title: Comprehensive bioinformatics analysis of cell-free protein synthesis: identification of multiple protein properties that correlate with successful expression.
abstract: High-throughput cell-free protein synthesis is being used increasingly in structural/functional genomics projects. However, the factors determining expression success are poorly understood. Here, we evaluated the expression of 3066 human proteins and their domains in a bacterial cell-free system and analyzed the correlation of protein expression with 39 physicochemical and structural properties of proteins. As a result of the bioinformatics analysis performed, we determined the 18 most influential features that affect protein amenability to cell-free expression. They include protein length; hydrophobicity; pI; content of charged, nonpolar, and aromatic residues;, cysteine content; solvent accessibility; presence of coiled coil; content of intrinsically disordered and structured (alpha-helix and beta-sheet) sequence; number of disulfide bonds and functional domains; presence of transmembrane regions; PEST motifs; and signaling sequences. This study represents the first comprehensive bioinformatics analysis of heterologous protein synthesis in a cell-free system. The rules and correlations revealed here provide a plethora of important insights into rationalization of cell-free protein production and can be of practical use for protein engineering with the aim of increasing expression success.-Kurotani, A., Takagi, T., Toyama, M., Shirouzu, M., Yokoyama, S., Fukami, Y., Tokmakov, A. A. Comprehensive bioinformatics analysis of cell-free protein synthesis: identification of multiple protein properties that correlate with successful expression.
authors: RIKEN Systems and Structural Biology Center, Yokohama, Japan.
authors: Atsushi
authors: A
authors: Kurotani
authors: Tetsuo
authors: T
authors: Takagi
authors: Mitsutoshi
authors: M
authors: Toyama
authors: Mikako
authors: M
authors: Shirouzu
authors: Shigeyuki
authors: S
authors: Yokoyama
authors: Yasuo
authors: Y
authors: Fukami
authors: Alexander A
authors: AA
authors: Tokmakov
mesh_terms: D020816:Amino Acid Motifs; D002474:Cell-Free System / Q000737:chemistry / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008962:Models, Theoretical; D014176:Protein Biosynthesis / Q000502:physiology*; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000096:biosynthesis* / Q000737:chemistry*
chemical_list: D011994:Recombinant Proteins