title: Attempt to simplify the amino-acid sequence of photoactive yellow protein with a set of simple rules.
abstract: 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 beta-scaffold region.
authors: Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
authors: Kumiko
authors: K
authors: Shirai
authors: Yoichi
authors: Y
authors: Yamazaki
authors: Hironari
authors: H
authors: Kamikubo
authors: Yasushi
authors: Y
authors: Imamoto
authors: Mikio
authors: M
authors: Kataoka
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D002942:Circular Dichroism; D019295:Computational Biology; D015870:Gene Expression; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D020283:Photoreceptors, Microbial / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D011489:Protein Denaturation; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D012996:Solutions; D013816:Thermodynamics; D014508:Urea
chemical_list: D001426:Bacterial Proteins; D020283:Photoreceptors, Microbial; D011994:Recombinant Proteins; D012996:Solutions; C050162:photoactive yellow protein, Bacteria; D014508:Urea