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Sequence co-evolution gives 3D contacts and structures of protein complexes.

Thomas A Hopf1, Charlotta P I Schärfe1, João P G L M Rodrigues2

  • 1Department of Systems Biology, Harvard University, Boston, United States.

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|September 26, 2014
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Summary

Analyzing evolutionary sequence changes reveals protein-protein interactions. This method accurately predicts 3D structures of protein complexes and can map interaction networks genome-wide.

Keywords:
E. colico-evolutionevolutionary biologygenomicsinteractionsprotein

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Protein-protein interactions are crucial for biological functions.
  • Experimental methods and structural biology provide insights but are limited in scope.
  • Evolutionary sequence data offers an alternative information source for protein interactions.

Purpose of the Study:

  • To develop and validate a method using evolutionary sequence analysis to predict protein-protein interactions and complex structures.
  • To assess the accuracy of predicting residue-level contacts in protein complexes.
  • To explore the application of this method for genome-wide interaction network elucidation.

Main Methods:

  • Analysis of correlated evolutionary sequence changes across proteins.
  • Prediction of residue proximity in 3D space based on evolutionary couplings.
  • Validation against known 3D structures of protein complexes.
  • Application to complexes with unknown structures.

Main Results:

  • Accurate identification of residues close in space, enabling 3D structure determination of protein complexes.
  • Successful prediction of protein-protein contacts in 32 complexes of unknown structure.
  • Demonstrated ability to distinguish interacting from non-interacting protein pairs within large complexes.

Conclusions:

  • Evolutionary sequence analysis is a powerful tool for predicting protein-protein interactions and structures.
  • The method shows high accuracy and broad applicability.
  • Future potential for genome-wide mapping of protein interaction networks at residue resolution.