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Related Experiment Videos

The network of sequence flow between protein structures.

Leonid Meyerguz1, Jon Kleinberg, Ron Elber

  • 1Department of Computer Science, Cornell University, Ithaca, NY 14853, USA.

Proceedings of the National Academy of Sciences of the United States of America
|June 29, 2007
PubMed
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Many protein sequences fold into a few structures, creating a directed graph. This study reveals that few sequences transition between folds, with beta-sheet-rich structures acting as "sinks" for sequence flow.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein sequence-structure relationships are asymmetric, with numerous sequences mapping to limited structures.
  • Understanding the "sequence space" for a given protein fold is crucial for protein design and evolution studies.
  • The possibility of interconverting protein folds via point mutations remains an open question.

Purpose of the Study:

  • To quantify the number of protein sequences that can fold into a specific structure.
  • To investigate the potential for switching between stable protein folds through point mutations.
  • To analyze the connectivity and flow of sequences within the protein sequence-structure landscape.

Main Methods:

  • Construction of a directed graph representing protein sequences and their corresponding structures.

Related Experiment Videos

  • Utilizing 2,060 experimentally determined protein structures from the Protein Data Bank (PDB).
  • Analysis of graph properties, including connectivity, "sinks," and strongly connected components.

    • Main Results:

    • The computed directed graph exhibits high connectivity at native energies, featuring "sinks" that attract sequences from diverse folds.
    • Beta-sheet-rich structures are identified as prominent sinks in the sequence-structure graph.
    • The number of sequences transitioning between folds is substantially lower than those remaining within their native fold.
    • Sequence flow into specific protein shapes correlates with their prevalence in empirically determined genomes.
    • Properties of strongly connected components align with protein length and secondary structure characteristics.

    Conclusions:

    • Protein sequence space is characterized by a significant asymmetry, with many sequences converging onto fewer structures.
    • The landscape of protein folds is relatively stable, with limited sequence plasticity for fold switching.
    • The observed sequence flow patterns provide insights into evolutionary constraints and the functional distribution of protein structures.