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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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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]
Total Authors: 5
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
Total Affiliations: 4
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 type: 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 type: 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 type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 18/24293-0 - Computational methods in optimization
Grantee:Sandra Augusta Santos
Support type: Research Projects - Thematic Grants
FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
Grantee:Munir Salomao Skaf
Support type: 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 type: Research Projects - Thematic Grants