Physicochemical factors for discriminating between soluble and membrane proteins: hydrophobicity of helical segments and protein length

Protein Eng. 1999 Nov;12(11):953-7. doi: 10.1093/protein/12.11.953.


The average hydrophobicity of a polypeptide segment is considered to be the most important factor in the formation of transmembrane helices, and the partitioning of the most hydrophobic (MH) segment into the alternative nonpolar environment, a membrane or hydrophobic core of a globular protein may determine the type of protein produced. In order to elucidate the importance of the MH segment in determining which of the two types of protein results from a given amino acid sequence, we statistically studied the characteristics of MH helices, longer than 19 residues in length, in 97 membrane proteins whose three-dimensional structure or topology is known, as well as 397 soluble proteins selected from the Protein Data Bank. The average hydrophobicity of MH helices in membrane proteins had a characteristic relationship with the length of the protein. All MH helices in membrane proteins that were longer than 500 residues had a hydrophobicity greater than 1.75 (Kyte and Doolittle scale), while the MH helices in membrane proteins smaller than 100 residues could be as hydrophilic as 0.1. The possibility of developing a method to discriminate membrane proteins from soluble ones, based on the effect of size on the type of protein produced, is discussed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Factual
  • Membrane Proteins / chemistry*
  • Protein Structure, Secondary
  • Sequence Homology, Amino Acid
  • Solubility


  • Membrane Proteins