Affiliations: Knowledge-Trail, Inc, 9 Charles Street, Natick, MA
01760, USA. E-mail: [email protected]; URL:
http://www.dcs.bbk.ac.uk/~galitsky
Abstract: In this study, I explain the observation that a rather limited
number of residues (about 10) establishes the immunoglobulin fold for the
sequences of about 100 residues. Immunoglobulin fold proteins (IgF) comprise
SCOP protein superfamilies with rather different functions and with less than
10% sequence identity; their alignment can be accomplished only taking into
account the 3D structure. Therefore, I believe that discovering the additional
common features of the sequences is necessary to explain the existence of a
common fold for these SCOP superfamilies. We propose a method for analysis of
pair-wise interconnections between residues of the multiple sequence alignment
which helps us to reveal the set of mutually correlated positions, inherent to
almost every superfamily of this protein fold. Hence, the set of constant
positions (comprising the hydrophobic common core) and the set of variable but
mutually correlated ones can serve as a basis of having the common 3D structure
for rather distinct protein sequences.
Keywords: protein sequence and structure, immunoglobulin fold, pair-wise correlation of sequence residues