Current Enzyme Inhibition, 2005, 1, 3-10 171 The Dilemma of Modern Functional Enzymology Carsten Kettner * and Martin G. Hicks Beilstein-Institut, 60487 Frankfurt/Main, Germany Abstract: Functional characterization of enzymes plays an essential role in one of the major areas 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. Here we describe the dilemma of modern enzymology which generates functional data from enzymes under non- standardized experimental conditions followed by suggestions how to remedy this situation by initiating broad discussions within the scientific community and introducing to a new initiative, called STRENDA. Keywords: Systems Biology, STRENDA, Functional Enzyme Data, Standardization of Experimental Conditions, Data Reporting. PROTEOMICS MEETS ENZYMOLOGY investigate the activity, reaction mechanism and rates of catalysis of enzymes. In comparison to proteomics, enzymology is an established field that has been making fundamental contributions to medicine and basic science long before structural biological disciplines came into being. The question whether enzymology is part of proteomics is more a question of the definition of proteomics. The term proteomics was first coined about ten years ago and was defined as the large-scale characterization of the entire protein complement of a cell line, tissue or organism [1]. Today, one can encounter two definitions of proteomics: the first being the more classical definition, restricting the large-scale analysis of gene products to studies involving only proteins; the second and broader definition combines protein studies with analyses that have a genetic readout such as mRNA analysis, genomics, and the yeast two-hybrid analysis [2]. However, irrespective of which definition is applied, the goal of proteomics remains the same, i.e. to obtain a comprehensive and integrated view of biology by studying all the proteins of a cell rather than each one individually. One of the challenges of modern enzymology is to generate structure-function relationships where the activity is intimately related to the molecular interactions between substrate molecule and components of the enzyme molecule and where the sequence of these interactions defines the catalytic mechanism. To address the questions of structure- function relationships two powerful collections of methodologies are routinely applied. The one is the use of biophysical probes of protein structure such as X-ray crystallography, NMR and magnetization transfer methods, optical and vibrational spectroscopy for the assessment of the three-dimensional structures of enzymes and ligands bound to the enzyme. The second collection contains molecular biological methods for cloning and heterologously expression of enzymes in foreign host organisms, which allows scientists to study, identified and isolated enzymes, to purify and to characterize them. Further tools of molecular biologists are used to manipulate amino acid sequences, i.e. site-directed mutagenesis or deletional mutagenesis, to pinpoint the chemical groups that are required for ligand binding and subsequent steps of enzyme catalysis. In proteomics it is of central importance to determine not just whether a protein is present but how much of the protein is present and how active it is. The activity of many proteins is regulated by interactions with other proteins that form complexes or catalyze structural modifications. Comprehensive proteomics, therefore, requires not only the determination of the protein functions but also a detailed understanding of protein-protein interactions within a cell and of protein modifications that regulate function, such as phosphorylation, glycosylation, etc. Most proteins are enzymes that catalyze specific chemical reactions. Thus, changes in gene expression are typically accompanied by changes in the levels of many cellular chemicals. The simultaneous measurement of these collective chemical changes is the emerging field of metabolomics. 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 data for the gene products, in particular for enzymes, has either limited accessibility or is not available. The problem is twofold; on the one hand, deriving data from experimental work is expensive and very time consuming. On the other hand, it is inherently very difficult to collect, interpret and standardize published data since they are widely distributed among journals covering a number of fields, and the data itself is It is only a small step from proteomics to enzymology. After proteins have been identified and their functions have been understood, it is then up to the enzymologists to *Address correspondence to this author at the Beilstein-Institut, 60487 Frankfurt/Main, Germany; Tel: +49-69-7167-3221; Fax.: +49-69-7167- 3219; E-Mail: ckettner@beilstein-institut.de 1573-4080/05 $50.00+.00 © 2005 Bentham Science Publishers Ltd.