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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 physical proximity to the heme groups may be a strong determinant of the selective pressure. The distance in angstroms of each COX I residue to the closest heme group was determined and the distribution of such a variable is shown for each category of residue (A). (B) shows, in yellow, those Exposed Noncontact residues that are not involved in the formation of interfaces, as well as their spatial proximity to the hemes a and a3, in white. In (C), it has been added, in green color, those Exposed Noncontact residues that form part of protein–protein interfaces. Finally, for comparative purposes, in (D) the Buried residues are shown in red.
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evu240-F7: The physical proximity to the heme groups may be a strong determinant of the selective pressure. The distance in angstroms of each COX I residue to the closest heme group was determined and the distribution of such a variable is shown for each category of residue (A). (B) shows, in yellow, those Exposed Noncontact residues that are not involved in the formation of interfaces, as well as their spatial proximity to the hemes a and a3, in white. In (C), it has been added, in green color, those Exposed Noncontact residues that form part of protein–protein interfaces. Finally, for comparative purposes, in (D) the Buried residues are shown in red.

Mentions: The structures shown in figures 2 and 7 were rendered using PyMol (http://www.pymol.org).Fig. 2.—


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 physical proximity to the heme groups may be a strong determinant of the selective pressure. The distance in angstroms of each COX I residue to the closest heme group was determined and the distribution of such a variable is shown for each category of residue (A). (B) shows, in yellow, those Exposed Noncontact residues that are not involved in the formation of interfaces, as well as their spatial proximity to the hemes a and a3, in white. In (C), it has been added, in green color, those Exposed Noncontact residues that form part of protein–protein interfaces. Finally, for comparative purposes, in (D) the Buried residues are shown in red.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu240-F7: The physical proximity to the heme groups may be a strong determinant of the selective pressure. The distance in angstroms of each COX I residue to the closest heme group was determined and the distribution of such a variable is shown for each category of residue (A). (B) shows, in yellow, those Exposed Noncontact residues that are not involved in the formation of interfaces, as well as their spatial proximity to the hemes a and a3, in white. In (C), it has been added, in green color, those Exposed Noncontact residues that form part of protein–protein interfaces. Finally, for comparative purposes, in (D) the Buried residues are shown in red.
Mentions: The structures shown in figures 2 and 7 were rendered using PyMol (http://www.pymol.org).Fig. 2.—

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