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Edited by George H. Lorimer, University of Maryland, College Park, MD, and approved January 26, 2009 (received for review November 23, 2008)
Article Figures & SI
Figures
- Fig. 1.
Schematic illustration of the experiment. Each ORF in the ASKA library, which has all of the E. coli ORFs, was amplified by PCR using 2 common primers to translate the gene in the cell-free translation system. The reconstituted cell-free translation system (the PURE system) contains no chaperones. After the 60-min translation, an aliquot of the translation mixture was centrifuged to obtain the soluble fraction. The uncentrifuged (Total) and supernatant (Sup) fractions were subjected to SDS/PAGE, and the translated products were quantified by autoradiography.
- Fig. 2.
Solubility distribution for quantified proteins. (A) Histogram of solubility for the 3,173 quantified proteins. The proteins with solubilities <30% and >70% were defined as the aggregation-prone (Agg, colored pink) and soluble (Sol, colored blue) groups, respectively. (B) Histogram of solubility for 2,277 predicted cytoplasmic proteins. (C) Histogram of solubility for essential proteins. (D) The ratio of subcellular location (predicted) in all quantified (Total), Agg, and Sol groups. Cyto, cytoplasmic proteins; IMP, integral membrane proteins; Peri, periplasmic proteins; MA, membrane-anchored proteins; OM, outer membrane lipoproteins and β-barrel proteins.
- Fig. 3.
Correlation between solubility and physicochemical properties. (A) Histograms of molecular mass in the Total, Agg, and Sol groups. (B) Scatter plot of solubility versus isoelectric point. (C) Histograms of the relative contents of negatively charged residues (Asp and Glu) (Left) and hydrophobic residues (Val, Leu and Ile) (Right) in the Total, Agg, and Sol groups.
- Fig. 4.
Correlation between solubility and tertiary structure. (A) Histograms of solubility in the SCOP classes. SCOP class abbreviations: all α proteins (a); all β proteins (b); α and β proteins (α/β) (c); α and β proteins (α+β) (d). (B) The ratio of the Agg and Sol proteins in each SCOP fold. Details of each fold and the assigned number of proteins with statistical significance (P values) in each fold are described in Table S2. (C) Histograms of solubility for the GroEL substrate proteins. The classification of the substrates is according to Kerner et al. (27), in which Classes I, II, and III are spontaneously foldable, chaperone-dependent (but partially GroEL-dependent) and obligate GroEL/ES-dependent substrates, respectively.
Data supplements
Supporting Information
Files in this Data Supplement:
Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins
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