ArticleProtein science : a publication of the Protein Society2006
Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure.
Article in Protein science : a publication of the Protein Society, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Increased sequence hydrophobicity reduces conformational specificity: A mutational case study of the Arc repressor protein.Proteins · 2019Article
- The Relation between α-Helical Conformation and Amyloidogenicity.Biophysical journal · 2018Article
- The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins.Bioinformatics and biology insights · 2014Article
- A polymetamorphic protein.Protein science : a publication of the Protein Society · 2013Article
- Amyloidogenic sequences in native protein structures.Protein science : a publication of the Protein Society · 2010Article
- Sequence periodicity and secondary structure propensity in model proteins.Protein science : a publication of the Protein Society · 2010Article
- Folding by numbers: primary sequence statistics and their use in studying protein folding.International journal of molecular sciences · 2009Review
- The distribution of residues in a polypeptide sequence is a determinant of aggregation optimized by evolution.Biophysical journal · 2007Article
- Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
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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 remains a viable explanation for the rarity of long hydrophobic runs in soluble proteins. Comparison between database editions reveals robustness of statistics on aqueous proteins despite an approximately twofold increase in nonredundant sequences. The expanded database does now allow us to explain several deviations of hydrophobicity statistics from models of random sequence in terms of requirements of specific secondary structure elements. Comparison to prior membrane-bound protein sequences, however, shows significant qualitative changes, with the average hydrophobicity and frequency of long runs of hydrophobic residues noticeably increasing between the database editions. These results suggest that the aqueous proteins of solved structure may represent an essentially complete sample of the universe of aqueous sequences, while the membrane proteins of known structure are not yet representative of the universe of membrane-associated proteins, even by relatively simple measures of hydrophobic patterns.
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