title: Systematic interpretation of cyclic nucleotide binding studies using KinetXBase.
abstract: 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.
authors.affiliation: Department of Biochemistry, University of Kassel, Kassel, Germany.
authors.forename: Sonja
authors.initials: S
authors.lastname: Schweinsberg
authors.forename: Daniela
authors.initials: D
authors.lastname: Moll
authors.forename: Nicole C G
authors.initials: NC
authors.lastname: Burghardt
authors.forename: Claudia
authors.initials: C
authors.lastname: Hahnefeld
authors.forename: Frank
authors.initials: F
authors.lastname: Schwede
authors.forename: Bastian
authors.initials: B
authors.lastname: Zimmermann
authors.forename: Stephan
authors.initials: S
authors.lastname: Drewianka
authors.forename: Lars
authors.initials: L
authors.lastname: Werner
authors.forename: Frank
authors.initials: F
authors.lastname: Kleinjung
authors.forename: Hans-Gottfried
authors.initials: HG
authors.lastname: Genieser
authors.forename: Johannes
authors.initials: J
authors.lastname: Schuchhardt
authors.forename: Friedrich W
authors.initials: FW
authors.lastname: Herberg
mesh_terms: D019295:Computational Biology / Q000379:methods; D000242:Cyclic AMP / Q000378:metabolism*; D017868:Cyclic AMP-Dependent Protein Kinases / Q000378:metabolism*; D011485:Protein Binding; D040901:Proteomics / Q000295:instrumentation / Q000379:methods; D012984:Software; D020349:Surface Plasmon Resonance
chemical_list: D000242:Cyclic AMP; D017868:Cyclic AMP-Dependent Protein Kinases