A many-body term improves the accuracy of effective potentials based on protein coevolutionary data

The study of correlated mutations in alignments of homologous proteins proved to be successful not only in the prediction of their native conformation but also in the development of a two-body effective potential between pairs of amino acids. In the present work, we extend the effective potential, i...

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Bibliographic Details
Published in:The Journal of chemical physics 2015-07, Vol.143 (2), p.025103-025103
Main Authors: Contini, A, Tiana, G
Format: Article
Language:English
Subjects:
Amino acids
Correlation analysis
Entropy
Homology
Hydrophobic and Hydrophilic Interactions
Hydrophobicity
Maximum entropy
Models, Chemical
Mutation
Physics
Predictions
Proteins
Proteins - chemistry
Proteins - genetics
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Summary:The study of correlated mutations in alignments of homologous proteins proved to be successful not only in the prediction of their native conformation but also in the development of a two-body effective potential between pairs of amino acids. In the present work, we extend the effective potential, introducing a many-body term based on the same theoretical framework, making use of a principle of maximum entropy. The extended potential performs better than the two-body one in predicting the energetic effect of 308 mutations in 14 proteins (including membrane proteins). The average value of the parameters of the many-body term correlates with the degree of hydrophobicity of the corresponding residues, suggesting that this term partly reflects the effect of the solvent.
ISSN:0021-9606
1089-7690
DOI:10.1063/1.4926665