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Functional flexibility of human cyclin‐dependent kinase‐2 and its evolutionary conservation
Author(s) -
Bártová Iveta,
Koča Jaroslav,
Otyepka Michal
Publication year - 2008
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.072951208
Subject(s) - cyclin dependent kinase 2 , kinase , biology , computational biology , cyclin dependent kinase complex , function (biology) , cyclin dependent kinase , flexibility (engineering) , microbiology and biotechnology , conserved sequence , biophysics , evolutionary biology , genetics , cell cycle , protein kinase a , peptide sequence , cell , gene , mathematics , statistics
Cyclin‐dependent kinase 2 (CDK2) is the most thoroughly studied of the cyclin‐dependent kinases that regulate essential cellular processes, including the cell cycle, and it has become a model for studies of regulatory mechanisms at the molecular level. This contribution identifies flexible and rigid regions of CDK2 based on temperature B ‐factors acquired from both X‐ray data and molecular dynamics simulations. In addition, the biological relevance of the identified flexible regions and their motions is explored using information from the essential dynamics analysis related to conformational changes of CDK2 and knowledge of its biological function(s). The conserved regions of CMGC protein kinases' primary sequences are located in the most rigid regions identified in our analyses, with the sole exception of the absolutely conserved G13 in the tip of the glycine‐rich loop. The conserved rigid regions are important for nucleotide binding, catalysis, and substrate recognition. In contrast, the most flexible regions correlate with those where large conformational changes occur during CDK2 regulation processes. The rigid regions flank and form a rigid skeleton for the flexible regions, which appear to provide the plasticity required for CDK2 regulation. Unlike the rigid regions (which as mentioned are highly conserved) no evidence of evolutionary conservation was found for the flexible regions.