Computational Biology CB_W0009

Title : Experimental and computational approaches for the study of calmodulin interactions
Author : A.S.N. Reddy a,?, Asa Ben-Hur b, Irene S. Day a
Year : 2011
Place of publish : ELSEVIER
Abstract :

 Ca2+, a universal messenger in eukaryotes, plays a major role in signaling pathways that control many
growth and developmental processes in plants as well as their responses to various biotic and abiotic
stresses. Cellular changes in Ca2+ in response to diverse signals are recognized by protein sensors that
either have their activity modulated or that interact with other proteins and modulate their activity. Calmodulins
(CaMs) and CaM-like proteins (CMLs) are Ca2+ sensors that have no enzymatic activity of their
own but upon binding Ca2+ interact and modulate the activity of other proteins involved in a large number
of plant processes. Protein–protein interactions play a key role in Ca2+/CaM-mediated in signaling
pathways. In this review, using CaM as an example, we discuss various experimental approaches and
computational tools to identify protein–protein interactions. During the last two decades hundreds of
CaM-binding proteins in plants have been identified using a variety of approaches ranging from simple
screening of expression libraries with labeled CaM to high-throughput screens using protein chips. However,
the high-throughput methods have not been applied to the entire proteome of any plant system.
Nevertheless, the data provided by these screens allows the development of computational tools to predict
CaM-interacting proteins. Using all known binding sites of CaM, we developed a computational
method that predicted over 700 high confidence CaM interactors in the Arabidopsis proteome. Most
(>600) of these are not known to bind calmodulin, suggesting that there are likely many more CaM targets
than previously known. Functional analyses of some of the experimentally identified Ca2+ sensor target
proteins have uncovered their precise role in Ca2+-mediated processes. Further studies on identifying
novel targets of CaM and CMLs and generating their interaction network – ‘‘calcium sensor interactome’’
– will help us in understanding how Ca2+ regulates a myriad of cellular and physiological processes.
2011 Elsevier Ltd. All rights reserved.