Affiliations: National Centre for Biological Sciences, UAS-GKVK
campus, Bellary Road, Bangalore 560 065, India | Avinashalingam Institute, Coimbatore 641 043,
India
Abstract: The presence of sequence homologues and the availability of
structural information of proteins enable better understanding of the
biological function of a protein family. A majority of entries in protein
structural databank are single member superfamilies for which it is hard to
derive motifs due to the paucity of structural homologues. Important conserved
segments for these superfamilies have been identified and compiled into a
database, SSToSS (Sequence Structural Templates of Single member Superfamily).
Conserved regions, recognized by permitted amino acid exchanges, are mapped on
the structure and various structural features (solvent accessibility, secondary
structure content, hydrogen bonding and residue packing) are examined. These
conserved segments with high structural feature content are projected as
sequence-structural templates for the particular superfamily member.
Interactive three-dimensional displays of the templates in three-dimensional
structure (in Chime® and RASMOL) are
provided for better understanding and visualization. In SSToSS database, we
also provide the application of sequence-structural templates in three
different areas: multiple-motif based sequence search, multiple sequence
alignment and homology modeling. In each case, the inclusion of the
sequence-structural templates can give rise to sensitive and accurate results.
This enables the inclusion of singletons to provide added value to the
recognition of additional members, comparative modeling and in designing
experiments.
Keywords: Conserved regions, motif-based database search, comparative modeling, spatial orientation of motifs, superfamily signatures, distant similarity, protein structure prediction
