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Related Experiment Videos

Multiple structural alignment for distantly related all beta structures using TOPS pattern discovery and simulated

A Williams1, D R Gilbert, D R Westhead

  • 1School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT.

Protein Engineering
|February 26, 2004
PubMed
Summary

Topsalign is a novel method for aligning diverse protein structures, even with low sequence identity. It effectively uses topological descriptions and pattern discovery to create accurate multiple structure alignments and superpositions.

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Structure Analysis

Background:

  • Protein superfolds share common structural scaffolds but exhibit low sequence identity and functional diversity.
  • Significant structural variations can exist within superfolds, challenging traditional alignment methods.

Purpose of the Study:

  • To introduce Topsalign, a new method for structurally aligning diverse protein structures.
  • To evaluate Topsalign's performance against established methods on challenging protein superfamilies.

Main Methods:

  • Topsalign utilizes topological protein descriptions and a pattern discovery algorithm to identify equivalent secondary structure elements.
  • An initial multiple structure alignment is generated, followed by optimization using simulated annealing.

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  • The method outputs a multiple structure-based sequence alignment and a 3D superposition of protein structures.

    • Main Results:

    • Topsalign successfully aligned diverse protein structures from three superfolds: beta-jelly roll, TIM (alpha/beta) barrel, and OB fold.
    • The method demonstrated superior performance compared to existing techniques, particularly for highly diverse structures.
    • Topsalign effectively aligned TIM (alpha/beta) barrel superfamilies, despite the pattern discovery focusing on beta strands.

    Conclusions:

    • Topsalign provides an effective approach for structural alignment of proteins with low sequence identity and high structural diversity.
    • The method's ability to handle mixed secondary structure elements (alpha-helices and beta-strands) enhances its applicability.