Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure.

ABSTRACT: Patterns of alternation of hydrophobic and polar residues are a profound aspect of amino acid sequences, but a feature not easily interpreted for soluble proteins. Here we report statistics of hydrophobicity patterns in proteins of known structure in a current protein database as compared with results from earlier, more limited structure sets. Previous studies indicated that long hydrophobic runs, common in membrane proteins, are underrepresented in soluble proteins. Long runs of hydrophobic residues remain significantly underrepresented in soluble proteins, with none longer than 16 residues observed. These long runs most commonly occur as buried alpha helices, with extended hydrophobic strands less common. Avoiding aggregation of partially folded intermediates during intracellular folding

SUBMITTER: Schwartz R 

PROVIDER: S-EPMC2242367 | biostudies-literature | 2006 Jan

REPOSITORIES: biostudies-literature