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Attempt to simplify the amino‐acid sequence of photoactive yellow protein with a set of simple rules
Author(s) -
Shirai Kumiko,
Yamazaki Yoichi,
Kamikubo Hironari,
Imamoto Yasushi,
Kataoka Mikio
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21331
Subject(s) - amino acid , sequence (biology) , peptide sequence , chemistry , protein structure , protein engineering , fusion protein , biochemistry , computational biology , combinatorial chemistry , stereochemistry , biology , gene , recombinant dna , enzyme
To understand the information encoded in an amino‐acid sequence, the authors have attempted to simplify the amino‐acid sequence of photoactive yellow protein (PYP) with a set of simple rules. The rules are designed to reduce overlapping structural information. The simplified PYP protein, which was composed of only nine species of amino acids (Ser, Val, Asp, Lys, Phe, Met, Gly, Pro, and Cys), took a completely different structure than the native conformation. Even after the evolutionarily conserved residues were restored in the simplified protein, the PYP variant did not properly fold, indicating that the information encoded in the conserved residues is insufficient for the structure formation. Additional restorations of the substituted hydrophilic or hydrophobic residues did not lead to a variant that formed the native structure. The structural properties of these variants and the wild‐type protein in aqueous solution differed. Partial simplification was successfully performed by creating chimeric proteins composed of combinations of wild‐type PYP and sPYPIII. The structural characterization of each chimeric protein indicates that the important information on the structure formation is encoded in the β‐scaffold region. Proteins 2007. © 2007 Wiley‐Liss, Inc.