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Structural Bridges through Fold Space.

Hannah Edwards1, Charlotte M Deane1

  • 1Department of Statistics, University of Oxford, Oxford, United Kingdom.

Plos Computational Biology
|September 16, 2015
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Summary
This summary is machine-generated.

Protein structure networks reveal evolutionary relationships between folds. Ancestral protein folds form the core of these networks, with newer structures on the periphery, suggesting evolutionary information is encoded in structural bridges.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Evolutionary biology

Background:

  • Existing protein structure classification schemes partition the protein universe into folds but lack global structural relationships.
  • Understanding the global organization of protein fold space is crucial for deciphering protein evolution and function.

Purpose of the Study:

  • To construct networks representing global relationships between protein folds using structural bridges.
  • To investigate the influence of different structural alignment methods on network topology.
  • To explore the correlation between fold age, network centrality, and evolutionary patterns.

Main Methods:

  • Generation of protein fold networks using four distinct structural alignment methods.
  • Application of multiple score thresholds to define structural bridges.
  • Projection of estimated fold ages onto network structures.
  • Analysis of fold centrality measures within the constructed networks.

Main Results:

  • Networks generated by different methods show consistent distances, indicating method-specific structural bridges.
  • All network representations consistently identify five principal community structures in fold space.
  • Unconnected folds exhibit greater age differences than bridged folds, increasing with network representation.
  • Ancestral folds are located in the core of the networks, while newer folds populate the periphery.
  • Four pivotal folds are identified as dominant topological features and key attractors.

Conclusions:

  • Protein fold space organization is robust across different structural alignment methods, despite some method-specific bridges.
  • Fold networks encode evolutionary information, with ancestral folds centrally located and newer folds peripheral.
  • The identified pivotal folds represent key evolutionary hubs within protein structural space.