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
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 user-editable 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.
Macromolecular hydrodynamics Bead modeling Analytical ultracentrifugation Protein structure and dynamics NMR spectroscopy X-ray crystallography
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We thank M. Nöllmann for providing his newAtoB code, and O. Byron for suggestions. The development of the UltraScan and US-SOMO is supported by the National Institute of Health Grant # RR022200 (to B. D.). M. R. gratefully acknowledges support from the Istituto Superiore della Sanità, program Italia-USA.
Demeler B (2005) UltraScan. A comprehensive data analysis software package for analytical ultracentrifugation experiments. In: Scott DJ, Harding SE, Rowe AJ (eds) Modern analytical ultracentrifugation: techniques and methods. Royal Society of Chemistry, UK, pp 210–229Google Scholar
Harding SE, Longman E, Carrasco B, Ortega A, García de la Torre J (2004) Studying antibody conformations by ultracentrifugation and hydrodynamic modeling. Methods Mol Biol 248:93–113PubMedGoogle Scholar
Rai N, Nöllmann M, Spotorno B, Tassara G, Byron O, Rocco M (2005) SOMO (SOlution MOdeler): differences between X-ray- and NMR-derived bead models suggest a role for side chain flexibility in protein hydrodynamics. Structure 13:723–734. doi:10.1016/j.str.2005.02.012CrossRefPubMedGoogle Scholar
Rocco M, Rosano C, Weisel JW, Horita DA, Hantgan RR (2008) Integrin conformational regulation: uncoupling extension/tail separation from changes in the head region by a multi-resolution approach. Structure 16:954–964. doi:10.1016/j.str.2008.02.019CrossRefPubMedGoogle Scholar
Spotorno B, Piccinini L, Tassara G, Ruggiero C, Nardini M, Molina F, Rocco M (1997) BEAMS (BEAds Modelling System): a set of computer programs for the generation, the visualization and the computation of the hydrodynamic and conformational properties of bead models of proteins. Eur Biophys J 25:373–384 Erratum 26:417CrossRefGoogle Scholar
Tanford C (1961) Physical chemistry of macromolecules. Wiley, New YorkGoogle Scholar
Tsodikov OV, Record MT Jr, Sergeev YV (2002) Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J Comput Chem 23:600–609. doi:10.1002/jcc.10061CrossRefPubMedGoogle Scholar
Zipper P, Durchschlag H (1997) Calculation of hydrodynamic parameters of proteins from crystallographic data using multibody approaches. Prog Colloid Polym Sci 107:58–71. doi:10.1007/BFb0118015CrossRefGoogle Scholar
Zipper P, Durchschlag H (1998) Recent advances in the calculation of hydrodynamic parameters from crystallographic data by multibody approaches. Biochem Soc Trans 26:726–731PubMedGoogle Scholar