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Computational analysis of sequence selection mechanisms.

Leonid Meyerguz1, Catherine Grasso, Jon Kleinberg

  • 1Department of Computer Science, 4130 Upson Hall, Cornell University, Ithaca, NY 14853, USA.

Structure (London, England : 1993)
|April 6, 2004
PubMed
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Protein foldability, a key evolutionary constraint, influences gene variation. This study reveals universal structure selection mechanisms for longer protein sequences, but not for shorter ones.

Area of Science:

  • Evolutionary biology
  • Biophysics
  • Structural biology

Background:

  • Gene variations drive species diversity and are central to evolutionary theory.
  • Protein foldability, ensuring thermodynamic stability of 3D structures, acts as a critical constraint on gene evolution.

Purpose of the Study:

  • To investigate the impact of protein foldability constraint on sequence evolution.
  • To develop a selection function predicting survival probability based on sequence fitness to protein structure.
  • To analyze properties of foldable protein sequences using a large dataset.

Main Methods:

  • Utilized 3660 protein structures from the Protein Data Bank (PDB).
  • Calculated sequence properties including density, entropy, and 'selection' temperature.

Related Experiment Videos

  • Computed the number of sequences with energies lower than native sequences for specific protein structures.

    • Main Results:

    • Identified an approximately universal mechanism of structure selection for protein sequences exceeding 200 amino acids.
    • Observed that this selection mechanism is not universal for shorter protein sequences.
    • Quantified sequence fitness to structure, density, and entropy.

    Conclusions:

    • Protein foldability significantly constrains evolutionary trajectories of gene sequences.
    • The universality of structure selection mechanisms differs based on protein sequence length.
    • Further research is needed to elucidate specific evolutionary mechanisms underlying length-dependent selection.