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Multidomain protein structure prediction using information about residues interacting on multimeric protein

Shumpei Matsuno1,2, Masahito Ohue1,3, Yutaka Akiyama1,3

  • 1Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.

Biophysics and Physicobiology
|June 9, 2020
PubMed
Summary

Predicting multidomain protein structures is challenging. This study introduces a novel computational method using domain docking and interaction scoring, successfully predicting 50 of 55 protein structures without whole templates.

Keywords:
conformations rerankinginteraction residue pairmultidomain proteinprotein tertiary structure predictionrigid-body docking

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biochemistry

Background:

  • Protein function prediction relies on 3D structures, but multidomain proteins often have unstable structures.
  • Existing computational methods for multidomain protein structure prediction depend heavily on available structural templates.
  • A lack of suitable templates significantly reduces prediction accuracy for multidomain proteins.

Purpose of the Study:

  • To develop and validate a novel computational method for predicting multidomain protein structures without requiring whole protein structural templates.
  • To improve the accuracy and applicability of structure prediction for challenging multidomain proteins.

Main Methods:

  • Implemented a rigid-body docking approach using individual domain structures.
  • Developed a new scoring function incorporating domain-domain interaction scores and docking-derived 3D structure scores.
  • Incorporated interaction residue pair information from protein-protein complex interfaces to guide domain reorganization.

Main Results:

  • Successfully predicted the 3D structures of 50 out of 55 multidomain proteins in the test dataset.
  • Demonstrated the effectiveness of the improved scoring function in reranking correct structures higher.
  • Validated the contribution of interaction residue pair information in cases lacking whole protein templates.

Conclusions:

  • The proposed method accurately predicts multidomain protein structures without whole templates, overcoming limitations of existing approaches.
  • Domain docking combined with novel scoring effectively addresses challenges posed by unstable or uncharacterized multidomain proteins.
  • This approach holds significant potential for elucidating the structures and functions of important multidomain proteins in biochemistry.