Local hydrophobicity stabilizes secondary structures in proteins

✍ Scribed by Minoru I. Kanehisa; Tian Yow Tsong

• Publisher: Wiley (John Wiley & Sons)
• Year: 1980
• Tongue: English
• Weight: 661 KB
• Volume: 19
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.1980.360190906

✦ Synopsis

Abstract

The probability of occurrence of helix and β‐sheet residues in 47 globular proteins was determined as a function of local hydrophobicity, which was defined by the sum of the Nozaki‐Tanford transfer free energies at two nearest‐neighbors on both sides of the amino acid sequence. In general, hydrophilic amino acids favor neither helix nor β‐sheet formations when neighbor residues are also hydrophilic but favor helix formation at higher local hydrophobicity. On the other hand, some hydrophobic amino acids such as Met, Leu, and Ile favor helix formation when neighbor residues are hydrophilic. None of the hydrophobic amino acids favor β‐sheet formation with hydrophilic neighbors, but most of them strongly favor β‐sheet formation at high local hydrophobicity. When the average of 20 amino acids is taken, both helix and β‐sheet residue probabilities are higher at higher local hydrophobicity, although the increase is steeper for β‐sheets. Therefore, β‐sheet formation is more influenced by local hydrophobicity than helix formation. Generally, helices are nearer the surface and tend to have hydrophilic and hydrophobic faces at opposite sides. The tendency of alternating regions of hydrophilic and hydrophobic residues in a helical sequence was revealed by calculating the correlation of the Nozaki‐Tanford values. Such amphipathic helices may be important in protein–protein and protein–lipid interactions and in forming hydrophilic channels in the membrane. The choice of 30 nonhomologous proteins as the data set did not alter the above results.