From Enzymology to Systems Biology and Back

7th Beilstein ESCEC Symposium 2015

14 18 September 2015

Hotel Jagdschloss Niederwald, Rüdesheim, Germany

Scientific Program: Carsten Kettner and Martin G. Hicks

Introduction

About twenty years ago, systems biology was far away from modeling large metabolic networks due to insufficient computational power to go beyond modeling the reaction kinetics of individual enzymes.
Today, after the enormous increases in the speed of computation and growth in data storage capabilities, systems biology is approaching its goal to be able to investigate complex biological systems be it individual cells, tissues, organs or even whole organisms. Furthermore, in systems biology, modeling of pathways not only includes single enzyme reaction kinetics but also higher-level controlling processes such as gene regulation and signal transduction making the in-silico reconstruction of such heterogeneous networks significantly more complicated.

However, these network studies strongly depend on the availability of interpretable and reliable data from mechanistic studies of enzyme activities, insights in gene regulation and from investigations of inter- and intracellular signaling. Systematic metabolic pathway studies require a well-founded mechanistic understanding supported by experimental data on single enzymes. The lack of this data has meant that researchers have often moved their focus to the study of the metabolom and reaction products. Studies from metabolic flux analysis have shown that calculated flux rates using metabolic models are relatively insensitive to large errors in kinetic parameters for most enzymes [1], thus justifying the use of metabolomics until better data becomes available. In addition, since large amounts of kinetic data are stored in databases such as BRENDA or SABIO-RK, applying mathematical quantification methods (e.g. as described by Liebermeister and Klipp [2,3]) to the value distributions of these parameters for particular reactions and specific organisms, allows determination of a set of data which can be used in dynamic pathway simulations.

Whilst modelling methods, such as those described above, are able to give very useful insights and be used to make predictions, they are nevertheless, not good enough to avoid the necessity to produce more accurate and comprehensive experimental data [4]. For example, time-resolved measurements allowing insights in the mechanistic activities of individual enzymes during the catalysis of chemical reactions lead to an increased understanding of correlations between conformational changes and chemical processes in temporal order which is extremely important for further progress in developing models and understanding events on single site in the protein.

Furthermore, additional experimental data with increased depth and accuracy will help to address current questions in health care and biotechnology. Developments in industrial biotechnology have shown that the design and redesign of enzyme catalysts requires sound modeling based on reliable structural-mechanistic knowledge.

The ESCEC Symposia embrace structural, computational and biological disciplines, and bring researchers (established and younger workers) together to discuss the limits and challenges of systems biology, considering where and when the mechanistic view should be favoured over the holistic one and how this discipline is making new and valuable discoveries.
This conference series also provides a platform to discuss standards in biochemistry in general and the STRENDA Guidelines in particular, aiming to improve the quality of data reporting in the scientific literature. All participants are invited to discuss latest results, approaches and methodologies in experimental, theoretic and bioinformatics enzymology.

 

 

 

 

[1] Cornish-Bowden, A. and Hofmeyr, J.-H.S. (2005) Kinetic characterization of enzymes for sytstems biology. The Biochemist, pp 11-14.

[2] Liebermeister, W. and Klipp, E. (2006) Bringing metabolic networks to life: integration of kinetic, metabolic and proteomic data. Theor. Biol. Med. Mode 3:42.

[3] Liebermeister, W. (2008) Validity and combination of biochemical models. In: Proceedings of the 3rd Beilstein ESCEC Symposium (Eds. Hicks, M.G. and Kettner, C.). Logos-Verlag, Berlin, pp. 163 – 179. http://www.beilstein-institut.de/download/656/liebermeister.pdf

[4] Cvijovic, M., Almquiest, J., Hagmar, J., Hohmann, S., Kaltenbach, H.-M., Klipp, E., Krantz, M.-, Mendes, P., Nelander, S., et al. (2014) Bridging the gaps in systems biology. Mol. Genet. Genomics 289(5):727-34.

Aspects covered by this symposium

  • Enzyme mediated cascade reactions
  • Protein engineering by directed evolution and/or rational design
  • Metabolomics and systems biology
  • Application of systems biology in the "coloured" biotechnologies (green, red, blue)
  • Manufacturing of chemical products using biocatalysis
  • Data analysis, storage and sharing

Summary

by Elisabeth Davioud-Charvet, Université de Strasbourg, France and

Peter Halling, University of Strathclyde, Glasgow, UK

The ESCEC symposia brought together the scientific communities working in biological chemistry, and enzymology to systems biology (and even back). Established and younger researchers from a wide range of areas - often outside chemistry - were invited to present the most advanced aspects of their work, with the aim of enhancing interdisciplinary communication and sharing new ideas and inspirations.

Enzymology

Pedro Martins (Porto) described a new mathematical treatment of the simple Henri-Michaelis-Menten-Briggs-Haldane kinetic network, avoiding the steady-state and other approximations. Oliver Ebenhöh (Dusseldorf) presented an investigation of starch synthesis and degradation processes along with mechanistic aspects of the enzymic reactions taking place at the granule surface. Amnon Kohen (Iowa) showed the value of measuring kinetic isotope effects, their temperature dependence, in understanding enzyme mechanisms. Shelley Copley (Boulder) showed how evolutionary change can be rapid and effective in microrganisms. Reinhard Sterner (Regensburg) described an enzyme, whose sequence was expected to be similar to that found in the last universal common ancestor. It functioned as an apparently quite sophisticated enzyme, suggesting that many fundamental properties had already been near optimised some 4 billion years ago. Manfred Konrad (Göttingen) presented a different practical application of enzymes in medicine, i.e. L-asparaginase as an effective treatment for various leukemias. Douglas Auld (Cambridge) presented the misinterpretation issue raised by high throughput inhibitor screening using luciferase-based reporter-gene assays for drug discovery. The comprehensive analysis allowed to set up dual luciferase-based reporter gene assays. Christian P. Whitman (Austin) reviewed the kinetic/structural/evolutionary mechanism of the hydratase-aldolase-enzymes of the bacterial meta fission pathway. Ming-Daw Tsai (Taipei) presented detailed studies on a viral DNA polymerase displaying significant mutagenic formation of G:G base pairs. Friedrich Förster (Martinsried) developed an algorithm for cryoelectron tomography to classify and then average shapes of different particles to study the function of large complexes (ribosome and proteasome).

Biocatalysis has emerged as a new field between modern enzymology and green chemistry. A session was dedicated to the most recent advanced biocatalytic processes for large scale preparation of valuable compounds of interest. Selection of enzyme variants as biocatalysts is the challenge of modern industry to produce valuable pharmaceuticals and agrochemicals, with high chemo-and stereo-selectivity, by low cost and green chemistry.

Daniel Mink (Geleen) reviewed the industrial enzymatic C-C bond biotransformations used by DSM Company for the cost-effective manufacturing of homochiral buiding-blocks. Selected key examples were presented to illustrate how the platform of biosynthetic engineering of wild-type enzymes can select mutants to build C-C bonds with high enantio- and diastero-selectivity from cheap chemicals under mild conditions. In the same vein, Dörte Rother (Jülich) showed how the combination of three classes of enzymes (wild-type and variants), catalyzing multi-step reactions in cascade, can be used to produce chiral buiding-blocks in a high yielding modular approach from inexpensive starting chemicals. Anthony Green (Manchester) presented examples of synthetic routes to produce high-value bio-inspired chemicals applied to natural product and medicinal chemistry.

Metabolomics, Proteomics, and Systems Biology are the emerging fields to study the complexity of large networks in individual cells and tissues, organs and in the whole organisms.

Monica Campillos (München) showed how new approaches to study systems biology of small molecules led to significant insights on the comprehensive interplay between mode of action of drugs – their phenotypic effects – and their roles in diseases. From various databases of small molecules, analysis of chemical genetics data allowed prediction of drug side-effects by integration of drug symptoms related to disease symptoms, of mouse genes related to mouse phenotypes, and disease symptoms related to drug-gene relationships. Barbara M. Bakker (Groningen) demonstrated how molecular competition at the enzyme level of the fatty acid oxidation pathway might explain the patient physiology with severe fatty-acid disorders found in the metabolic syndrome. Johann M. Rohwer (Stellenbosch) showed how modeling redox networks place the kinetics of cellular redox processes into a systems biology context. Redox systems should be modeled as redox couples with mass action model. Ulrike Kusebauch (Seattle) developed the recent advances in mass spectrometry techniques, resources, and tools to allow comprehensive quantitative proteomics. Olaf Wolkenhauer (Rostock) opened our horizons with the modeling of life complexicity at multi-levelness applied to the self-organization of the tissues. There is a functional organization of the tissues via interplay between gene, cell and tissue functions, which governs a progressive cell-to-tissue determination (emergence), and regressive determination coordination.

Scientific Program

Enzyme Function Initiative:
Tools and Strategies for Discovering Novel Enzymes & Metabolic Pathways
John A. Gerlt, University of Illinois, Urbana-Champaign

Finding Homes for Orphan Enzymes
Frank M. Raushel, Texas A&M University, College Station

Poster Session #1
Oral Poster Presentations

In Search of Lost Time Constants and of non-Michaelis-Menten Parameters
Pedro M. Martins, Universidade do Porto

Specificity and Promiscuity in Enzyme Superfamilies
Karen N. Allen, Boston University

The STRENDA Presentation
The STRENDA Commission

The Reactome Pathways Project
Henning Hermjakob, European Bioinformatics Institute, Cambridge

Evidence for the Existence of Elaborate Enzyme Complexes in the LUCA Era
Reinhard Sterner, University of Regensburg

E. coli can Navigate a Rugged Fitness Landscpae to Reconstitute PLP Synthesis within 320 Generations after Deletion of pdxB - How?
Shelley D. Copley, University of Colorado, Boulder

Enzymatic Activites in Microcapsules and Microfluidic Droplets
Manfred Konrad, MPI for Biophysical Chemistry, Göttingen

Impact of Luciferase Reporter Enzymes on Drug Discovery Efforts
Douglas Auld, Novartis Institutes of Biomedical Research, Cambridge, MA

Industrial Enzymatic C-C Bond Formation
Daniel Mink, Royal DSM, Geleen

Poster/Software Session #2
Oral Poster and Software Presentations

Modular Synthetic Enzyme Cascades for the Production of Pharmaceutically Potent Chiral Building Blocks
Dörte Rother, Forschungszentrum Jülich

The Hydratase/Aldolase-catalyzed Reactions in the Bacterial Degradation of Polycyclic Aromatic Hydrocarbons: Analysis and Implications
Christian P. Whitman, University of Texas at Austin

Biocatalytic Retrosynthesis: Redesignin Synthetic Routes to High-value Chemicals
Anthony Green, University of Manchester

Systems Biology of Small Molecules
Monica Campillos, Helmholtz Zentrum München

Living on the Edge: Molecular Competition Explains Loss of Robustness in Fatty-acid Oxidation Disorders
Barbara M. Bakker, University Medical Center Groningen

Optimality Principles in Plants: Towards Synthetic Starch
Oliver Ebenhoeh, Heinrich-Heine University Dusseldorf

Abstraction as an Approach to Infer Organizing Principles from Cellular Processes
Olaf Wolkenhauer, University of Rostock

Modelling Redoxin Networks: Placing the Kinetics of Cellular Redox Processes into a Systems Biology Context
Johann M. Rohwer, University of Stellenbosch

Development of Comprehensive Quantitative Proteome Resources
Ulrike Kusebauch, Institute for Systems Biology, Seattle

The Enigmatic Conservation of Enzyme Dynamics in Evolution
Amnon Kohen, The University of Iowa, Iowa City

How some Low-fidelity DNA Polymerases Choose non-Watson-Crick from Watson-Crick Incorporation
Ming-Daw Tsai, Academia Sinica, Taipei

Analyzing the Co-translational Protein Translocation Machinery in situ Using Cryo-electron Tomography
Friedrich Förster, MPI for Biochemistry, Martinsried

Oral Poster Presentations

Gilles Curien / D-Phy-Chloro Team, CNRS, UMR 5168, Laboratoire de Physiologie Cellulaire et Végétale, Grenoble, France

Ulrike Wittig / Heidelberg Institute for THeoretical Studies (HITS), Germany

Elisabeth Davioud-Charvet / UMR 7509, CNRS-Université de Strasbourg, European School of Chemistry, Polymers and Materials, Strasbourg, France

Neil Swainston / Centre for Synthetic Biology of Fine and Speciality Chemicals, The University of Manchester, UK

Photo Gallery

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