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Systematic interpretation of cyclic nucleotide binding studies using KinetXBase
Author(s) -
Schweinsberg Sonja,
Moll Daniela,
Burghardt Nicole C. G.,
Hahnefeld Claudia,
Schwede Frank,
Zimmermann Bastian,
Drewianka Stephan,
Werner Lars,
Kleinjung Frank,
Genieser HansGottfried,
Schuchhardt Johannes,
Herberg Friedrich W.
Publication year - 2008
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200700731
Subject(s) - isothermal titration calorimetry , computational biology , protein–protein interaction , surface plasmon resonance , allosteric regulation , protein kinase a , chemistry , computer science , biophysics , biology , biochemistry , nanotechnology , kinase , materials science , enzyme , nanoparticle
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.