Physicochemical factors for discriminating between soluble and membrane proteins: hydrophobicity of helical segments and protein length.
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.
Mitaku
S
S
Tokyo University of Agriculture and Technology, Department of Biotechnology, Koganei, Tokyo 184-8588, Japan. mitaku@cc.tuat.ac.jp
Hirokawa
T
T
D016208:Databases, Factual; D008565:Membrane Proteins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid; D012995:Solubility
D008565:Membrane Proteins