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Modeling, predicting and mining metabolism at atom-level resolution

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The Laboratory in a Droplet

Kai Johnsson

In this issue of Chem. & Biol., the groups of Tawfik and Griffiths present fluorescence-activated cell sorting of double emulsions as a generally applicable screen for enzyme activity. This novel methodol. increases the throughput of a typical enzyme scree ...

2005

Computational discovery of biochemical routes to specialty chemicals

Vassily Hatzimanikatis

A computational framework has been developed for the construction and evaluation of metabolic pathways given input substrates and knowledge of enzyme-catalyzed reactions. Application of the framework creates new and existing routes to both chems. known to ...

2004

Metabolic networks: enzyme function and metabolite structure

Vassily Hatzimanikatis

A review and discussion. Metab. is one of the most complex cellular processes. Connections between biochem. reactions via substrate and product metabolites create complex metabolic networks that may be analyzed using network theory, stoichiometric anal., a ...

2004

Metabolic control analysis under uncertainty: Framework development and case studies

Vassily Hatzimanikatis

Information about the enzyme kinetics in a metabolic network will enable understanding of the function of the network and quant. prediction of the network responses to genetic and environmental perturbations. Despite recent advances in exptl. techniques, s ...

2004

A computational framework for the discovery of novel biotransformations

Vassily Hatzimanikatis

The large no. of chem. transformations involved in biochem. pathways and the even larger no. of enzymes that catalyze these transformations contribute to the complexity of biol. systems. Anal. of the available genome sequences, as well as results from prio ...

2003

Quantification and characterization of uncertainty in metabolic engineering

Vassily Hatzimanikatis

One of the central problems in metabolic engineering deals with the identification of the "rate limiting steps", i.e. enzymes whose activities one should manipulate towards the achievement of a desirable performance. However, uncertainty about the kinetic ...

2003

Reaction mechanism of caspases: Insights from QM/MM Car-Parrinello simulations

Ursula Röthlisberger

Caspases are fundamental targets for pharmaceutical interventions in a variety of diseases involving disregulated apoptosis. Here, we present a quantum mechanics/mol. mechanics Car-Parrinello study of key steps of the enzymic reaction for a representative ...

2003

Mixed quantum mechanical/molecular mechanical simulation of biological systems

Ursula Röthlisberger

During the last decade the field of computational chem. has experienced an enormous progress. Due to the exponential increase in computer power and the development of new computational methods it has now become possible to treat many complex chem. and biol ...

2003

The "aryne" route to biaryls featuring uncommon substituent patterns

The reaction of 1-bromo-3-halo-2-iodobenzene (I; X = Cl) with butyllithium gives 62% (II; X = Cl) similarly reaction of [I; X = F(III)] gave 64% II (X = F). These reactions involve the immediate intermediacy of the halolithiobiphenyl (IV) and the penultima ...

2002

Nonlinear metabolic control analysis

Vassily Hatzimanikatis

Math. description of metabolic systems allows the calcn. of the expected responses of metab. to genetic modifications and the identifications of the most promising targets for metabolic engineering. Metabolic control anal. (MCA) provides such a description ...

1999