Protein Structure Meets Enzyme Kinetics

5th Beilstein ESCEC Symposium 2011

12 – 16 September 2011

Hotel Jagdschloss Niederwald, Rüdesheim, Germany

Scientific program: Carsten Kettner and Martin G. Hicks


Proceedings of this Beilstein ESCEC Symposium.


The multi-disciplinary approach of systems biology combines a variety of modern experimental techniques which lead to an increased accuracy of measurements of enzyme structures and activities by the application of advanced analysis methods.

Due to these technological inventions in turn huge amounts of data and large data sets are generated and subsequently published in electronic data repositories and in written papers. However, all these data in both the literature and in databases suffer from the fact that they are incomparable due to incomplete and fragmented descriptions of materials and methods, and therefore are, to some extent, unreliable. Furthermore, if the experimental conditions are not clearly and fully stated, the values of the functional data of enzyme activities are of little use for, in particular, systems biology applications.

Moreover, experimental results have been collected under quite disparate conditions so that researchers often are faced with the problem of the range of method-specific enzyme data. This causes problems when data move between researchers whose data are supplied by laboratories that use different methods, and can, in the worst case, lead to misinterpretations of laboratory findings.

Since 2003 the STRENDA Commission (Standards for Reporting Enzyme Data) is concerned with the improvement of the quality of reporting functional enzyme data to support the community with the efficient application of enzyme kinetics in the in vivo, in vitro and in silico investigation of biological systems. The Commission has two major goals: One is the development of a set of guidelines for the reporting of data in publications. These guidelines have already been adopted by a number of biochemistry journals. The second goal is the development of an electronic data submission tool which incorporates the STRENDA Guidelines, and which is intended to act as a portal for the submission of enzyme kinetics data to a freely accessible, public database.

This 5th ESCEC symposium, organized by the Beilstein-Institut together with the STRENDA Commission, provides a platform to discuss standards in biochemistry in general and the STRENDA Guidelines in particular. The meeting also brings together representatives from diverse standardizations initiatives and systems biology groups such as MIBBI, YSBN, EFB and SYSMO, and the editorial board members from journals. Additionally experts from all fields of experimental, theoretic and bioinformatics enzymology and metabolic network investigation are invited to present and discuss new results, approaches and methodologies.

Aspects covered by this symposium

  • Systems Biology
  • Sequence, Structure and Kinetics
  • Physiological Meaning of Enzyme Kinetics
  • Network Modelling
  • Enzymes in Metabolic Collaboration
  • Pitfalls in Data Reproduction
  • Standard Data Repositories

Scientific Program

Functional Annotation for Members of the Amidohydrolase Superfamily
Frank M. Raushel, Texas A&M University, College Station, TX, USA

Catalysis without Chemistry: Structure and Function of Transmembrane Solute Transporters
Gary Rudnick, Yale University, New Haven, CT, USA

IMP Dehydrogenase: The Dynamics of Reaction Specificity
Lizbeth Hedstrom, Brandeis University, Waltham, MA, USA

Glutathione Reductase-catalyzed Cascade of Redox Reactions to Bioactivate Potent Antimalarial 1,4-Naphtoquinone - A New Strategy to Combat Malarial Parasites
Elisabeth Davioud-Charvet, University of Strasbourg and CNRS, France

Structure and Function of Membran-bound Enzymes Probed with Backbone Amide Hydrogen/Deuterium Exchange Mass Spectrometry
Richard N. Armstrong, Vanderbilt University, Nashville, TN, USA

The pH-induced Metabolic Shift from Acidogenesis to Solventogenesis - From Experiments to Models
Thomas Millat, University of Rockstock, Germany

The EnzymePortal - Unifying Access to EBI's Enzyme-related Resource
Christoph Steinbeck, European Bioinformatics Institute, Cambridge, UK

Slow Enzyme-modifier Interactions. Mechanisms, Physiological and Pharmalogical Significance, Pitfalls and Data Reporting
Antonio Baici, University of Zurich, Switzerland

BioSharing and MIBBI
Christopher F. Taylor, European Bioinformatics Institute, Cambridge, UK

Ontology-based Search in SABIO-RK
Ulrike Wittig, Heidelberg Institut for Theoretical Studies, Germany



Theoretical and Experimental Aspects of Genome-sized Metabolic Models
Dietmar Schomburg, Technical University Braunschweig, Germany

Challenges and Opportunities for Systems Biology in 21st Century Healthcare
Adriano Henney, University of Heidelberg, Germany

Protein Design as a Tool to Study the Relationship between Structure, Function and Stability of a Metabolic Enzyme
Reinhard Sterner, University of Regensburg, Germany

Computational Approaches to Leverage Enzyme Structures to Predict Function
Matthew P. Jacobson, University of California, San Francisco, CA, USA

Successes and Challenges in Functional Assignment in a Superfamily of Phosphatases
Karen N. Allen, Boston University, MA, USA

Functional (Mis)Assignment in the Tomaymycin Biosynthetic Pathway
Christian P. Whitman, The University of Texas at Austin, TX, USA

Enhancing Allosteric Response in Thermus thermophilus Phosphofructokinase
Gregory D. Reinhard, Texas A&M University, College Station, TX, USA

Modelling of an Allostericall-controlled Branched Metabolic Systems
Gilles Curien, CNRS, Grenoble, France

The Role of Mixing Entropy in Carbohydrate Metabolism
Oliver Ebenhoeh, University of Edinburgh, UK

Metal-selectivity in Metal Sensing
Nigel J. Robinson, University of Durham, UK

Metal Binding Sites in Proteins
Vladimir Sobolev, Weizmann Institute of Science, Rehovot, Israel


Oral Poster Presentations

Raphael Alcàntara / European Bioinformatics Institute, Cambridge, UK

Ida Schomburg / Technical University Braunschweig, Germany

Ian Cook / Albert Einstein College of Medicine, Bronx, NY, USA

Sandra Schlee / University of Regensburg, Germany

Monika Meier / University of Regensburg, Germany

Nikhilesh Sanyal / University of Nebraska-Lincoln, Lincoln, NE, USA

Mehran Miroliaei / University of Isfahan, Iran