Discovery of protein substructures in EM maps

  • Authors:

  • Keren Lasker;Oranit Dror;Ruth Nussinov;Haim Wolfson

  • Affiliations:

  • School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel;School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel;Sackler Inst. of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel;School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel

  • Venue:
  • WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
  • Year:
  • 2005

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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.