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Modeling repetitive, non-globular proteins.

Koli Basu1, Robert L Campbell1, Shuaiqi Guo1

  • 1Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada.

Protein Science : a Publication of the Protein Society
|February 26, 2016
PubMed
Summary
This summary is machine-generated.

Modeling repetitive protein structures is challenging but achievable. Knowledge of consensus sequences and secondary structures aids in building novel protein models, even with ab initio methods.

Keywords:
Beta-solenoidantifreeze proteinmolecular dynamicsprotein modelingrepetitive proteintandem repeat

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Ab initio protein structure modeling is complex and not yet routine.
  • Proteins with repetitive sequences often display repetitive structures.
  • Modeling these repetitive proteins is feasible with additional sequence information.

Purpose of the Study:

  • To review methods for successfully modeling repetitive protein structures.
  • To highlight the utility of consensus sequence and secondary structure information.
  • To demonstrate the creation of novel protein folds using these approaches.

Main Methods:

  • Utilizing knowledge of the consensus sequence within repeats.
  • Incorporating understanding of probable secondary structures.
  • Applying these insights to ab initio modeling of repetitive proteins.

Main Results:

  • Successful construction of models for repetitive protein structures.
  • Generation of models with novel, previously uncharacterized folds.
  • Demonstration of feasibility for de novo modeling of specific protein classes.

Conclusions:

  • Ab initio modeling of repetitive protein structures is viable.
  • Consensus sequence and secondary structure prediction are key.
  • This approach facilitates the discovery of novel protein folds.