A common root for coevolution and substitution rate variability in protein sequence evolution
We introduce a simple model that describes the average occurrence of point variations in a generic protein sequence. This model is based on the idea that mutations are more likely to be fixed at sites in contact with others that have mutated in the recent past. Therefore, we extend the usual assumpt...
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| Veröffentlicht in: | Scientific reports 2019-12, Vol.9 (1), p.18032-10, Article 18032 |
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| creator | Rizzato, Francesca Zamuner, Stefano Pagnani, Andrea Laio, Alessandro |
| description | We introduce a simple model that describes the average occurrence of point variations in a generic protein sequence. This model is based on the idea that mutations are more likely to be fixed at sites in contact with others that have mutated in the recent past. Therefore, we extend the usual assumptions made in protein coevolution by introducing a time dumping on the effect of a substitution on its surrounding and makes correlated substitutions happen in avalanches localized in space and time. The model correctly predicts the average correlation of substitutions as a function of their distance along the sequence. At the same time, it predicts an among-site distribution of the number of substitutions per site highly compatible with a negative binomial, consistently with experimental data. The promising outcomes achieved with this model encourage the application of the same ideas in the field of pairwise and multiple sequence alignment. |
| doi_str_mv | 10.1038/s41598-019-53958-w |
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| subjects | 631/114 631/114/2397 631/181/2474 631/181/2481 639/766/747 Amino Acid Sequence - genetics Amino Acid Substitution Codon - genetics Coevolution Evolution, Molecular Humanities and Social Sciences Humans Landslides Models, Genetic multidisciplinary Nucleotide sequence Point Mutation Proteins Science Science (multidisciplinary) Sequence Alignment |
| title | A common root for coevolution and substitution rate variability in protein sequence evolution |
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