Comprehensive bioinformatics analysis of cell-free protein synthesis: identification of multiple protein properties that correlate with successful expression.
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.
Kurotani
Atsushi
A
RIKEN Systems and Structural Biology Center, Yokohama, Japan.
Takagi
Tetsuo
T
Toyama
Mitsutoshi
M
Shirouzu
Mikako
M
Yokoyama
Shigeyuki
S
Fukami
Yasuo
Y
Tokmakov
Alexander A
AA
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*
D011994:Recombinant Proteins