European Biophysics Journal

, Volume 39, Issue 3, pp 423–435

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

  • Emre Brookes
  • Borries Demeler
  • Camillo Rosano
  • Mattia Rocco
Original Paper

DOI: 10.1007/s00249-009-0418-0

Cite this article as:
Brookes, E., Demeler, B., Rosano, C. et al. Eur Biophys J (2010) 39: 423. doi:10.1007/s00249-009-0418-0

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 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.

Keywords

Macromolecular hydrodynamics Bead modeling Analytical ultracentrifugation Protein structure and dynamics NMR spectroscopy X-ray crystallography 

Supplementary material

249_2009_418_MOESM_ESM.pdf (778 kb)
Supplementary material (PDF 777 kb)

Copyright information

© European Biophysical Societies' Association 2009

Authors and Affiliations

  • Emre Brookes
    • 1
  • Borries Demeler
    • 1
  • Camillo Rosano
    • 2
  • Mattia Rocco
    • 3
  1. 1.Department of BiochemistryThe University of Texas Health Science Center at San AntonioSan AntonioUSA
  2. 2.NanobiotecnologieIstituto Nazionale per la Ricerca sul Cancro (IST)GenoaItaly
  3. 3.Biopolimeri e ProteomicaIstituto Nazionale per la Ricerca sul Cancro (IST)GenoaItaly

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