Title: Magnitude and spatial orientation of the hydrophobic moments of multi-domain proteins

Authors: Ruhong Zhou, Ajay Royyuru, Prasanna Athma, Frank Suits, B. David Silverman

Addresses: IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA. ' IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA. ' IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA. ' IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA. ' IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA

Abstract: The distributions of residue hydrophobicity for individual domains as well as for the aggregates of domains on a single chain have been found to exhibit well-defined second-order hydrophobic moment profiles. This indicates that most of the domains do fold into a stable entity with a core composed predominantly of hydrophobic residues as well as a prevalence of hydrophobic residues at the interface between domains. A simple scoring function based upon the relative hydrophobic moment dipole orientations shows that 80% of the dipoles of adjacent domains point to each other, highlighting hydrophobic residue prevalence at the domain interfaces.

Keywords: amino acid hydrophobicity; hydrophobic moments; spatial orientation; hydrophobic ratio; multi-domain proteins; hydrophobic residues; dipoles; domain interfaces; multi-domain protein folding; bioinformatics.

DOI: 10.1504/IJBRA.2006.009766

International Journal of Bioinformatics Research and Applications, 2006 Vol.2 No.2, pp.161 - 176

Published online: 09 May 2006 *

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