Evolutionary models of amino acid substitutions based on the tertiary structure of their neighborhoods.
Proteins
; 89(11): 1565-1576, 2021 11.
Article
em En
| MEDLINE
| ID: mdl-34278605
ABSTRACT
Intra-protein residual vicinities depend on the involved amino acids. Energetically favorable vicinities (or interactions) have been preserved during evolution, while unfavorable vicinities have been eliminated. We describe, statistically, the interactions between amino acids using resolved protein structures. Based on the frequency of amino acid interactions, we have devised an amino acid substitution model that implements the following idea amino acids that have similar neighbors in the protein tertiary structure can replace each other, while substitution is more difficult between amino acids that prefer different spatial neighbors. Using known tertiary structures for α-helical membrane (HM) proteins, we build evolutionary substitution matrices. We constructed maximum likelihood phylogenies using our amino acid substitution matrices and compared them to widely-used methods. Our results suggest that amino acid substitutions are associated with the spatial neighborhoods of amino acid residuals, providing, therefore, insights into the amino acid substitution process.
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Texto completo:
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Base de dados:
MEDLINE
Assunto principal:
Algoritmos
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Software
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Evolução Molecular
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Substituição de Aminoácidos
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Aminoácidos
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Proteínas de Membrana
Idioma:
En
Revista:
Proteins
Assunto da revista:
BIOQUIMICA
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
Grécia