Proceedings of the 1st International Beilstein Workshop on EXPERIMENTAL STANDARD CONDITIONS OF ENZYME CHARACTERIZATIONS October, 5th - 8th 2003 Rüdesheim/Rhein, Germany Edited by Martin G. Hicks and Carsten Kettner ESCEC, Oct. 5th - 8th 2003, Rüdesheim, Germany BEILSTEIN-INSTITUT ZUR FÖRDERUNG DER CHEMISCHEN WISSENSCHAFTEN Trakehner Str. 7 – 9 60487 Frankfurt Germany Telephone: +49 (0)69 7167 3211 E-Mail: [email protected] Fax: +49 (0)69 7167 3219 Web-Page: www.beilstein-institut.de IMPRESSUM Experimental Standard Conditions of Enzyme Characterizations, Martin G. Hicks and Carsten Kettner (Eds.), Proceedings of the Beilstein-Institut Workshop, October 5th - 8th 2003, Rüdesheim, Germany. Copyright © 2004 Beilstein-Institut zur Förderung der Chemischen Wissenschaften. Copyright of this compilation by the Beilstein-Institut zur Förderung der Chemischen Wissenschaften. The copyright of specific articles exists with the author(s). 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Bibliographic information published by Die Deutsche Bibliothek Die Deutsche Bibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data is available in the internet at http://dnb.ddb.de ISBN Layout by: Beilstein-Institut Printed by: Logos Verlag Berlin Comeniushof, Gubener Str. 47 Cover Illustration: Joelle Heyer 10243 Berlin Beilstein GmbH Tel: +49 (0) 30 42 85 10 90 Fax: +49 (0) 30 42 85 10 92 Internet: http://www.logos-verlag.de I ESCEC, Oct. 5th - 8th 2003, Rüdesheim, Germany PREFACE The Beilstein Institute organises and sponsors scientific meetings, workshops and seminars, with the aim to catalyse advances in chemical and biological science by facilitating the interdisciplinary exchange and communication of ideas amongst the attendees. Functional characterization of enzymes and the subsequent computational analysis and modelling of the cellular metabolism and the interaction of cells within tissues and organs led to the foundation of a new branch within the life sciences called systems biology. At the present time, data from metabolic simulations show broad value ranges with high uncertainty because the accessible experimental data have been obviously generated under non-standardized experimental conditions. Successful biological analysis requires, however, comparable and reliable data from both enzyme and physiological interactions collected under standardized experimental conditions. The standardization or recommendation of experimental conditions firstly needs broad discussions within the scientific community, which hopefully will lead to enough common acceptance so that each researcher will carry out his/her experiments in accord with these recommendations. Participants, as well as speakers were confronted with the following complex questions from experimental and theoretical enzymology: - are any standards used in the field of functional characterization of enzymes? - are there any standard procedures or instructions for experimental conditions? - is it possible to define laboratory procedures for common use? - do current repositories for enzyme characterization data meet the demands of users? - which data types for metabolic simulations are necessary? -are there any demands for the transfer of standardized experimental data to journals or databases? Over the three days of the workshop, the participants not only heard excellent talks, took part in lively discussions, but in the time between the official sessions of the scientific program, exchanged ideas and thoughts and generally made a valuable and personal contribution to find a way out of the dilemma mentioned above. Whilst this meeting did not find answers to all questions, it succeeded in initiating a dialog between scientists from the different areas of enzymology. One notable outcome is the foundation of the STRENDA commission (see also http://www.strenda.org) under the auspices of the Beilstein-Institut. http://www.beilstein-institut.de/escec2003/proceedings/Preface.pdf II Preface We would like to thank particularly the authors who provided us with written versions of the papers that they presented. Special thanks also to all those involved with the preparation and organization of the workshop, to the chairmen who directed us successfully through the sessions, and to the speakers and participants for their contribution in making this workshop a success. Frankfurt/Main, October 2004 Martin G. Hicks Carsten Kettner III ESCEC, Oct. 5th - 8th 2003, Rüdesheim, Germany CONTENTS Page Kettner, C. and Hicks, M.G. Chaos in the World of Enzymes - How Valid is Functional Characterization without Methodological Experimental Data?.............................................................................. 1 Boyce, S., Tipton, K. and McDonald, A.G. Extending Enzyme Classification with Metabolic and Kinetic Data: Some Difficulties to be Resolved................................................................................... 17 Bock, H.G., Körkel, S., Kostina, E. and Schlöder, J.P. Methods of Design of Optimal Experiments with Application to Parameter Estimation in Enzyme Catalytic Processes .................................................................... 45 Fernie, A.R. and Sweetlove, L.J. Borad-Range Metabolite Analysis: Integration into Genomic Programs ...................... 71 Schlüter, H., Jankowski, J., Thieman, A., Rykl, J., Kurzawski, S. and Runge D. Determination of Enzyme Activities by Mass Spectrometry - Benefits and Limitations ................................................................................................ 87 Holzhütter, H.-G. Studying Enzyme Kinetics by Means of Progress-Curve Analysis ............................... 99 Schuster, S. and Zevedei-Oancea, I. Multifunctional Enzymes and Pathway Modelling........................................................ 115 Snoep, J.L. Olivier, B.G. and Westerhoff, H.V. JES Online Cellular Systems Modelling and the Silicon Cell ....................................... 129 Degtyarenko, K. Controlled Vocabularies and Ontologies in Enzymology .............................................. 143 Andreassi, J.L. and Leyh, T. Profiles of Molecular Function - Genomic Enzymology............................................... 175 http://www.beilstein-institut.de/escec2003/proceedings/Contents.pdf IV ESCEC, Oct. 5th - 8th 2003, Rüdesheim, Germany Schomburg, I., Chang, A., Ebeling, C., Huhn, G., Hofmann, O. and Schomburg, D. Experimental Enzyme Data as Presented in BRENDA - a Database for Metabolic Research, Enzyme Technology and Systems Biology ................................................... 185 Cammack, R. Systematic Names for Systems Biology ........................................................................ 203 Biographies ................................................................................................................... 215 Index .............................................................................................................................. 225 1 ESCEC, Oct. 5th - 8th 2003, Rüdesheim, Germany CHAOS IN THE WORLD OF ENZMYES - HOW VALID IS FUNCTIONAL CHARACTERIZATION WITHOUT METHODOLOGICAL EXPERIMENTAL DATA? CARSTEN KETTNER AND MARTIN G. HICKS Beilstein-Institut, D-60487 Frankfurt/Main, Germany E-Mail: [email protected] Received: 15th April 2004 / Published: 1st Ocotber 2004 ABSTRACT Functional characterization of enzymes plays an essential role in one of the major aims of proteomics research: the modelling of sections of the cellular metabolism with a view to being able to model the whole cellular metabolism and the interaction of cells within tissues and organs. With these purposes in mind, the scientific community established a new branch within the life sciences, called systems biology. However, meaningful modelling by necessity requires comparable and reliable data from standardized enzyme characterizations. From a short, but detailed, investigation of the BRENDA database, it is shown here that the quality of experimental data of enzymes is insufficient for the needs of theoretical biology. The first step to remedy the situation is to ensure that measurements carried out on enzymes are done so under standard conditions and that all the important information is recorded. With the aim of arriving at an acceptable set of recommendations for experimental conditions, the Beilstein Institut has initiated broad discussions within the scientific community and is further willing to organize and present them as long as appropriate and there is sufficient support. http://www.beilstein-institut.de/ESCEC2003/proceedings/Kettner/Kettner.pdf 2 Kettner, C. & Hicks, M.G. QUO VADIS, SYSTEMS BIOLOGY? Continuous advances and improvements have enabled proteome analyses to proceed with increased depth and efficiency. However, whilst the large international genome sequencing projects elicited considerable public attention with the creation of huge sequence databases, it has become increasingly apparent that functional