6 Molecular Evolution Within Protease Family C2, or Calpains Liudmila Lysenko and Nina Nemova Institute of Biology, KarRC of Russian Academy of Science Russian Federation 1. Introduction Calpains, or the intracellular Ca 2+ -dependent proteases (EC 3.4.22.17, family C2, cysteine protease clan CA) are one of the most important proteolytic systems in cytosol of eukaryotic and some prokaryotic cells (reviews: Croall & DeMartino, 1991; Goll et al., 2003; Sorimachi et al., 2011a). Calpain family is ancient and diverse since highly variable modules flanking conservative proteolytic core are found in the structure of these proteins. Linking of protease catalytic domain with ancillary domains, i.e. specialized functional modules with their own spectrum of non-proteolytic activities and binding partners, expands calpain functions on multiple cellular processes. Calpains are processing proteases cleaving their specific substrates at one or a limited number of sites to modulate their structure and activity rather than degrade it. Calpains are versatile proteases that have been implicated in diverse cellular signaling pathways mediated by calcium, such as cytoskeleton remodeling, cell-cycle regulation, differentiation, and death (Croall & DeMartino, 1991; Carafoli & Molinari, 1998; Goll et al., 2003; Nemova et al., 2010). Calpains were also considered to participate in chromosome rearrangements during mitosis (Schollmeyer, 1988), microtubule assembly and disassembly (Billger et al., 1988), intracellular signaling, motility, and vesicle traffic (Choi et al., 1997; Huttenlocher et al., 1997; Lu et al., 2002; Li & Iyengar, 2002). In mammals and plants it is clear that calpains are of critical importance for development (Wang et al., 2003; Dutt et al., 2006; Sorimachi et al., 2010). Furthermore, impaired calpain activity due to mutations or misregulation of the calpains has been implicated in a variety of pathological conditions including muscular dystrophy, ischemia, diabetes mellitus, cancer, and neurodegenerative disease (Tidball & Spencer, 2000; Huang & Wang, 2001; Crocker et al., 2003; Mamoune et al., 2003; Suzuki et al., 2004; Zatz & Starling, 2005). Calpains have attracted much attention because of the recent discovery of correlations between calpain gene mutations and human diseases, together with elucidation of its three-dimensional structure (Hosfield et al., 1999; Strobl et al., 2000) and Ca 2+ -induced activation mechanisms (Moldoveanu et al., 2002; 2004). Because the enzyme participates not only in normal intracellular signal transduction cascades but also in various pathological states, calpain research has attracted tremendous interest in wide areas of life sciences in both basic and clinical terms. 2. Distribution and diversity of calpains A variety of identified sequences of calpains and calpain-like polypeptides was found in all eukaryotes and a few bacteria since 1964 when the first protein of this family (later named