Amino Acid metabolism conflicts with protein diversity.
Bottom Line: The 20 protein-coding amino acids are found in proteomes with different relative abundances.More than 100 organisms reach comparable solutions to the trade-off by different combinations of proteome cost and sequence diversity.Quantifying the interplay between proteome size and entropy shows that proteomes can get optimally large and diverse.
Affiliation: Departamento de Matemática, Facultad de Ciencias Exactas y Naturales and IMAS-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina.Show MeSH
Related in: MedlinePlus
Mentions: We postulate a model in which living organisms maximize a target function f that equals the entropy of the amino acid distribution in the proteome h minus the average metabolic cost of an amino acid . This gives rise to a trade-off between both terms. Figure 3 displays this trade-off for all organisms in DS1 (white symbols) and DS2 (black symbols). The figure also shows the expectation for the genetic code model (red symbols); figure 3A shows that most natural proteomes present lower metabolic costs than the genetic code model. Similarly, the entropies of natural proteomes are in the same order as the genetic code model or higher (fig. 3B). Finally, the target function f takes higher values in most natural proteomes than in the genetic code model (fig. 3C).Fig. 3.
Affiliation: Departamento de Matemática, Facultad de Ciencias Exactas y Naturales and IMAS-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina.