EM∩IM: software for relating ion mobility mass spectrometry and electron microscopy data

Abstract

(2016) 'EMIM : software for relating ion mobility mass spectrometry and electron microscopy data.', Analyst., 141 (1). pp. 70-75. Further information on publisher's website:https://doi.org/10.1039/c5an01636cPublisher's copyright statement:Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. We present EM!IM, software that allows the calculation of collision cross-sections from electron density maps obtained for example by means of transmission electron microscopy. This allows the validation of structures other than those described by atomic coordinates with ion mobility mass spectrometry data, and provides a new means for contouring and validating electron density maps. EM!IM thereby facilitates the use of data obtained in the gas phase within structural biology studies employing diverse experimental methodologies.Ion mobility mass spectrometry (IM-MS) can be used to investigate the structure of large biomolecules and the complexes they assemble into [1][2][3][4][5][6] . While the MS experiment provides a mass measurement, the IM dimension reports on the ability of an ion to traverse a region of low pressure that, depending on the experimental implementation 7, 8 , may be quantified through an orientationally averaged collision cross-section (CCS). The CCS can subsequently be exploited to validate existing atomic coordinates, assess differing candidate structures, or to guide model building directly [1][2][3][4][5][6] .A number of different algorithms 9-14 , tailored to specific applications, have been written to calculate the CCS of a given threedimensional structure, allowing the relation of IM measurements to structures derived from X-ray crystallography, NMR spectroscopy, or atomic modelling [15][16][17] An electron density map is typically a three-dimensional grid, with each voxel having a certain density value. In general, such a map is displayed as a volume demarcated by an isodensity surface, which is generated by specifying a contour-level, the lower electron density threshold (!*) for a voxel to be considered occupied. The more stringent this threshold is, the fewer voxels match the electron density criterion, and the smaller the resultant volume. Furthermore, as the electron density is typically anisotropic 18 , changing the threshold can result in different shapes. Yet, despite its importance, defining the appropriate threshold is difficult, and particularly so for low resolution maps (>10Å), where secondary structure elements are not readily identifiable 20 .Our fundamental premise in d...

Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM

“…In this model, the active sites of DacA protomers are occluded through binding to the GlmM protein (Fig 8D), while the GlmM active sites are still accessible. To validate the SAXS analysis, the reconstructed envelopes were used to calculate theoretical Collision Cross Section (CCS) values using the program EM∩IM [44]. These theoretical values were subsequently compared to those experimentally determined by Ion-Mobility Mass Spectrometry.…”

Fundamentals of ion mobility spectrometry

“…Omission of long-range interactions make EHSS and PA invariant to temperature, although temperaturedependent atom radii can circumvent this problem to some degree [39,52]. PA lends itself for analysis of non-atomistic structures, including bead models [53] and electron-densities [38,54].…”

Mass spectrometry-enabled structural biology of membrane proteins

“…Whilst initial experiments focused on the use of native MS as a tool to discern protein complex stoichiometry [60], the advent of IMS-MS has significantly enhanced the structural information accessible [37,74,138,145,153]. Despite the relatively low structural resolution afforded from IMS measurements, knowledge of a protein's collision cross section can provide critical information that can be used to refine structural models and to map conformational changes [16,33,79,80,145,[160][161][162]. This is especially useful in the study of protein dynamics and structural interconversions, as co-populated species with different m/z and/or CCS can be interrogated individually without ensemble averaging.…”