Structural complementarity of distance constraints obtained from chemical cross-linking and amino acid coevolution

Author(s)

dos Santos, Ricardo N. ^{[1, 2]} ; Bottino, Guilherme F. ^{[1, 2]} ; Gozzo, Fabio C. ^[1] ; Morcos, Faruck ^{[3, 4]} ; Martinez, Leandro ^{[1, 2]}

Affiliation

^[1] Univ Estadual Campinas, Inst Chem, Campinas, SP - Brazil

^[2] Univ Estadual Campinas, Ctr Comp Engn & Sci, Campinas, SP - Brazil

^[3] Univ Texas Dallas, Dept Biol Sci, Richardson, TX 75083 - USA

^[4] Univ Texas Dallas, Dept Bioengn, Richardson, TX 75083 - USA

• Document type: Journal article
• Source: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS; v. 88, n. 4 NOV 2019.
• Web of Science Citations: 0

Abstract

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. (AU)

• FAPESP's process: 18/14274-9 - Protein Structure Determination from Distance Constraints Derived from Chemical Cross-linking: Computational Methods and Applications
• Grantee: Leandro Martinez
• Support Opportunities: Regular Research Grants
• FAPESP's process: 10/16947-9 - Correlations between dynamics, structure and function in protein: computer simulations and algorithms
• Grantee: Leandro Martinez
• Support Opportunities: Regular Research Grants
• FAPESP's process: 15/13667-9 - Studies of multimeric protein systems through cross-linking, mass spectrometry and molecular modeling
• Grantee: Ricardo Nascimento dos Santos
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 18/24293-0 - Computational methods in optimization
• Grantee: Sandra Augusta Santos
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
• Grantee: Munir Salomao Skaf
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• FAPESP's process: 14/17264-3 - New frontiers in structural proteomics: characterizing protein and protein complex structures by mass spectrometry
• Grantee: Fabio Cesar Gozzo
• Support Opportunities: Research Projects - Thematic Grants