title: QUAFIT: a novel method for the quaternary structure determination from small-angle scattering data.
abstract: The new QUAFIT method for determining the quaternary structure of biological macromolecular assemblies by analyzing x-ray or neutron small-angle scattering data is presented. The method is based on the idea that asymmetric monomers, formed by rigid domains of known atomic structure possibly connected by flexible linkers of known sequence, are assembled according to a point-group symmetry combined with a screw axis. Scattering amplitudes of domains and linkers are determined by means of a spherical harmonics expansion and combined to get the form factor of the assembly. To avoid any overlap among domains, the contact distance between two asymmetric domains is determined as a function of their orientation by a new algorithm, based on Stone's Invariants expansion. To account for continuity and compactness of the whole assembly, an anisotropic Lennard-Jones potential among domains, written in terms of the contact distances, is included in the merit function. QUAFIT allows for the simultaneous presence of oligomerization intermediates as well as of monomers distributed over multiple conformations. QUAFIT has been tested by studying the structure of a high molecular weight protein, the hemocyanin from Octopus vulgaris, under solution conditions that stabilize the decameric form or induce dissociation into monomers, respectively. Results are in very good agreement with the structural model derived from electron microscopy observations.
authors.affiliation: Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, Ancona, Italy. Electronic address: f.spinozzi@univpm.it.
authors.forename: Francesco
authors.initials: F
authors.lastname: Spinozzi
authors.affiliation: Dipartimento di Biologia, Università di Padova, Padova, Italy.
authors.forename: Mariano
authors.initials: M
authors.lastname: Beltramini
mesh_terms: D000818:Animals; D006433:Hemocyanins / Q000737:chemistry*; D008958:Models, Molecular; D033363:Neutron Diffraction; D049831:Octopodiformes; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D015203:Reproducibility of Results; D053838:Scattering, Small Angle; D012984:Software; D013223:Statistics as Topic / Q000379:methods*; D014961:X-Ray Diffraction
chemical_list: D006433:Hemocyanins