Terminal Sequence Importance of De Novo Proteins from Binary- Patterned Library: Stable Artificial Proteins with 11- or 12-Amino Acid Alphabet

Hiromichi      Okura; Tsuyoshi      Takahashi; Hisakazu      Mihara

doi:10.2174/092986612800494101

Abstract

Successful approaches of de novo protein design suggest a great potential to create novel structural folds and to understand natural rules of protein folding. For these purposes, smaller and simpler de novo proteins have been developed. Here, we constructed smaller proteins by removing the terminal sequences from stable de novo vTAJ proteins and compared stabilities between mutant and original proteins. vTAJ proteins were screened from an α3β3 binary-patterned library which was designed with polar/ nonpolar periodicities of α-helix and β-sheet. vTAJ proteins have the additional terminal sequences due to the method of constructing the genetically repeated library sequences. By removing the parts of the sequences, we successfully obtained the stable smaller de novo protein mutants with fewer amino acid alphabets than the originals. However, these mutants showed the differences on ANS binding properties and stabilities against denaturant and pH change. The terminal sequences, which were designed just as flexible linkers not as secondary structure units, sufficiently affected these physicochemical details. This study showed implications for adjusting protein stabilities by designing N- and C-terminal sequences.

Keywords: Protein, De novo design, N- and C-terminal sequences, Binary patterning, Limited amino acid alphabet, amino acid sequences, leader sequence, bioinformatics, binary-patterned library, fluorescence