Helical assemblies: structure determinants

J Theor Biol. 2015 Mar 21;369:80-84. doi: 10.1016/j.jtbi.2015.01.012. Epub 2015 Jan 19.

Abstract

Protein structural motifs such as helical assemblies and α/β barrels combine secondary structure elements with various types of interactions. Helix-helix interfaces of assemblies - Ankyrin, ARM/HEAT, PUM, LRR, and TPR repeats - exhibit unique amino acid composition and patterns of interactions that correlate with curvature of solenoids, surface geometry and mutual orientation of the helical edges. Inner rows of ankyrin, ARM/HEAT, and PUM-HD repeats utilize edges (i-1, i) and (i+1, i+2) for the interaction of the given α-helix with preceding and following helices correspondingly, whereas outer rows of these proteins and LRR repeats invert this pattern and utilize edges (i-1, i) and (i-3, i-2). Arrangement of contacts observed in protein ligands that bind helical assemblies has to mimic the assembly pattern to provide the same curvature as a determinant of binding specificity. These characteristics are important for understanding fold recognition, specificity of protein-protein interactions, and design of new drugs and materials.

Keywords: Assembly; Enantiomer-selective ligand binding; Helix–helix interface; Protein conformation; Repeats.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Ankyrins / chemistry
  • Databases, Protein
  • Molecular Sequence Data
  • Protein Binding
  • Protein Structure, Secondary
  • Proteins / chemistry*

Substances

  • Ankyrins
  • Proteins