title: Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis.
abstract: A general method is presented to characterize the helical properties of potentially irregular helices, such as those found in protein secondary and tertiary structures and nucleic acids. The method was validated using artificial helices with varying numbers of points, points per helical turn, pitch, and radius. The sensitivity of the method was validated by applying increasing amounts of random perturbation to the coordinates of these helices; 399 360 helices in total were evaluated. In addition, the helical parameters of protein secondary structure elements and nucleic acid helices were analyzed. Generally, at least seven points were required to recapitulate the parameters of a helix using our method. The method can also be used to calculate the helical parameters of nucleic acid-binding proteins, like TALE, enabling direct analysis of their helix complementarity to sequence-dependent DNA distortions.
authors.affiliation: Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Kevin
authors.initials: K
authors.lastname: Hauser
authors.affiliation: Great Neck South High School , Great Neck, New York 11023, United States.
authors.forename: Yiqing
authors.initials: Y
authors.lastname: He
authors.affiliation: Department of Pharmacological Sciences, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Miguel
authors.initials: M
authors.lastname: Garcia-Diaz
authors.affiliation: Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.|Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Carlos
authors.identifier: 0000-0002-7252-4730
authors.initials: C
authors.lastname: Simmerling
authors.affiliation: Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States.|Department of Applied Mathematics and Statistics, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Evangelos
authors.identifier: 0000-0003-2910-9125
authors.initials: E
authors.lastname: Coutsias
mesh_terms: D004247:DNA / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D000072756:Protein Conformation, alpha-Helical; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D012399:Rotation
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA