Systematic interpretation of cyclic nucleotide binding studies using KinetXBase.
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.
Schweinsberg
Sonja
S
Department of Biochemistry, University of Kassel, Kassel, Germany.
Moll
Daniela
D
Burghardt
Nicole C G
NC
Hahnefeld
Claudia
C
Schwede
Frank
F
Zimmermann
Bastian
B
Drewianka
Stephan
S
Werner
Lars
L
Kleinjung
Frank
F
Genieser
Hans-Gottfried
HG
Schuchhardt
Johannes
J
Herberg
Friedrich W
FW
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
D000242:Cyclic AMP; D017868:Cyclic AMP-Dependent Protein Kinases