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Sequence-Similar Protein Domain Pairs With Structural or Topological Dissimilarity.

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  • 1Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.

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Summary
This summary is machine-generated.

Protein structures with similar sequences can have different topologies. BCAlign identifies these topological variations, crucial for understanding protein function and evolution, especially between X-ray and NMR structures.

Keywords:
chain topologymetric on sequence alignmentsnonredundantstructure alignmentstructure comparison

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational chemistry

Background:

  • Protein structure analysis often clusters by sequence similarity, discarding redundant structures.
  • Sequence similarity usually implies structural similarity, but significant variations exist, often with functional implications.
  • Backbone movements can alter protein chain topology and folding pathways.

Purpose of the Study:

  • To identify protein domains with alternate chain topologies within sequence families.
  • To develop a method (BCAlign) for aligning protein backbone curves that accounts for both structural and sequence-based derivations.
  • To investigate the relationship between sequence similarity, structural variation, and topological differences in protein structures.

Main Methods:

  • Utilized the CATH4.2 database to search for domains with alternate chain topologies.
  • Developed BCAlign to optimize alignments by combining structural and sequence-based derivations.
  • Employed an algorithm to detect steric and topological obstructions during curve deformation.
  • Compared sequence-based and structure-based alignments for highly sequence-similar domains.

Main Results:

  • Identified domains with alternate chain topologies across CATH4.2 sequence families, largely independent of sequence identity or RMSD.
  • BCAlign effectively aligns protein backbone curves, revealing structural and topological variations.
  • Sequence-based alignment highlighted greater structural and topological variations in highly sequence-similar domains compared to structure-based alignment.
  • Alternate chain topologies were most frequently observed between X-ray and NMR structures.

Conclusions:

  • Representative protein structure sets should include sequence-similar domains exhibiting topological variations.
  • BCAlign provides a novel approach for analyzing protein backbone flexibility and topological changes.
  • Understanding topological variations is essential for comprehensive protein structure-function relationship studies.
  • The prevalence of altered topology between X-ray and NMR structures suggests underrepresentation of such variations in databases.