On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies

Degiacomi, Matteo T.

Abstract

Ion mobility mass spectrometry (IM/MS) can provide structural information on intact protein complexes. Such data, including connectivity and collision cross sections (CCS) of assemblies’ subunits, can in turn be used as a guide to produce representative super coarse-grained models. These models are constituted by ensembles of overlapping spheres, each representing a protein subunit. A model is considered plausible if the CCS and sphere-overlap levels of its subunits fall within predetermined confidence intervals. While the first is determined by experimental error, the latter is based on a statistical analysis on a range of protein dimers. Here, we first propose a new expression to describe the overlap between two spheres. Then we analyze the effect of specific overlap cutoff choices on the precision and accuracy of super coarse-grained models. Finally, we propose a method to determine overlap cutoff levels on a per-case scenario, based on collected CCS data, and show that it can be applied to the characterization of the assembly topology of symmetrical homo-multimers.

Citation

Degiacomi, M. T. (2019). On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies. Journal of The American Society for Mass Spectrometry, 30(1), 113-117. https://doi.org/10.1007/s13361-018-1974-2

• Journal Article Type: Article
• Acceptance Date: Apr 18, 2018
• Online Publication Date: May 7, 2018
• Publication Date: Jan 31, 2019
• Deposit Date: May 8, 2018
• Publicly Available Date: May 8, 2018
• Journal: Journal of The American Society for Mass Spectrometry
• Print ISSN: 1044-0305
• Electronic ISSN: 1879-1123
• Publisher: American Chemical Society
• Peer Reviewed: Peer Reviewed
• Volume: 30
• Issue: 1
• Pages: 113-117
• DOI: https://doi.org/10.1007/s13361-018-1974-2
• Public URL: https://durham-repository.worktribe.com/output/1331811