Book of Abstracts: Albany 2005
Protein Modules: The Closed Loop Prototype Database
Series of works by Berezovsky et al. has suggested that proteins in early evolution has gone through a stage of closed loop elements with a typical contour size of 25-35 residues. These closed loops are still the elementary protein units to these days, and can be used to spell out protein sequence and structure in the alphabet of a relatively small number of protein prototypes.
In this study we aimed to identify the sequences that are used to lock the loop ends to one another, and to show how an extensive dictionary of such locking pairs can be created using positional correlation data from a large proteome database, and structural data from PDB databases.
The modules identified by this locking pair motifs correlation analysis are added to a growing list of the prototype elements derived by other techniques, and a comprehensive database consisting of the prototype elements in the form of closed loops is constructed. Few examples of these sequence-structure prototype elements (along with their simple consensus sequences) are presented in the figure below.
This database of elementary protein units can be extremely usefull in reconstructing the evolutionary pathway modern proteins have gone through in the distant past, as well as in identifying structural closed loop elements in proteins whose 3D structure is yet unknown, thus paving the way for sequence based protein structuture prediction.
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