SOMO (SOlution MOdeler)

• DOI: 10.1016/j.str.2005.02.012
• Publication Date: 2005-05-15T05:40:42Z
• Authors: Nithin Rai; Marcelo Nöllmann; Bruno Spotorno; Giovanni Tassara; Olwyn Byron; Mattia Rocco
• Keywords: Models, Molecular; 0303 health sciences; 03 medical and health sciences; Magnetic Resonance Spectroscopy; Structural Biology; Protein Conformation; Proteins; Crystallography, X-Ray; Molecular Biology; Algorithms

Reduced numbers of frictional/scattering centers are essential for tractable hydrodynamic and small-angle scattering data modeling. We present a method for generating medium-resolution models from the atomic coordinates of proteins, basically by using two nonoverlapping spheres of differing radii per residue. The computed rigid-body hydrodynamic parameters of BPTI, RNase A, and lysozyme models were compared with a large database of critically assessed experimental values. Overall, very good results were obtained, but significant discrepancies between X-ray- and NMR-derived models were found. Interestingly, they could be accounted for by properly considering the extent to which highly mobile surface side chains differently affect translational/rotational properties. Models of larger structures, such as fibrinogen fragment D and citrate synthase, also produced consistent results. Foremost among this method's potential applications is the overall conformation and dynamics of modular/multidomain proteins and of supramolecular complexes. The possibility of merging data from high- and low-resolution structures greatly expands its scope.