title: ESPRESSO: a system for estimating protein expression and solubility in protein expression systems.
abstract: Recombinant protein technology is essential for conducting protein science and using proteins as materials in pharmaceutical or industrial applications. Although obtaining soluble proteins is still a major experimental obstacle, knowledge about protein expression/solubility under standard conditions may increase the efficiency and reduce the cost of proteomics studies. In this study, we present a computational approach to estimate the probability of protein expression and solubility for two different protein expression systems: in vivo Escherichia coli and wheat germ cell-free, from only the sequence information. It implements two kinds of methods: a sequence/predicted structural property-based method that uses both the sequence and predicted structural features, and a sequence pattern-based method that utilizes the occurrence frequencies of sequence patterns. In the benchmark test, the proposed methods obtained F-scores of around 70%, and outperformed publicly available servers. Applying the proposed methods to genomic data revealed that proteins associated with translation or transcription have a strong tendency to be expressed as soluble proteins by the in vivo E. coli expression system. The sequence pattern-based method also has the potential to indicate a candidate region for modification, to increase protein solubility. All methods are available for free at the ESPRESSO server (http://mbs.cbrc.jp/ESPRESSO).
authors: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan. hirose-shuichi@aist.go.jp
authors: Shuichi
authors: S
authors: Hirose
authors: Tamotsu
authors: T
authors: Noguchi
mesh_terms: D000595:Amino Acid Sequence; D002474:Cell-Free System / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D006801:Humans; D020407:Internet; D015233:Models, Statistical; D014176:Protein Biosynthesis; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012984:Software; D012995:Solubility; D014158:Transcription, Genetic
chemical_list: D011994:Recombinant Proteins