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Discovery of Protein Substructures in EM Maps

  • Keren Lasker
  • Oranit Dror
  • Ruth Nussinov
  • Haim Wolfson
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3692)

Abstract

Cryo-EM has become an increasingly powerful technique for elucidating the structure, dynamics and function of large flexible macromolecule assemblies that cannot be determined at atomic-resolution. A major challenge in analyzing EM maps of complexes is the identification of their subunits. We propose a fully automated highly efficient method for discovering high-resolution subunits of a complex, given as an intermediate resolution map, without prior knowledge of their boundaries and content. The method extracts helices from an EM map and uses their spatial arrangement to detect candidate subunits. The method was tested successfully on several simulated 8.0Å resolution maps. The obtained spatial helix arrangement was sufficient for the discovery of the correct subunits from a dataset of 887 SCOP representatives.

Keywords

Structural bioinformatics intermediate resolution cryo EM maps 3D alignment of secondary structures macromolecular assemblies 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Keren Lasker
    • 1
  • Oranit Dror
    • 1
  • Ruth Nussinov
    • 2
    • 3
  • Haim Wolfson
    • 1
  1. 1.School of Computer Science, Raymond and Beverly Sackler Faculty of Exact SciencesTel Aviv UniversityTel AvivIsrael
  2. 2.Sackler Inst. of Molecular Medicine, Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
  3. 3.Lab. of Experimental and Computational BiologyBasic Research Program, SAIC-Frederick, IncFrederickUSA

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