title: Functionally compensating coevolving positions are neither homoplasic nor conserved in clades.
abstract: We demonstrated that a pair of positions in phosphoglycerate kinase that score highly by three nonparametric covariation measures are important for function even though the positions can be occupied by aliphatic, aromatic, or charged residues. Examination of these pairs suggested that the majority of the covariation scores could be explained by within-clade conservation. However, an analysis of diversity showed that the conservation within clades of covarying pairs was indistinguishable from pairs of positions that do not covary, thus ruling out both clade conservation and extensive homoplasy as means to identify covarying positions. Mutagenesis showed that the residues in the covarying pair were epistatic, with the type of epistasis being dependent on the initial pair. The results show that nonconserved covarying positions that affect protein function can be identified with high precision.
authors.affiliation: Department of Biochemistry, University of Western Ontario, London, Ontario, Canada. ggloor@uwo.ca
authors.forename: Gregory B
authors.initials: GB
authors.lastname: Gloor
authors.forename: Gaurav
authors.initials: G
authors.lastname: Tyagi
authors.forename: Dana M
authors.initials: DM
authors.lastname: Abrassart
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Kingston
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Fernandes
authors.forename: Stanley D
authors.initials: SD
authors.lastname: Dunn
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Brandl
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000235:genetics; D017124:Conserved Sequence; D030562:Databases, Protein; D019143:Evolution, Molecular; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016296:Mutagenesis / Q000235:genetics; D050505:Mutant Proteins / Q000378:metabolism; D010735:Phosphoglycerate Kinase / Q000737:chemistry; D010802:Phylogeny; D011489:Protein Denaturation; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000201:enzymology / Q000254:growth & development; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013696:Temperature
chemical_list: D000596:Amino Acids; D050505:Mutant Proteins; D010735:Phosphoglycerate Kinase