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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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Structural view of mitochondrially encoded COX residues. COX core, consisting of COX subunits I (chain A in green), II (chain B in yellow), and III (chain C in orange) is shown at the top of the figure. The spatial distribution of those residues in close contact with nDNA-encoded subunits (ABCMt-nu_Contact) is also shown. The set formed by mtDNA-encoded residues that are not in contact with nDNA-encoded subunits, (ABCMt-nu_Contact)c, was partitioned into three disjoint subsets: ABCMt-mt_Contact, which is formed by those residues contacting only with other mtDNA-encoded residues; ABCExposed_Noncontact, encompassing residues accessible to the solvent that are not involved in intersubunit contacts; and ABCBuried_Noncontact, which contains all those residues that being buried inside the protein are not available for intersubunit contacts. The spatial distributions of the residues belonging to each of these subsets are shown at the bottom of the figure.
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evu240-F2: Structural view of mitochondrially encoded COX residues. COX core, consisting of COX subunits I (chain A in green), II (chain B in yellow), and III (chain C in orange) is shown at the top of the figure. The spatial distribution of those residues in close contact with nDNA-encoded subunits (ABCMt-nu_Contact) is also shown. The set formed by mtDNA-encoded residues that are not in contact with nDNA-encoded subunits, (ABCMt-nu_Contact)c, was partitioned into three disjoint subsets: ABCMt-mt_Contact, which is formed by those residues contacting only with other mtDNA-encoded residues; ABCExposed_Noncontact, encompassing residues accessible to the solvent that are not involved in intersubunit contacts; and ABCBuried_Noncontact, which contains all those residues that being buried inside the protein are not available for intersubunit contacts. The spatial distributions of the residues belonging to each of these subsets are shown at the bottom of the figure.

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)

Structural view of mitochondrially encoded COX residues. COX core, consisting of COX subunits I (chain A in green), II (chain B in yellow), and III (chain C in orange) is shown at the top of the figure. The spatial distribution of those residues in close contact with nDNA-encoded subunits (ABCMt-nu_Contact) is also shown. The set formed by mtDNA-encoded residues that are not in contact with nDNA-encoded subunits, (ABCMt-nu_Contact)c, was partitioned into three disjoint subsets: ABCMt-mt_Contact, which is formed by those residues contacting only with other mtDNA-encoded residues; ABCExposed_Noncontact, encompassing residues accessible to the solvent that are not involved in intersubunit contacts; and ABCBuried_Noncontact, which contains all those residues that being buried inside the protein are not available for intersubunit contacts. The spatial distributions of the residues belonging to each of these subsets are shown at the bottom of the figure.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu240-F2: Structural view of mitochondrially encoded COX residues. COX core, consisting of COX subunits I (chain A in green), II (chain B in yellow), and III (chain C in orange) is shown at the top of the figure. The spatial distribution of those residues in close contact with nDNA-encoded subunits (ABCMt-nu_Contact) is also shown. The set formed by mtDNA-encoded residues that are not in contact with nDNA-encoded subunits, (ABCMt-nu_Contact)c, was partitioned into three disjoint subsets: ABCMt-mt_Contact, which is formed by those residues contacting only with other mtDNA-encoded residues; ABCExposed_Noncontact, encompassing residues accessible to the solvent that are not involved in intersubunit contacts; and ABCBuried_Noncontact, which contains all those residues that being buried inside the protein are not available for intersubunit contacts. The spatial distributions of the residues belonging to each of these subsets are shown at the bottom of the figure.
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