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Structural complementarity of distance constraints obtained from chemical cross‐linking and amino acid coevolution
Author(s) -
Santos Ricardo N.,
Bottino Guilherme F.,
Gozzo Fábio C.,
Morcos Faruck,
Martínez Leandro
Publication year - 2020
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25843
Subject(s) - complementarity (molecular biology) , coevolution , amino acid residue , protein tertiary structure , low resolution , constraint (computer aided design) , protein structure , amino acid , computer science , resolution (logic) , computational biology , biological system , algorithm , mathematics , chemistry , high resolution , biology , evolutionary biology , peptide sequence , artificial intelligence , genetics , geography , biochemistry , geometry , remote sensing , gene
The analysis of amino acid coevolution has emerged as a practical method for protein structural modeling by providing structural contact information from alignments of amino acid sequences. In parallel, chemical cross‐linking/mass spectrometry (XLMS) has gained attention as a universally applicable method for obtaining low‐resolution distance constraints to model the quaternary arrangements of proteins, and more recently even protein tertiary structures. Here, we show that the structural information obtained by XLMS and coevolutionary analysis are effectively complementary: the distance constraints obtained by each method are almost exclusively associated with non‐coincident pairs of residues, and modeling results obtained by the combination of both sets are improved relative to considering the same total number of constraints of a single type. The structural rationale behind the complementarity of the distance constraints is discussed and illustrated for a representative set of proteins with different sizes and folds.