Fit EM2EM—Tools for Low Resolution Study of Macromolecular Assembly and Dynamics Ziv Frankenstein1, Joseph Sperling 2 , Ruth Sperling 3 , Miriam Eisenstein4* 1 Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel, 2 Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel, 3 Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel, 4 Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel Abstract Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for comparing (matching) and docking of low resolution structures, based on shape complementarity. The matched or docked objects are represented by three dimensional grids where the value of each grid point depends on its position with regard to the interior, surface or exterior of the object. The grids are correlated using fast Fourier transformations producing either matches of related objects or docking models depending on the details of the grid representations. The procedures incorporate thickening and smoothing of the surfaces of the objects which effectively compensates for differences in the resolution of the matched/docked objects, circumventing the need for resolution modification. The presented matching tool FitEM2EMIN successfully fitted electron microscopy structures obtained at different resolutions, different conformers of the same structure and partial structures, ranking correct matches at the top in every case. The differences between the grid representations of the matched objects can be used to study conformation differences or to characterize the size and shape of substructures. The presented low-to-low docking tool FitEM2EMOUT ranked the expected models at the top. Citation: Frankenstein Z, Sperling J, Sperling R, Eisenstein M (2008) FitEM2EM—Tools for Low Resolution Study of Macromolecular Assembly and Dynamics. PLoS ONE 3(10): e3594. doi:10.1371/journal.pone.0003594 Editor: Che John Connon, University of Reading, United Kingdom Received July 10, 2008; Accepted October 9, 2008; Published October 31, 2008 Copyright: 2008 Frankenstein et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: ZF is partially supported by the Kimmelman Center for Macromolecular Structure and Assembly at the Weizmann Institute of Science. JS and RS thank the US NIH, grant GM079549. The funding source had no role in the design and execution of the computations or in the analyses of the results or the preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: miriam.eisenstein@weizmann.ac.il Introduction The structures of large and flexible macromolecules and macromolecular assemblies are hard to determine and the current experimental techniques often produce only medium to low resolution models. Single particle electron microscopy (EM) is one such technique that produces models at resolutions as high as 4 A˚ [1,2]. Other techniques that produce low resolution structures are atomic force microscopy (AFM) [3,4] and small angle X-ray scattering (SAXS) [5,6]. Recently, single particle EM in vitrified ice (cryo-EM) was used to study the structural heterogeneity of macromolecules and assemblies, exploiting the fact that the fast vitrification traps samples at different conformations and different stages of activity [7–9]. Characterizing and analyzing structural heterogeneity of macromolecules is challenging as it requires comparison of low resolution models obtained at different resolutions and sometimes using different techniques, each carrying its typical experimental error. Currently such comparisons are customarily done by manual fitting of the models (e.g. [10–13]). Similarly, manual fitting is commonly used in assembly modeling studies (e.g. [14–16]). Many programs that match atomic structures to EM maps have been previously presented (reviewed in [17]) however these tools were not tested for matching of one EM map to another. A computerized tool for comparing low resolution 3D models is evidently necessary. It is however a non-trivial task because maps at resolutions lower than 15 A˚ do not carry enough features for density comparison [18–20]; in addition experimental error, density cutoff uncertainty and resolution differences must by considered [18,21]. Recently it was shown that the combination of shape matching with maximization of density overlap provides a superior tool for matching atomic resolution models to EM maps in the resolution range of 12–25 A˚ (high-to-low resolution matching) [22]. We present here new tools designed for comparing and matching low resolution models (FitEM2EMIN for low-to-low resolution matching) and for docking of such models (FitEM2EM- OUT). The tools are based on the shape complementarity algorithm, MolFit [23]. Hence, we employ three dimensional (3D) grid representations of the low resolution objects and use fast Fourier transformations (FFT) to match or dock them. We tested FitEM2EMIN on ten pairs of related EM maps and found that it can efficiently match EM maps obtained at different resolutions and using different EM techniques. Moreover, models of different conformers were successfully matched and partial structures were fitted into larger assemblies. The difference between the grid representations of the matched models can be used to study conformation changes or to predict the shape and size of substructures. Docking of low resolution EM maps with FitE- M2EMOUT identified the expected positions and ranked them at the top of the list of predicted models. Results The matching and docking tools FitEM2EMIN and FitEM2EM- OUT test many relative orientations of the matched/docked PLoS ONE | www.plosone.org 1 October 2008 | Volume 3 | Issue 10 | e3594