Studies on the principle of protein architecture by the simplification of amino acid sequence

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In order to understand the information encoded in an amino-acid sequence, we have created variants of photoactive yellow protein (PYP) with simplified amino-acid sequences. We simplified the amino-acid sequence of PYP using a simple set of rules to reduce overlapping structural information. The simplified PYP protein (sPYP0), which was composed of only nine species of amino acids (Ser,Val,Asp,Lys,Phe,Met,Gly,Pro, and Cys), showed a completely different structure than the native conformation. Even after the evolutionarily conserved residues were restored in the simplified protein (sPYPI), the PYP variant did not properly fold. Additional restorations of the substituted hydrophobic (sPYPII) or hydrophilic residues (sPYPIII) did not lead to a variant that formed the native structure. sPYPIII only shows the tendency of helical formation by TFE. Partial simplification was successfully performed by creating chimeric proteins composed of combinations of wild-type PYP and sPYPIII. Hybrid mutants containing a wild-type β scaffold adopted native-like structures. In contrast, the hybrid mutants that contained the simplified β scaffold demonstrated a tendency to adopt non-native conformations, suggesting that there is a wealth of information about the formation of the structure in the β scaffold. 5 hydrophobic residues in the β scaffold were identified to be responsible for the structure formation. It is also demonstrated that sPYPII takes amyloid-like fibril structure.