Investigating the structure of the factor B vWF-A domain/CD55 protein–protein complex using DEER spectroscopy: successes and pitfalls

Abstract

The electron paramagnetic resonance technique of double electron-electron resonance (DEER) was used to measure nanometre-scale distances between nitroxide spin labels attached to the complement regulatory protein CD55 (also known as decay accelerating factor) and the von Willebrand factor A (vWF-A) domain of factor B. Following a thorough assessment of the quality of the data, distances obtained from good-quality measurements are compared to predicted distances from a previously hypothesised model for the complex and are found to be incompatible. The success of using these distances as restraints in multi-body docking routines is presented critically.

Keywords:

• DEER
• distance restraints
• CD55
• vWF-A
• decay acceleration

Acknowledgements

We would like to thank Christian Bauer at MPI Mainz and Dr Jeff Harmer in Oxford (now at the University of Queensland) for EPR technical support. We thank Dr Jo Nettleship at the Oxford Protein Production Facility for mass spectrometry and Oxford Biochemistry DNA Sequencing Service for DNA sequencing. We gratefully acknowledge Prof. Axel Brunger at Stanford University for providing us with the CNS docking scripts and offering further support and advice. JEL thanks the Royal Society for a University Research Fellowship and University College Oxford for a Junior Research Fellowship.

Supplemental data

Supplemental data for this article can be accessed online.

Additional information

Funding

We thank the EPSRC for funding the Centre for Advanced Electron Spin Resonance and this work [grant number EP\DO48559\1]. The Wellcome Trust are thanked for funding to SML and her group.