title: Helical assemblies: structure determinants.
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.
authors.affiliation: The School of Theoretical Modeling, 1629 K St NW s 300, Washington, DC 20006, United States. Electronic address: info@schtm.org.
authors.forename: Natalya A
authors.initials: NA
authors.lastname: Kurochkina
authors.affiliation: 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.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Iadarola
mesh_terms: D000595:Amino Acid Sequence; D017487:Ankyrins / Q000737:chemistry; D030562:Databases, Protein; D008969:Molecular Sequence Data; D011485:Protein Binding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D017487:Ankyrins; D011506:Proteins
keywords: Assembly; Enantiomer-selective ligand binding; Helix–helix interface; Protein conformation; Repeats