Comprehensive bioinformatics analysis of cell-free protein synthesis: identification of multiple protein properties that correlate with successful expression

FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology
Atsushi KurotaniAlexander A Tokmakov

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 pr...Continue Reading

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Citations

Jun 8, 2012·The Journal of Biological Chemistry·Alexander A TokmakovShigeyuki Yokoyama
Jun 16, 2015·FEBS Letters·Rebecca B BerlowPeter E Wright
Apr 30, 2014·Chemical Reviews·Robin van der LeeM Madan Babu
Sep 12, 2015·Scientific Reports·Alexander A TokmakovShigeyuki Yokoyama
Aug 21, 2019·BMC Molecular and Cell Biology·Atsushi KurotaniTetsuya Sakurai
Mar 7, 2020·The Biochemical Journal·Prakash KalwaniAnand Ballal
Oct 3, 2019·Biotechnology and Applied Biochemistry·Xumeng Ge, Jianfeng Xu
Feb 5, 2019·Frontiers in Molecular Biosciences·Steffen P Graether

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