Structural Complementarity of Distance Constraints Obtained from Chemical Crosslinking and Amino Acid Coevolution

Abstract

In recent years, the analysis of amino acid coevolution has emerged as a practical method for protein structural modeling by providing structural contact information from the alignment 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 orthogonal, in the sense that the distance constraints obtained by each method are almost exclusively associated with non-coincident pairs of residues. Therefore, the combination of the two methods has an unanticipated potential to improve structural modeling results. 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.