Protein Engineering, Vol. 15, No. 12, 967-977,
December 2002
© 2002 Oxford University Press
Identification of conserved residue patterns in small ß-barrel proteins
Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500 076, India
Our abilities to predict three-dimensional conformation of a polypeptide, given its amino acid sequence, remain limited despite advances in structure analysis. Analysis of structures and sequences of protein families with similar secondary structural elements, but varying topologies, might help in addressing this problem. We have studied the small ß-barrel class of proteins characterized by four strands (n = 4) and a shear number of 8 (S = 8) to understand the principles of barrel formation. Multiple alignments of the various protein sequences were generated for the analysis. Positional entropy, as a measure of residue conservation, indicated conservation of non-polar residues at the core positions. The presence of a type II ß-turn among the various barrel proteins considered was another strikingly invariant feature. A conserved glycyl-aspartyl dipeptide at the ß-turn appeared to be important in guiding the protein sequence into the barrel fold. Molecular dynamics simulations of the type II ß-turn peptide suggested that aspartate is a key residue in the folding of the protein sequence into the barrel. Our study suggests that the conserved type II ß-turn and the non-polar residues in the barrel core are crucial for the folding of the protein’s primary sequence into the ß-barrel conformation.
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