Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues.

ABSTRACT: Patterns of hydrophobic and hydrophilic residues play a major role in protein folding and function. Long, predominantly hydrophobic strings of 20-22 amino acids each are associated with transmembrane helices and have been used to identify such sequences. Much less attention has been paid to hydrophobic sequences within globular proteins. In prior work on computer simulations of the competition between on-pathway folding and off-pathway aggregate formation, we found that long sequences of consecutive hydrophobic residues promoted aggregation within the model, even controlling for overall hydrophobic content. We report here on an analysis of the frequencies of different lengths of contiguous blocks of hydrophobic residues in a database of amino acid sequences of proteins of known structure.

SUBMITTER: Schwartz R 

PROVIDER: S-EPMC2374206 | biostudies-literature | 2001 May

REPOSITORIES: biostudies-literature