A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices.
amino acid substitution
exchangeabilities
protein evolution
protein stability
replacement matrices
Journal
Protein science : a publication of the Protein Society
ISSN: 1469-896X
Titre abrégé: Protein Sci
Pays: United States
ID NLM: 9211750
Informations de publication
Date de publication:
10 2021
10 2021
Historique:
revised:
25
06
2021
received:
17
03
2021
accepted:
29
06
2021
pubmed:
5
7
2021
medline:
25
12
2021
entrez:
4
7
2021
Statut:
ppublish
Résumé
Proteins evolve under a myriad of biophysical selection pressures that collectively control the patterns of amino acid substitutions. These evolutionary pressures are sufficiently consistent over time and across protein families to produce substitution patterns, summarized in global amino acid substitution matrices such as BLOSUM, JTT, WAG, and LG, which can be used to successfully detect homologs, infer phylogenies, and reconstruct ancestral sequences. Although the factors that govern the variation of amino acid substitution rates have received much attention, the influence of thermodynamic stability constraints remains unresolved. Here we develop a simple model to calculate amino acid substitution matrices from evolutionary dynamics controlled by a fitness function that reports on the thermodynamic effects of amino acid mutations in protein structures. This hybrid biophysical and evolutionary model accounts for nucleotide transition/transversion rate bias, multi-nucleotide codon changes, the number of codons per amino acid, and thermodynamic protein stability. We find that our theoretical model accurately recapitulates the complex yet universal pattern observed in common global amino acid substitution matrices used in phylogenetics. These results suggest that selection for thermodynamically stable proteins, coupled with nucleotide mutation bias filtered by the structure of the genetic code, is the primary driver behind the global amino acid substitution patterns observed in proteins throughout the tree of life.
Identifiants
pubmed: 34218472
doi: 10.1002/pro.4155
pmc: PMC8442976
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2057-2068Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM096053
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM132499
Pays : United States
Informations de copyright
© 2021 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.
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