Identification of the Core Aspartic Protease: The Minimal Unit for Aspartic Protease Function

REVUELTA MV; ARJEN TEN HAVE

Buenos AIres

Workshop; Fronteras en Biociencias; 2012

Ministerio de Ciencia, Tecnología e Innovación Productiva y Sociedad Max-Planck

Eukaryotic Aspartic proteases (APs, A01, EC 3.4.23) constitute one of the seven families of proteolytic enzymes that are distinguished. They are classified into the A01A and A01B subfamilies (Rawlings et al., 2010).        To widen our knowledge of AP function, one first needs to make a reliable classification in subfamilies. According to our results, at least eight AP monophyletic subfamilies can be discriminated in the eukaryotic genomes available for screening. Most of the subfamilies are exclusive to fungi, probably as a result of the variety of lifestyles that fungi exhibit. Subsequently one can characterize them by means of comparative genomics. Knowing what parts of the protease correspond to general AP features, and which parts are related to its particular characteristics as a member of a certain subfamily are key points to study in this field. Two types of particular characteristics can be distinguished. First, specialization of function can be the result of specific residues at specific positions. A second cause of specialization is found in the many (surface) loops APs can have. For this reason, we are interested in the hypothetical core of an aspartic protease able to sustain catalytic activity. That knowledge would provide tools to further develop synthetic protein design.       In order to study the AP core, the different AP subfamily loops have to be identified. Sequence Alignment Trimming software, like BMGE (Criscuolo & Gribaldo, 2010), are useful tools to perform that task. The columns that BMGE does not consider overall conserved are mainly subfamily specific loops and are likely not required for protease activity.       Once the core has been described we will intend to determine the most probable residues for each position in the core sequence. Both the knowledge of the minimal AP skeleton and the ancestral sequence features will help understand the basis of aspartic protease function.