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Ratio of membrane proteins in total proteomes of prokaryota

View Article: PubMed Central - PubMed

ABSTRACT

The numbers of membrane proteins in the current genomes of various organisms provide an important clue about how the protein world has evolved from the aspect of membrane proteins. Numbers of membrane proteins were estimated by analyzing the total proteomes of 248 prokaryota, using the SOSUI system for membrane proteins (Hirokawa et al., Bioinformatics, 1998) and SOSUI-signal for signal peptides (Gomi et al., CBIJ, 2004). The results showed that the ratio of membrane proteins to total proteins in these proteomes was almost constant: 0.228. When amino acid sequences were randomized, setting the probability of occurrence of all amino acids to 5%, the membrane protein/total protein ratio decreased to about 0.085. However, when the same simulation was carried out, but using the amino acid composition of the above proteomes, this ratio was 0.218, which is nearly the same as that of the real proteomic systems. This fact is consistent with the birth, death and innovation (BDI) model for membrane proteins, in which transmembrane segments emerge and disappear in accordance with random mutation events.

No MeSH data available.


The number density of hydrophobic amino acids (A) and amphiphilic amino acids (B) were calculated for five sets of proteomes. It is already known that hydrophobic and amphiphilic clusters in amino acid sequences directly affect the membrane translocation of proteins. The distribution of both parameters systematically changed according to the variation of the factor α. Hydrophobic amino acids in this diagram include isoleucine, leucine, methionine, phenylalanine and valine, and amphiphilic amino acids are arginine, glutamine, glutamate, histidine and lysine. Because both types contain five amino acids, the probability of occurrence of both types of amino acids is 0.25 for the system of the uniform amino acid composition.
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f6-3_37: The number density of hydrophobic amino acids (A) and amphiphilic amino acids (B) were calculated for five sets of proteomes. It is already known that hydrophobic and amphiphilic clusters in amino acid sequences directly affect the membrane translocation of proteins. The distribution of both parameters systematically changed according to the variation of the factor α. Hydrophobic amino acids in this diagram include isoleucine, leucine, methionine, phenylalanine and valine, and amphiphilic amino acids are arginine, glutamine, glutamate, histidine and lysine. Because both types contain five amino acids, the probability of occurrence of both types of amino acids is 0.25 for the system of the uniform amino acid composition.

Mentions: In order to confirm the strong correlation between the amino acid composition and the membrane protein/total protein ratio, we carried out a third simulation, this time changing the amino acid composition according to equation (2). The numbers of membrane proteins after 400 mutational steps for the entire set of organisms are plotted in Figure 5A as a function of the numbers of proteins in the total proteomes. As the fraction of the real amino acid composition decreased, the ratio of membrane proteins to total proteins monotonically decreased (Fig. 5C). In accordance with the change in this ratio, the distribution of the deviation became gradually sharper (Fig. 5B). The distributions of hydrophobic and amphiphilic amino acids changed according to the variation in the fraction of the real amino acid compositions, as shown in Figures 6A and 6B, respectively. These results indicate that the membrane protein/total protein ratio in the simulations is determined by the amino acid compositions through variation of the hydrophobicity and the amphiphilicity, both physicochemical properties.


Ratio of membrane proteins in total proteomes of prokaryota
The number density of hydrophobic amino acids (A) and amphiphilic amino acids (B) were calculated for five sets of proteomes. It is already known that hydrophobic and amphiphilic clusters in amino acid sequences directly affect the membrane translocation of proteins. The distribution of both parameters systematically changed according to the variation of the factor α. Hydrophobic amino acids in this diagram include isoleucine, leucine, methionine, phenylalanine and valine, and amphiphilic amino acids are arginine, glutamine, glutamate, histidine and lysine. Because both types contain five amino acids, the probability of occurrence of both types of amino acids is 0.25 for the system of the uniform amino acid composition.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036657&req=5

f6-3_37: The number density of hydrophobic amino acids (A) and amphiphilic amino acids (B) were calculated for five sets of proteomes. It is already known that hydrophobic and amphiphilic clusters in amino acid sequences directly affect the membrane translocation of proteins. The distribution of both parameters systematically changed according to the variation of the factor α. Hydrophobic amino acids in this diagram include isoleucine, leucine, methionine, phenylalanine and valine, and amphiphilic amino acids are arginine, glutamine, glutamate, histidine and lysine. Because both types contain five amino acids, the probability of occurrence of both types of amino acids is 0.25 for the system of the uniform amino acid composition.
Mentions: In order to confirm the strong correlation between the amino acid composition and the membrane protein/total protein ratio, we carried out a third simulation, this time changing the amino acid composition according to equation (2). The numbers of membrane proteins after 400 mutational steps for the entire set of organisms are plotted in Figure 5A as a function of the numbers of proteins in the total proteomes. As the fraction of the real amino acid composition decreased, the ratio of membrane proteins to total proteins monotonically decreased (Fig. 5C). In accordance with the change in this ratio, the distribution of the deviation became gradually sharper (Fig. 5B). The distributions of hydrophobic and amphiphilic amino acids changed according to the variation in the fraction of the real amino acid compositions, as shown in Figures 6A and 6B, respectively. These results indicate that the membrane protein/total protein ratio in the simulations is determined by the amino acid compositions through variation of the hydrophobicity and the amphiphilicity, both physicochemical properties.

View Article: PubMed Central - PubMed

ABSTRACT

The numbers of membrane proteins in the current genomes of various organisms provide an important clue about how the protein world has evolved from the aspect of membrane proteins. Numbers of membrane proteins were estimated by analyzing the total proteomes of 248 prokaryota, using the SOSUI system for membrane proteins (Hirokawa et al., Bioinformatics, 1998) and SOSUI-signal for signal peptides (Gomi et al., CBIJ, 2004). The results showed that the ratio of membrane proteins to total proteins in these proteomes was almost constant: 0.228. When amino acid sequences were randomized, setting the probability of occurrence of all amino acids to 5%, the membrane protein/total protein ratio decreased to about 0.085. However, when the same simulation was carried out, but using the amino acid composition of the above proteomes, this ratio was 0.218, which is nearly the same as that of the real proteomic systems. This fact is consistent with the birth, death and innovation (BDI) model for membrane proteins, in which transmembrane segments emerge and disappear in accordance with random mutation events.

No MeSH data available.