a method is developed to dissect the hierarchical regulation into contributions by transcription, translation, protein degradation, and posttranslational modification. The method was applied to the regulation of fluxes through individual glycolytic enzymes when the yeast Saccharomyces cerevisiae was confronted with the absence of oxygen and the presence of benzoic acid depleting its ATP. Metabolic regulation largely contributed to the ≈10-fold change in flux through the glycolytic enzymes. This contribution varied from 50 to 80%, depending on the glycolytic step and the cultivation condition tested. Within the 50–20% hierarchical regulation of fluxes, transcription played a minor role, whereas regulation of protein synthesis or degrada...

Proceedings of the National Academy of Sciences, 2006

An important question is to what extent metabolic fluxes are regulated by gene expression or by m... more An important question is to what extent metabolic fluxes are regulated by gene expression or by metabolic regulation. There are two distinct aspects to this question: ( i ) the local regulation of the fluxes through the individual steps in the pathway and ( ii ) the influence of such local regulation on the pathway’s flux. We developed regulation analysis so as to address the former aspect for all steps in a pathway. We demonstrate the method for the issue of how Saccharomyces cerevisiae regulates the fluxes through its individual glycolytic and fermentative enzymes when confronted with nutrient starvation. Regulation was dissected quantitatively into ( i ) changes in maximum enzyme activity ( V max , called hierarchical regulation) and ( ii ) changes in the interaction of the enzyme with the rest of metabolism (called metabolic regulation). Within a single pathway, the regulation of the fluxes through individual steps varied from fully hierarchical to exclusively metabolic. Existin...

Parasitology, 2010

SUMMARYAfrican trypanosomes have emerged as promising unicellular model organisms for the next ge... more SUMMARYAfrican trypanosomes have emerged as promising unicellular model organisms for the next generation of systems biology. They offer unique advantages, due to their relative simplicity, the availability of all standard genomics techniques and a long history of quantitative research. Reproducible cultivation methods exist for morphologically and physiologically distinct life-cycle stages. The genome has been sequenced, and microarrays, RNA-interference and high-accuracy metabolomics are available. Furthermore, the availability of extensive kinetic data on all glycolytic enzymes has led to the early development of a complete, experiment-based dynamic model of an important biochemical pathway. Here we describe the achievements of trypanosome systems biology so far and outline the necessary steps towards the ambitious aim of creating a ‘Silicon Trypanosome’, a comprehensive, experiment-based, multi-scale mathematical model of trypanosome physiology. We expect that, in the long run, ...

Nature Communications, 2010

The field of systems biology is often held back by difficulties in obtaining comprehensive, highq... more The field of systems biology is often held back by difficulties in obtaining comprehensive, highquality, quantitative data sets. In this paper, we undertook an interlaboratory effort to generate such a data set for a very large number of cellular components in the yeast Saccharomyces cerevisiae, a widely used model organism that is also used in the production of fuels, chemicals, food ingredients and pharmaceuticals. With the current focus on biofuels and sustainability, there is much interest in harnessing this species as a general cell factory. In this study, we characterized two yeast strains, under two standard growth conditions. We ensured the high quality of the experimental data by evaluating a wide range of sampling and analytical techniques. Here we show significant differences in the maximum specific growth rate and biomass yield between the two strains. on the basis of the integrated analysis of the highthroughput data, we hypothesize that differences in phenotype are due to differences in protein metabolism.

FEMS Yeast Research, 2005

A novel method dissecting the regulation of a cellular function into direct metabolic regulation ... more A novel method dissecting the regulation of a cellular function into direct metabolic regulation and hierarchical (e.g., geneexpression) regulation is applied to yeast starved for nitrogen or carbon. Upon nitrogen starvation glucose influx is down-regulated hierarchically. Upon carbon starvation it is down-regulated both metabolically and hierarchically. The method is expounded in terms of its implications for diverse types of regulation. It is also fine-tuned for cases where isoenzymes catalyze the flux through a single metabolic step.

FEBS Letters, 2013

Enzymology tends to focus on highly specific effects of substrates, allosteric modifiers, and pro... more Enzymology tends to focus on highly specific effects of substrates, allosteric modifiers, and products occurring at low concentrations, because these are most informative about the enzyme's catalytic mechanism. We hypothesized that at relatively high in vivo concentrations, important molecular monitors of the state of living cells, such as ATP, affect multiple enzymes of the former and that these interactions have gone unnoticed in enzymology. We test this hypothesis in terms of the effect that ATP, ADP, and AMP might have on the major free-energy delivering pathway of the yeast Saccharomyces cerevisiae. Assaying cell-free extracts, we collected a comprehensive set of quantitative kinetic data concerning the enzymes of the glycolytic and the ethanol fermentation pathways. We determined systematically the extent to which the enzyme activities depend on the concentrations of the adenine nucleotides. We found that the effects of the adenine nucleotides on enzymes catalysing reactions in which they are not directly involved as substrate or product, are substantial. This includes effects on the Michaelis-Menten constants, adding new perspective on these, 100 years after their introduction.