Figure 1.
The red line represents the aggregation profile of a putative protein with 35 amino acids. The blue line indicates the hot spot threshold, according to the individual aggregation propensity of the 20 natural amino acids and their frequency in natural proteins [28]. The green line corresponds to the average aggregation propensity of the putative protein. The aggregation-prone areas over the threshold are filled in red (A and B). a4v is the aggregation propensity average over a sliding window of 5 to 11 residues [10]. The aggregation propensity of each amino acid results from the depositional analysis of a set of amyloid polypeptides in the E. coli cytoplasm [25], [28].
Figure 2.
Relationship between the cytosolic proteins abundance and the AGGRESCAN aggregation parameters.
Cumulative distributions of the NnHS (A), THSAr (B) and Na4vSS (C) parameters in the 10% most abundant cytosolic proteins (black) and the 10% least abundant ones (grey). D) Correlation between protein abundance, measured as LN(emPAI), and protein aggregation propensity, measured as Na4vSS, in the complete cytosolic protein set. The 875 cytosolic proteins were divided in 45 groups according to their LN(emPAI) values. Each point in the graphic represents the average value of the corresponding group. Standard errors for aggregation and abundance measurements are shown.
Figure 3.
Relationship between the cytosolic proteins abundance and their intrinsic properties.
A) Amino acid abundance in high-abundant (pale grey) and low-abundant (dark grey) sequences relative to the expected frequencies in natural proteins as deduced from Swiss-Prot [82]. B) Comparison between the proteins pI and Na4vSS values. C) Correlation between proteins hydropathicity (GRAVY) and Na4vSS values.
Figure 4.
Comparison between cytosolic proteins theoretical expression levels and their aggregation parameters.
A) Cumulative distributions of Na4vSS values in the 10% cytosolic proteins with the highest (black) and lowest (grey) Codon Adaptation Index (CAI) values. B) Correlation between the CAI and the Na4vSS values. Each point represents the average value over all the sequences having a CAI value comprised in an interval of 0.03.
Figure 5.
Dependence of proteins length on their aggregation properties and chaperone binding affinity.
A) Dot plot distribution represents the relationship between the molecular weight and Na4vSS. Columns show the size distribution of polypeptides that bind to GroEL (grey) or DnaK (white) in E. coli according to the data in [61]. B) Relationship between the molecular weight and the NnHS. Each point corresponds to the average value over all the sequences having a length comprised in an interval of 1.9 kDa.
Figure 6.
Amino acid composition of cytosolic proteins hot spots and their flanks.
A) Amino acid frequencies relative to their average frequency in natural proteins as deduced from Swiss-Prot [82]. A relative frequency of 0 for a given residue at a given position means that the residue occupies that position with a frequency identical to that in natural proteins. Residues enrichment in the hot spots (B) and at the flanks (C) relative to their frequency in natural proteins. Values above or below 1.0 point denote increases or decreases in frequency, respectively.
Figure 7.
Proteins encoded by the same operon display related aggregation propensities.
Standard deviation of Na4vSS values in the 25 analysed operons. The standard deviation in the complete cytosolic set is 7.72 (dashed line). Low standard deviation within an operon indicates that the aggregation propensity of its proteins is similar.
Table 1.
Different operons regulate proteins with different aggregation propensity and biological function.
Figure 8.
Disordered sequence stretches display reduced protein aggregation.
Cumulative distributions of NnHS and Na4vSS values in ribosomal proteins (A and B), intrinsically unstructured proteins (C and D) and disordered fragments in cytosolic proteins (E and F) are compared with the distribution in the complete cytosolic set (grey).
Figure 9.
Relationship between subcellular localisation and protein aggregation propensity.
Cumulative distribution of NnHS (A), THSAr (B) and Na4vSS (C) of proteins located in the cytoplasm (C, red), outer membrane (OM, dark green), periplasm (P, blue). D) Dot distribution of the Na4vSS values of the proteins in the previous four protein sets as well as those located in the inner membrane (IM, pale green); the vertical lines correspond to the Na4vSS mean in each protein set. Cumulative distribution of NnHS (E) and Na4vSS (F) in cytosolic and inner membrane proteins.
Figure 10.
The inner membrane contains proteins with different number of transmembrane segments and associated aggregation propensities.
Diagram of the inner membrane protein set showing the Na4vSS value and the number of transmembrane segments.
Figure 11.
Inner membrane proteins with differential aggregation propensities are involved in different biological functions.
Percentage of inner membrane proteins associated with the biological functions described in FunCat (A) and UniProtKB (B). The inner membrane proteins were divided in two groups according to their Na4vSS value: Na4vSS <6 (42 proteins; pale grey) or Na4vSS ≥6 (43 proteins; dark grey).