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Understanding the functional difference between growth arrest-specific protein 6 and protein S: an evolutionary approach.

Studer RA, Opperdoes FR, Nicolaes GA, Mulder AB, Mulder R - Open Biol (2014)

Bottom Line: Sites experiencing functional divergence tend to express a greater diversity of stabilizing/destabilizing effects than sites that do not experience such functional divergence.Three electrostatic patches in the LG1/LG2 domains were found to differ between GAS6 and PROS1.These results may help researchers to analyse disease-causing mutations in the light of evolutionary and structural constraints, and link genetic pathology to clinical phenotypes.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

ABSTRACT
Although protein S (PROS1) and growth arrest-specific protein 6 (GAS6) proteins are homologous with a high degree of structural similarity, they are functionally different. The objectives of this study were to identify the evolutionary origins from which these functional differences arose. Bioinformatics methods were used to estimate the evolutionary divergence time and to detect the amino acid residues under functional divergence between GAS6 and PROS1. The properties of these residues were analysed in the light of their three-dimensional structures, such as their stability effects, the identification of electrostatic patches and the identification potential protein-protein interaction. The divergence between GAS6 and PROS1 probably occurred during the whole-genome duplications in vertebrates. A total of 78 amino acid sites were identified to be under functional divergence. One of these sites, Asn463, is involved in N-glycosylation in GAS6, but is mutated in PROS1, preventing this post-translational modification. Sites experiencing functional divergence tend to express a greater diversity of stabilizing/destabilizing effects than sites that do not experience such functional divergence. Three electrostatic patches in the LG1/LG2 domains were found to differ between GAS6 and PROS1. Finally, a surface responsible for protein-protein interactions was identified. These results may help researchers to analyse disease-causing mutations in the light of evolutionary and structural constraints, and link genetic pathology to clinical phenotypes.

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Phylogenetic consensus tree with and without molecular clock of GAS6, PROS1 and SHBG sequences. (a) Tree without a molecular clock model. The GAS6 clade is coloured in red, the PROS1 clade is in blue and the SHBG clade is in green. Values at the nodes indicate posterior probabilities. Only values different from 1.00 are indicated. The lengths of the axes are proportional to the estimated number of mutations per site. (b) Phylogenetic tree under a relaxed clock model. The tree topology is the same as that of the tree in panel (a). The estimated times of divergence of the more important nodes are indicated in electronic supplementary material, table S1. The blue error bars at the nodes represent the 95% confidence limits.
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RSOB140121F1: Phylogenetic consensus tree with and without molecular clock of GAS6, PROS1 and SHBG sequences. (a) Tree without a molecular clock model. The GAS6 clade is coloured in red, the PROS1 clade is in blue and the SHBG clade is in green. Values at the nodes indicate posterior probabilities. Only values different from 1.00 are indicated. The lengths of the axes are proportional to the estimated number of mutations per site. (b) Phylogenetic tree under a relaxed clock model. The tree topology is the same as that of the tree in panel (a). The estimated times of divergence of the more important nodes are indicated in electronic supplementary material, table S1. The blue error bars at the nodes represent the 95% confidence limits.

Mentions: Phylogenetic analyses producing trees reflecting the evolutionary history of this family were carried out using three different methods: (i) a neighbour-joining (NJ) distance matrix tree with exclusion of regions containing insertions and deletions, and correction for multiple substitutions with 1000 bootstrap samplings, created using the Tree option of ClustalX; (ii) a maximum-likelihood (ML) analysis with 100 bootstrap samplings using the JTT evolutionary substitution model with gamma rate distribution carried using with the program PhyML [54]; and finally, (iii) a phylogenetic tree inferred by Bayesian analysis using the program MrBayes v. 3.2 [55]. The model using the JTT substitution matrix and a gamma rate distribution with four substitution rate categories was the best-fitting model to our data. To estimate Bayesian posterior probabilities, Markov chain Monte Carlo (MCMC) chains were run for 100 000 generations and sampled every 100 generations (burn-in: 25%). The resulting tree was rooted using mid-point rooting (figure 1; electronic supplementary material, table S1). Strict and relaxed molecular clock models were applied to the same dataset running, respectively, 100 000 and 400 000 generations (MrBayes). The molecular clock was time calibrated as follows: from the divergence times of various pairs of taxa obtained from the TimeTree web resource (http://www.timetree.org/) [56] the clock rates, in substitutions per site per Myr, were estimated and an average clock rate was calculated. Best results were obtained with the relaxed clock model.FigureĀ 1.


Understanding the functional difference between growth arrest-specific protein 6 and protein S: an evolutionary approach.

Studer RA, Opperdoes FR, Nicolaes GA, Mulder AB, Mulder R - Open Biol (2014)

Phylogenetic consensus tree with and without molecular clock of GAS6, PROS1 and SHBG sequences. (a) Tree without a molecular clock model. The GAS6 clade is coloured in red, the PROS1 clade is in blue and the SHBG clade is in green. Values at the nodes indicate posterior probabilities. Only values different from 1.00 are indicated. The lengths of the axes are proportional to the estimated number of mutations per site. (b) Phylogenetic tree under a relaxed clock model. The tree topology is the same as that of the tree in panel (a). The estimated times of divergence of the more important nodes are indicated in electronic supplementary material, table S1. The blue error bars at the nodes represent the 95% confidence limits.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4221892&req=5

RSOB140121F1: Phylogenetic consensus tree with and without molecular clock of GAS6, PROS1 and SHBG sequences. (a) Tree without a molecular clock model. The GAS6 clade is coloured in red, the PROS1 clade is in blue and the SHBG clade is in green. Values at the nodes indicate posterior probabilities. Only values different from 1.00 are indicated. The lengths of the axes are proportional to the estimated number of mutations per site. (b) Phylogenetic tree under a relaxed clock model. The tree topology is the same as that of the tree in panel (a). The estimated times of divergence of the more important nodes are indicated in electronic supplementary material, table S1. The blue error bars at the nodes represent the 95% confidence limits.
Mentions: Phylogenetic analyses producing trees reflecting the evolutionary history of this family were carried out using three different methods: (i) a neighbour-joining (NJ) distance matrix tree with exclusion of regions containing insertions and deletions, and correction for multiple substitutions with 1000 bootstrap samplings, created using the Tree option of ClustalX; (ii) a maximum-likelihood (ML) analysis with 100 bootstrap samplings using the JTT evolutionary substitution model with gamma rate distribution carried using with the program PhyML [54]; and finally, (iii) a phylogenetic tree inferred by Bayesian analysis using the program MrBayes v. 3.2 [55]. The model using the JTT substitution matrix and a gamma rate distribution with four substitution rate categories was the best-fitting model to our data. To estimate Bayesian posterior probabilities, Markov chain Monte Carlo (MCMC) chains were run for 100 000 generations and sampled every 100 generations (burn-in: 25%). The resulting tree was rooted using mid-point rooting (figure 1; electronic supplementary material, table S1). Strict and relaxed molecular clock models were applied to the same dataset running, respectively, 100 000 and 400 000 generations (MrBayes). The molecular clock was time calibrated as follows: from the divergence times of various pairs of taxa obtained from the TimeTree web resource (http://www.timetree.org/) [56] the clock rates, in substitutions per site per Myr, were estimated and an average clock rate was calculated. Best results were obtained with the relaxed clock model.FigureĀ 1.

Bottom Line: Sites experiencing functional divergence tend to express a greater diversity of stabilizing/destabilizing effects than sites that do not experience such functional divergence.Three electrostatic patches in the LG1/LG2 domains were found to differ between GAS6 and PROS1.These results may help researchers to analyse disease-causing mutations in the light of evolutionary and structural constraints, and link genetic pathology to clinical phenotypes.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

ABSTRACT
Although protein S (PROS1) and growth arrest-specific protein 6 (GAS6) proteins are homologous with a high degree of structural similarity, they are functionally different. The objectives of this study were to identify the evolutionary origins from which these functional differences arose. Bioinformatics methods were used to estimate the evolutionary divergence time and to detect the amino acid residues under functional divergence between GAS6 and PROS1. The properties of these residues were analysed in the light of their three-dimensional structures, such as their stability effects, the identification of electrostatic patches and the identification potential protein-protein interaction. The divergence between GAS6 and PROS1 probably occurred during the whole-genome duplications in vertebrates. A total of 78 amino acid sites were identified to be under functional divergence. One of these sites, Asn463, is involved in N-glycosylation in GAS6, but is mutated in PROS1, preventing this post-translational modification. Sites experiencing functional divergence tend to express a greater diversity of stabilizing/destabilizing effects than sites that do not experience such functional divergence. Three electrostatic patches in the LG1/LG2 domains were found to differ between GAS6 and PROS1. Finally, a surface responsible for protein-protein interactions was identified. These results may help researchers to analyse disease-causing mutations in the light of evolutionary and structural constraints, and link genetic pathology to clinical phenotypes.

Show MeSH