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Ratio of membrane proteins in total proteomes of prokaryota

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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.

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Changes in an amino acid sequence gives rise to the transformation between soluble and membrane proteins. The rate constants, km→s and ks→m, can be defined as the numbers of transformations from soluble to membrane proteins and of the inverse process per a given number of mutations, respectively.
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f7-3_37: Changes in an amino acid sequence gives rise to the transformation between soluble and membrane proteins. The rate constants, km→s and ks→m, can be defined as the numbers of transformations from soluble to membrane proteins and of the inverse process per a given number of mutations, respectively.

Mentions: In the case of membrane proteins, the model can be described by Figure 7. When mutations are introduced into the amino acid sequence, a protein transforms from a membrane protein to a soluble protein and vice-versa. If the current proteomes have been formed by such reversible reactions during the process of extensive mutations, then our results support the idea that these proteomes have already reached an equilibrium state. If so, the numbers of soluble proteins Ns and membrane proteins Nm are related by the following equation,


Ratio of membrane proteins in total proteomes of prokaryota
Changes in an amino acid sequence gives rise to the transformation between soluble and membrane proteins. The rate constants, km→s and ks→m, can be defined as the numbers of transformations from soluble to membrane proteins and of the inverse process per a given number of mutations, respectively.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5036657&req=5

f7-3_37: Changes in an amino acid sequence gives rise to the transformation between soluble and membrane proteins. The rate constants, km→s and ks→m, can be defined as the numbers of transformations from soluble to membrane proteins and of the inverse process per a given number of mutations, respectively.
Mentions: In the case of membrane proteins, the model can be described by Figure 7. When mutations are introduced into the amino acid sequence, a protein transforms from a membrane protein to a soluble protein and vice-versa. If the current proteomes have been formed by such reversible reactions during the process of extensive mutations, then our results support the idea that these proteomes have already reached an equilibrium state. If so, the numbers of soluble proteins Ns and membrane proteins Nm are related by the following equation,

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.


Related in: MedlinePlus