SOMO (SOlution MOdeler): Differences between X-ray- and NMR-derived bead models suggest a role for side chain flexibility in protein hydrodynamics

Nithin Rai, Marcelo Nöllmann, Bruno Spotorno, Giovanni Tassara, Olwyn Byron, Mattia Rocco

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish
Pages (from-to)723-734
Number of pages12
JournalStructure
Volume13
Issue number5
DOIs
Publication statusPublished - May 2005

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

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