A Mean-Field Description of Protein Folding: Evolutional Conservation of Hydrophobicity Profile and Folding Nuclei

Abstract

Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D (3-dimensional) information of the structure is considered and it is found that a 3D hydrophobicity profile is essential to specify the folding nuclei and evolutionally conserved. This profile is maintained by the interaction, including entropic effect, among amino acids realized in the native state structure. Experimentally observed phi-value is correlated to this 3D hydrophobicity profile after taking into account the effect of the contact distance in amino-acid sequence.