Revealing the Set of Mutually Correlated Positions for the Protein Families of Immunoglobulin Fold

Article type: Research Article

Authors: Galitsky, Boris

Affiliations: Knowledge-Trail, Inc, 9 Charles Street, Natick, MA 01760, USA. E-mail: galitsky@dcs.bbk.ac.uk; 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

Journal: In Silico Biology, vol. 3, no. 3, pp. 241-264, 2003