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Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
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The elusive π-helix.

R Peter Riek1, Robert M Graham

  • 1Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, 2010 NSW, Australia. p.riek@victorchang.edu.au

Journal of Structural Biology
|September 11, 2010
PubMed
Summary
This summary is machine-generated.

Researchers discovered that protein structures previously thought to be pi-helices are actually wide turns. These structures mimic pi-helix radius without an energetically unfavorable central hole, enabling new protein functionalities.

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Area of Science:

  • Protein structure and bioinformatics
  • Biophysics
  • Structural biology

Background:

  • Protein secondary structures, such as alpha-helices, are crucial for protein architecture.
  • Alpha-helices constitute 30-40% of protein domains, featuring 3.6 residues per turn.
  • Pi-helices, with 4.4 residues per turn, have been proposed but present energetic challenges due to a central void.

Purpose of the Study:

  • To investigate the true nature of protein structures proposed as pi-helices.
  • To understand the structural and functional implications of these helical regions.
  • To resolve the energetic paradox associated with proposed pi-helical structures.

Main Methods:

  • Analysis of protein structural data.
  • Computational modeling of polypeptide backbone arrangements.
  • Examination of van der Waals interactions within helical structures.

Main Results:

  • Helical regions previously identified as putative pi-helices are composed of concatenated wide turns with elliptical configurations.
  • These structures possess a larger helical radius similar to pi-helices but avoid an energetically unfavorable central void.
  • Favorable cross-core van der Waals interactions are maintained.

Conclusions:

  • The identified wide turns represent a novel structural motif in proteins.
  • This structural arrangement obviates the helical void issue associated with pi-helices.
  • These structures contribute to protein functionality, including metal ion coordination, flexibility, and enzyme-substrate interactions.