title: A unified convention for biological assemblies with helical symmetry.
abstract: Assemblies with helical symmetry can be conveniently formulated in many distinct ways. Here, a new convention is presented which unifies the two most commonly used helical systems for generating helical assemblies from asymmetric units determined by X-ray fibre diffraction and EM imaging. A helical assembly is viewed as being composed of identical repetitive units in a one- or two-dimensional lattice, named 1-D and 2-D helical systems, respectively. The unification suggests that a new helical description with only four parameters [n(1), n(2), twist, rise], which is called the augmented 1-D helical system, can generate the complete set of helical arrangements, including coverage of helical discontinuities (seams). A unified four-parameter characterization implies similar parameters for similar assemblies, can eliminate errors in reproducing structures of helical assemblies and facilitates the generation of polymorphic ensembles from helical atomic models or EM density maps. Further, guidelines are provided for such a unique description that reflects the structural signature of an assembly, as well as rules for manipulating the helical symmetry presentation.
authors.affiliation: Basic Science Program, SAIC-Frederick Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA. tsaic@mail.nih.gov
authors.forename: Chung Jung
authors.initials: CJ
authors.lastname: Tsai
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
mesh_terms: D001435:Bacteriophages / Q000737:chemistry; D036022:Capsid Proteins / Q000737:chemistry; D018360:Crystallography, X-Ray / Q000379:methods*; D015497:HIV-1 / Q000737:chemistry; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D040681:Structural Homology, Protein
chemical_list: D036022:Capsid Proteins