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Structure alignment based on coding of local geometric measures.

Peter L Chang1, Andrew W Rinne, T Gregory Dewey

  • 1Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA. peter_chang@kgi.edu

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Summary
This summary is machine-generated.

A novel method uses the writhing number to encode protein structures as a 20-letter alphabet, transforming structure alignment into sequence alignment. This approach enables efficient, high-quality protein structure comparisons.

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biophysics

Background:

  • Protein structure alignment is crucial for understanding function and evolution.
  • Existing methods in Cartesian coordinates struggle with subtle structural variations like twists and bends.
  • A new local geometric property, the writhing number, is introduced as a measure.

Purpose of the Study:

  • To develop a novel protein structure alignment method using local geometric properties.
  • To transform the 3D structure alignment problem into a 2D sequence alignment problem.
  • To improve the accuracy and efficiency of pairwise and multiple structure alignments.

Main Methods:

  • The writhing number, derived from knot theory, is calculated along the protein chain using a sliding window.
  • Protein geometries are encoded into a 20-letter alphabet based on writhing number distributions.
  • Standard sequence alignment algorithms (Smith-Waterman and CLUSTALW) are adapted for the geometric alphabet sequences.

Main Results:

  • Pairwise local alignment (TLOCAL) and multiple alignment (TCLUSTALW) programs were developed.
  • TLOCAL demonstrated high-quality alignments comparable to existing methods on difficult protein sets and hinged structures.
  • TCLUSTALW identified conserved regions in protein kinases, consistent with manual alignments.

Conclusions:

  • Encoding protein geometry via the writhing number enables high-quality structure alignments using sequence alignment algorithms.
  • This method offers computationally efficient algorithms for rapid database searching and multiple structure alignment.
  • The geometric approach allows for alignment exploration across different length scales by varying window sizes.