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Research article2007Peer reviewed

Resolving the geometry of biomolecules imaged by cryo electron tomography

Bongini L, Fanelli D, Svensson S, Gedda M, Piazza F, Skoglund U

Abstract

In this paper, we describe two methods for computerized analysis of cryo electron tomography reconstructions of biomolecules. Both methods aim at quantifying the degree of structural flexibility of macromolecules and eventually resolving the inner dynamics through automatized protocols. The first method performs a Brownian dynamics evolution of a simplified molecular model into a fictitious force field generated by the tomograms. This procedure enables us to dock the simplified model into the experimental profiles. The second uses a fuzzy framework to delineate the subparts of the proteins and subsequently determine their interdomain relations. The two methods are discussed and their complementarities highlighted with reference to the case of the immonoglobulin antibody. Both artificial maps, constructed from immunoglobulin G entries in the Protein Data Bank and real tomograms are analyzed. Robustness issues and agreement with previously reported measurements are discussed

Keywords

brownian dynamic; fuzzy sets; immunoglobulin G; principle component analysis; protein data bank; volume images

Published in

Journal of Microscopy
2007, Volume: 228, number: 2, pages: 174-184 Publisher: BLACKWELL PUBLISHING

      SLU Authors

    • Svensson, Stina

      • Centre for Image Analysis, Swedish University of Agricultural Sciences

    Publication identifier

    DOI: https://doi.org/10.1111/j.1365-2818.2007.01839.x

    Permanent link to this page (URI)

    https://res.slu.se/id/publ/17107