Hydrophilic framework in proteins?
The spatial neighborhood composition of residues was determined in a 511-structure set by taking only side-chain atoms into account to generate a hydrophobicity scale. This scale is symmetrical and has been divided into seven functional groups. Hydrophobic (LIVFMCAWYG) and hydrophilic (PTHSQRNKED) residues obey an equipartition rule: not only are they found in equal proportions, but they play equivalent roles in many of their properties. The nearest neighbors of all residues are always hydrophilic. However, hydrophobic residues are mostly surrounded by other hydrophobic residues located at a peak at 3.9 A, while hydrophilic residues show three peaks at 5.0, 6.5, and 8.0 A, suggesting a hydrophilic structural framework. This leads us to question the importance of hydrophobic cores believed to be at the origin of protein folding.
Jésior
J C
JC
TIMC Laboratory, Institut Albert Bonniot, Faculté de Médecine, La Tronche, France. jean-claude.jesior@imag.fr
D000595:Amino Acid Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D005998:Glycine / Q000737:chemistry; D008432:Mathematical Computing; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D010507:Periodicity; D011487:Protein Conformation; D017510:Protein Folding; D012995:Solubility
D010455:Peptides; D005998:Glycine