Hydrophobic moments of protein structures: spatially profiling the distribution.
It is generally accepted that globular proteins fold with a hydrophobic core and a hydrophilic exterior. Might the spatial distribution of amino acid hydrophobicity exhibit common features? The hydrophobic profile detailing this distribution from the protein interior to exterior has been examined for 30 relatively diverse structures obtained from the Protein Data Bank, for 3 proteins of the 30S ribosomal subunit, and for a simple set of 14 decoys. A second-order hydrophobic moment has provided a simple measure of the spatial variation. Shapes of the calculated spatial profiles of all native structures have been found to be comparable. Consequently, profile shapes as well as particular profile features should assist in validating predicted protein structures and in discriminating between different protein-folding pathways. The spatial profiles of the 14 decoys are clearly distinguished from the profiles of their native structures.
Silverman
B D
BD
IBM Thomas J. Watson Research Center, P.O. Box 218, Yorktown Heights, NY 10598, USA. silverma@us.ibm.com
D000596:Amino Acids / Q000032:analysis / Q000737:chemistry; D019295:Computational Biology; D016384:Consensus Sequence; D019992:Databases as Topic; D008958:Models, Molecular; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D021122:Protein Subunits; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D015203:Reproducibility of Results; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism; D055672:Static Electricity; D013499:Surface Properties
D000596:Amino Acids; D021122:Protein Subunits; D011506:Proteins