The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule

Abstract

The interpretation of solution hydrodynamic data in terms of macromolecular structural parameters is not a straightforward task. Over the years, several approaches have been developed to cope with this problem, the most widely used being bead modeling in various flavors. We report here the implementation of the SOMO (SOlution MOdeller; Rai et al. in Structure 13:723-734, 2005) bead modeling suite within one of the most widely used analytical ultracentrifugation data analysis software packages, UltraScan (Demeler in Modern analytical ultracentrifugation: techniques and methods, Royal Society of Chemistry, UK, 2005). The US-SOMO version is now under complete graphical interface control, and has been freed from several constraints present in the original implementation. In the direct beads-per-atoms method, virtually any kind of residue as defined in the Protein Data Bank (e.g., proteins, nucleic acids, carbohydrates, prosthetic groups, detergents, etc.) can be now represented with beads whose number, size and position are all defined in usereditable tables. For large structures, a cubic grid method based on the original AtoB program (Byron in Biophys J 72:408-415, 1997) can be applied either directly on the atomic structure, or on a previously generated bead model. The hydrodynamic parameters are then computed in the rigid-body approximation. An extensive set of tests was conducted to further validate the method, and the results are presented here. Owing to its accuracy, speed, and versatility, US-SOMO should allow to fully take advantage of the potential of solution hydrodynamics as a complement to higher resolution techniques in biomacromolecular modeling.Correspondence to: Mattia Rocco, mattia.rocco@istge.it.

Characterization of Conformational Changes and Protein-Protein Interactions of Rod Photoreceptor Phosphodiesterase (PDE6)

“…This corresponds to a Stokes radius of 2.0 ϫ 10 Ϫ7 cm and an axial ratio of 1.3, indicating that the protein is essentially a spherical globular protein in solution. Our results are consistent with the predicted hydrodynamic properties of PrBP/␦ based on modeling the x-ray crystal structure (Protein Data Bank entry 1KSH, chain B) using SOMO (35,36), supporting the characterization of PrBP/␦ as a tightly organized, immunoglobulin-like fold protein (53).…”

“…The predicted hydrodynamic behavior for those proteins for which crystallographic data were available was determined using Solution Modeler (SOMO) (35,36).…”

Dimerization of Bacterial Diaminopimelate Epimerase Is Essential for Catalysis

“…Sedimentation equilibrium data were fitted to a monomer-dimer self-association model using SEDPHAT (35). Bead modeling was conducted using the SOMO method incorporated in the UltraScan III software suite (36,37).…”

Characterization of Pgp3, aChlamydia trachomatisPlasmid-Encoded Immunodominant Antigen

“…The running buffer used for the native gels also contained 0.01% (wt/vol) SDS, which did not affect the stability of Pgp3 trimers but allowed clear separation of protein bands. Protein samples run on denaturing gels were subjected to heat denaturing by boiling for 5 all from Sigma) and incubated on ice for 30 min. The mixtures were centrifuged at 21,000 ϫ g for 15 min at 4°C, and the remaining supernatant was collected for loading into gels.…”