mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL

Abstract

Nanometer distance measurements based on electron paramagnetic resonance methods in combination with site-directed spin labelling are powerful tools for the structural analysis of macromolecules. The software package mtsslSuite provides scientists with a set of tools for the translation of experimental distance distributions into structural information. The package is based on the previously published mtsslWizard software for in silico spin labelling. The mtsslSuite includes a new version of MtsslWizard that has improved performance and now includes additional types of spin labels. Moreover, it contains applications for the trilateration of paramagnetic centres in biomolecules and for rigid-body docking of subdomains of macromolecular complexes. The mtsslSuite is tested on a number of challenging test cases and its strengths and weaknesses are evaluated.

Keywords:

• DEER
• PELDOR
• triangulation
• EPR
• FRET
• docking

Acknowledgements

We would like to thank Jason Vertrees and Thomas Holder for help concerning PyMOL programming and Damien Farrell for help with the tkinterTable class for mtsslDock. This work has been supported by the SFB813 projects C8 and A6 of the Deutsche Forschungsgemeinschaft (DFG) and the Wellcome Trust (091825/Z/10/Z).

Note added in proof

While this paper went into production, the K1 spin label [42] was added to mtsslWizard upon user request. Supplementary Figure 7 shows a comparison between predicted and experimental distance distributions derived from this spin label.