Rational identification of aggregation hotspots based on secondary structure and amino acid hydrophobicity

Daisuke Matsui, Shogo Nakano, Mohammad Dadashipour, Yasuhisa Asano

Research output: Contribution to journalArticlepeer-review

24 Citations (Scopus)
31 Downloads (Pure)


Insolubility of proteins expressed in the Escherichia coli expression system hinders the progress of both basic and applied research. Insoluble proteins contain residues that decrease their solubility (aggregation hotspots). Mutating these hotspots to optimal amino acids is expected to improve protein solubility. To date, however, the identification of these hotspots has proven difficult. In this study, using a combination of approaches involving directed evolution and primary sequence analysis, we found two rules to help inductively identify hotspots: the α-helix rule, which focuses on the hydrophobicity of amino acids in the α-helix structure, and the hydropathy contradiction rule, which focuses on the difference in hydrophobicity relative to the corresponding amino acid in the consensus protein. By properly applying these two rules, we succeeded in improving the probability that expressed proteins would be soluble. Our methods should facilitate research on various insoluble proteins that were previously difficult to study due to their low solubility.

Original languageEnglish
Pages (from-to)9558
JournalScientific Reports
Issue number1
Publication statusPublished - 25 Aug 2017
Externally publishedYes


  • Amino Acid Motifs
  • Amino Acids/chemistry
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Protein Aggregates
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Structure, Secondary
  • Proteins/chemistry
  • Solubility
  • Structure-Activity Relationship


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