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

18 Pages Posted: 2 May 2019 Sneak Peek Status: Review Complete

See all articles by Ricardo N. dos Santos

Ricardo N. dos Santos

Universidade Estadual de Campinas (UNICAMP) - Institute of Chemistry

Fábio C. Gozzo

Universidade Estadual de Campinas (UNICAMP) - Institute of Chemistry

Faruck Morcos

University of Texas at Dallas - Department of Biological Sciences

Leandro Martinez

Universidade Estadual de Campinas (UNICAMP) - Institute of Chemistry

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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.

Keywords: protein modeling, chemical crosslinking, mass spectrometry, coevolution, distance constraints

Suggested Citation

dos Santos, Ricardo N. and Gozzo, Fábio C. and Morcos, Faruck and Martinez, Leandro, Structural Complementarity of Distance Constraints Obtained from Chemical Crosslinking and Amino Acid Coevolution (April 26, 2019). STRUCTURE-D-19-00099. Available at SSRN: https://ssrn.com/abstract=3378282 or http://dx.doi.org/10.2139/ssrn.3378282
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Ricardo N. Dos Santos

Universidade Estadual de Campinas (UNICAMP) - Institute of Chemistry ( email )

Campinas
Brazil

Fábio C. Gozzo

Universidade Estadual de Campinas (UNICAMP) - Institute of Chemistry

Campinas
Brazil

Faruck Morcos

University of Texas at Dallas - Department of Biological Sciences ( email )

Richardson, TX
United States

Leandro Martinez (Contact Author)

Universidade Estadual de Campinas (UNICAMP) - Institute of Chemistry ( email )

Campinas
Brazil

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