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Protein-protein interfaces from cytochrome c oxidase I evolve faster than nonbinding surfaces, yet negative selection is the driving force.

Aledo JC, Valverde H, Ruíz-Camacho M, Morilla I, López FD - Genome Biol Evol (2014)

Bottom Line: Herein, using evolutionary data in combination with structural information of COX, we show that failing to discern the effects of interaction from other structural and functional effects can lead to deceptive conclusions such as the "optimizing hypothesis." Once spurious factors have been accounted for, data analysis shows that mtDNA-encoded residues engaged in contacts are, in general, more constrained than their noncontact counterparts.This differential behavior cannot be explained on the basis of predicted thermodynamic stability, as interactions between mtDNA-encoded subunits contribute more weakly to the complex stability than those interactions between subunits encoded by different genomes.Therefore, the higher conservation observed among mtDNA-encoded residues involved in intragenome interactions is likely due to factors other than structural stability.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Spain caledo@uma.es.

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The behavior of Exposed Noncontact residues from COX I diverges from those exhibited by their counterparts in COX II and COX III. For each mtDNA-encoded chain, the codons from the multiple sequence alignment were randomly sorted to form a subset of the same size as the original Exposed Noncontact subset of the corresponding chain. Afterwards, ΣdN was computed using this random subset. For each chain, the random resampling was performed 104 times to build up empirical distributions, which were used to contrast the ΣdN values computed in the real Exposed Noncontact subsets, which are indicated by arrows on the abscissa axis.
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evu240-F4: The behavior of Exposed Noncontact residues from COX I diverges from those exhibited by their counterparts in COX II and COX III. For each mtDNA-encoded chain, the codons from the multiple sequence alignment were randomly sorted to form a subset of the same size as the original Exposed Noncontact subset of the corresponding chain. Afterwards, ΣdN was computed using this random subset. For each chain, the random resampling was performed 104 times to build up empirical distributions, which were used to contrast the ΣdN values computed in the real Exposed Noncontact subsets, which are indicated by arrows on the abscissa axis.

Mentions: The statistical support for the conclusion that Exposed Noncontact residues from COX I exhibit a unique behavior, provided in figure 4, was obtained by randomly sampling on the data set of each mtDNA-encoded subunit (chains A, B, and C corresponding to COX I, COX II, and COX III, respectively), which are the larger subunits from complex IV (514, 227, and 261 residues, respectively). Thus, reliable random distribution of ΣdN was generated. To this end, the codons from multiple sequence alignments of each chain were randomly sorted to form a subset of the same size as the original Exposed Noncontact subset of the corresponding chain. Afterwards, ΣdN was computed using this random subset as explained above. For each chain, the random resampling was performed 104 times to build up empirical distributions, which were used to contrast the ΣdN values computed in the real Exposed Noncontact subsets.


Protein-protein interfaces from cytochrome c oxidase I evolve faster than nonbinding surfaces, yet negative selection is the driving force.

Aledo JC, Valverde H, Ruíz-Camacho M, Morilla I, López FD - Genome Biol Evol (2014)

The behavior of Exposed Noncontact residues from COX I diverges from those exhibited by their counterparts in COX II and COX III. For each mtDNA-encoded chain, the codons from the multiple sequence alignment were randomly sorted to form a subset of the same size as the original Exposed Noncontact subset of the corresponding chain. Afterwards, ΣdN was computed using this random subset. For each chain, the random resampling was performed 104 times to build up empirical distributions, which were used to contrast the ΣdN values computed in the real Exposed Noncontact subsets, which are indicated by arrows on the abscissa axis.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4255772&req=5

evu240-F4: The behavior of Exposed Noncontact residues from COX I diverges from those exhibited by their counterparts in COX II and COX III. For each mtDNA-encoded chain, the codons from the multiple sequence alignment were randomly sorted to form a subset of the same size as the original Exposed Noncontact subset of the corresponding chain. Afterwards, ΣdN was computed using this random subset. For each chain, the random resampling was performed 104 times to build up empirical distributions, which were used to contrast the ΣdN values computed in the real Exposed Noncontact subsets, which are indicated by arrows on the abscissa axis.
Mentions: The statistical support for the conclusion that Exposed Noncontact residues from COX I exhibit a unique behavior, provided in figure 4, was obtained by randomly sampling on the data set of each mtDNA-encoded subunit (chains A, B, and C corresponding to COX I, COX II, and COX III, respectively), which are the larger subunits from complex IV (514, 227, and 261 residues, respectively). Thus, reliable random distribution of ΣdN was generated. To this end, the codons from multiple sequence alignments of each chain were randomly sorted to form a subset of the same size as the original Exposed Noncontact subset of the corresponding chain. Afterwards, ΣdN was computed using this random subset as explained above. For each chain, the random resampling was performed 104 times to build up empirical distributions, which were used to contrast the ΣdN values computed in the real Exposed Noncontact subsets.

Bottom Line: Herein, using evolutionary data in combination with structural information of COX, we show that failing to discern the effects of interaction from other structural and functional effects can lead to deceptive conclusions such as the "optimizing hypothesis." Once spurious factors have been accounted for, data analysis shows that mtDNA-encoded residues engaged in contacts are, in general, more constrained than their noncontact counterparts.This differential behavior cannot be explained on the basis of predicted thermodynamic stability, as interactions between mtDNA-encoded subunits contribute more weakly to the complex stability than those interactions between subunits encoded by different genomes.Therefore, the higher conservation observed among mtDNA-encoded residues involved in intragenome interactions is likely due to factors other than structural stability.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Spain caledo@uma.es.

Show MeSH