Systematic interpretation of cyclic nucleotide binding studies using KinetXBase

• Published in: Proteomics (Weinheim) Vol. 8; no. 6; pp. 1212 - 1220
• Main Authors: Schweinsberg, Sonja, Moll, Daniela, Burghardt, Nicole C.G, Hahnefeld, Claudia, Schwede, Frank, Zimmermann, Bastian, Drewianka, Stephan, Werner, Lars, Kleinjung, Frank, Genieser, Hans-Gottfried, Schuchhardt, Johannes, Herberg, Friedrich W
• Format: Journal Article
• Language: English
• Published: Weinheim Wiley-VCH Verlag 01.03.2008; WILEY-VCH Verlag; WILEY‐VCH Verlag
• Subjects: Biomolecular interaction analysis; cAMP dependent protein kinase; Computational Biology - methods; Cyclic AMP - metabolism; Cyclic AMP-Dependent Protein Kinases - metabolism; Functional proteomics; PKA; Protein Binding; Proteomics - instrumentation; Proteomics - methods; Software; Surface Plasmon Resonance
• ISSN: 1615-9853; 1615-9861
• DOI: 10.1002/pmic.200700731

Functional proteomics aims to describe cellular protein networks in depth based on the quantification of molecular interactions. In order to study the interaction of adenosine-3',5'-cyclic monophosphate (cAMP), a general second messenger involved in several intracellular signalling networks, with one of its respective target proteins, the regulatory (R) subunit of cAMP dependent protein kinase (PKA), a number of different methods was employed. These include fluorescence polarisation (FP), isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), amplified luminescence proximity homogeneous assay (ALPHA-screen), radioligand binding or activity-based assays. Kinetic, thermodynamic and equilibrium binding data of a variety of cAMP derivatives to several cAMP binding domains were integrated in a single database system, we called KinetXBase, allowing for very distinct data formats. KinetXBase is a practical data handling system for molecular interaction data of any kind, providing a synopsis of data derived from different technologies. This supports ongoing efforts in the bioinformatics community to devise formal concepts for a unified representation of interaction data, in order to enable their exchange and easy comparison. KinetXBase was applied here to analyse complex cAMP binding data and highly site-specific cAMP analogues could be identified. The software package is free for download by academic users.