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

Helical assemblies: structure determinants.

Author information

1
The School of Theoretical Modeling, 1629 K St NW s 300, Washington, DC 20006, United States. Electronic address: info@schtm.org.
2
Anesthesia Section, Department of Perioperative Medicine, Clinical Center, NIH, Building 10, Room 2C401, 10 Center Drive, MSC 1510, Bethesda, MD 20892, United States. Electronic address: michael.iadarola@nih.gov.

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

PMID:
25613414
DOI:
10.1016/j.jtbi.2015.01.012
[Indexed for MEDLINE]

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