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Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
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The GD box: a widespread noncontiguous supersecondary structural element.

Vikram Alva1, Stanislaw Dunin-Horkawicz, Michael Habeck

  • 1Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany.

Protein Science : a Publication of the Protein Society
|July 18, 2009
PubMed
Summary
This summary is machine-generated.

Researchers identified the GD box, a novel supersecondary protein structure element. This widespread motif, found in various protein folds, aids in understanding protein structure formation and prediction.

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Area of Science:

  • Structural biology
  • Protein bioinformatics

Background:

  • Understanding protein tertiary structure relies on identifying recurring supersecondary structural elements.
  • Noncontiguous elements are crucial for protein folding but less understood than contiguous ones.

Purpose of the Study:

  • To identify and characterize a novel noncontiguous supersecondary structural element, the GD box.
  • To assess the prevalence and distribution of the GD box across diverse protein folds.

Main Methods:

  • Structure-based analysis of protein domains from the SCOP database.
  • Sequence and structural comparison to define the GD box motif.

Main Results:

  • The GD box, comprising two beta-strands and a beta-turn, was identified.
  • 518 instances of the GD box were found in 3771 protein domains.
  • The motif exists in homologous beta-barrels and diverse nonhomologous folds.

Conclusions:

  • The GD box is a widespread supersecondary structural element beyond its initial discovery in cradle-loop barrels.
  • Systematic identification of noncontiguous elements like the GD box is valuable for protein structure modeling and prediction.