Application of HMM to the Study of Three-Dimensional Protein Structure

Reynès, Christelle; Regad, Leslie; Pérot, Stéphanie; Camproux, Anne‐Claude

doi:10.5772/14503

Cited by 1 publication

(1 citation statement)

References 43 publications

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“…The presence of EF-hand calcium-binding motifs in CDPK sequences ( Supplementary Table S1) was predicted using six different methods: Pfam [26], SMART [27], Prosite [28] and PatternScan through the software InterProScan [29] (http://www.ebi.ac.uk/Tools/pfa/iprscan/), Blocks Searcher [30] (http://blocks.fhcrc.org/blocks/blocks_search.html) and a prediction method recently developed, based on a structural alphabet [31,32]. From the prediction results, a consensus score s has been assigned for each calcium-binding site as follows: s = 0 if a maximum of two methods predict the binding site, s = 2 if three or four methods predict the binding site, and s = 5 if five or six methods predict the binding site.…”

Section: Prediction Of Calcium-binding Motifsmentioning

confidence: 99%

Characterization of Arabidopsis calcium-dependent protein kinases: activated or not by calcium?

Boudsocq

Droillard

Regad

et al. 2012

Biochemical Journal

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120

109

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CDPKs (calcium-dependent protein kinases), which contain both calmodulin-like calcium binding and serine/threonine protein kinase domains, are only present in plants and some protozoans. Upon activation by a stimulus, they transduce the signal through phosphorylation cascades to induce downstream responses, including transcriptional regulation. To understand the functional specificities of CDPKs, 14 Arabidopsis CPKs (CDPKs in plants) representative of the three main subgroups were characterized at the biochemical level, using HA (haemagglutinin)-tagged CPKs expressed in planta. Most of them were partially or mainly associated with membranes, in agreement with acylation predictions. Importantly, CPKs displayed highly variable calcium-dependences for their kinase activities: seven CPKs from subgroups 1 and 2 were clearly sensitive to calcium with different intensities, whereas six CPKs from subgroup 3 exhibited low or no calcium sensitivity to two generic substrates. Interestingly, this apparent calcium-independence correlated with significant alterations in the predicted EF-hands of these kinases, although they all bound calcium. The noticeable exception, CPK25, was calcium-independent owing to the absence of functional EF-hands. Taken together, the results of the present study suggest that calcium binding differentially affects CDPK isoforms that may be activated by distinct molecular mechanisms.

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