CONFORMATION OF PROTEINS - HYDROPHOBIC ORDERING OF STRANDS IN BETA-PLEATED SHEETS

[摘要] The influence of hydrophobic free energy on strand order .beta.-pleated sheets was studied. A hydrophobic free energy was assigned to each type of amino acid. The total hydrophobicity of each strand in a sheet was calculated by summing the energies for all residues in that strand. In 30 of the 39 sheets studied, there was evidence that the strands with greatest hydrophobic potential tend to occur in the center of the sheet, while the more hydrophilic strands occupied the edge positions in the sheet. In 20 of the 30 sheets, the most hydrophobic strand was buried and the remaining strands were arranged in order of decreasing hydrophobicity outwards in both directions. The total hydrophobicity of a strand reflected not only the amino acid composition of the strand, but also its length. Longer strands were potentially more hydrophobic and occured most frequently in the center of the sheet. This suggested that hydrophobic ordering was one important factor in determining strand order, possibly reflecting hydrophobic nucleation. The total hydrophobicities of opposite sides of the sheets were calculated. There was a good correlation between the observed relative exposure to solvent and the calculated hydrophobicities. These observations underlined the importance of hydrophobic free energy in determining the tertiary structure of the protein. Clearly hydrophobic nucleation should be taken into account in the prediction of the tertiary fold from secondary structure.