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

被引:12
作者
Contini, A. [1 ]
Tiana, G. [1 ,2 ]
机构
[1] Univ Milan, Dept Phys, I-20133 Milan, Italy
[2] Ist Nazl Fis Nucl, I-20133 Milan, Italy
关键词
TRANSITION-STATE; AMINO-ACIDS; STABILITY; MUTATIONS; DOMAIN; MODEL;
D O I
10.1063/1.4926665
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
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. (C) 2015 AIP Publishing LLC.
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页数:7
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