WorkPackage 1: Theory
SPIDoc's applies the theoretical study of protein orientation for single particle imaging experiments by quantum mechanics/molecular modelling and hybrid-molecular dynamics simulations. Additionally, a rigid rotor model is used to study the influence of protein dipole and field strength to predict protein orientation.
The work of WP1 is carried out by DC6 and DC7 (both at Uppsala University).
WorkPackage 2: Instrumentation
The development of MS components, as well as the adaption of the prototype developed within the MS SPIDOC project, contributes to the better characterization of small and large protein species. The instrument development has the main feature of versatility to be adapted to different applications and beamline. Specficially, the design of an optimized MS-based sample delivery system results in the TXI prototype which has been tested at the beamline. Along with instrument development, an important aspect to be considered is data analysis, which is addressed by the development of a software package for native MS data analysis.
The work of WP2 is carried out by DC1 (University of Lübeck), the DC9 and DC10 (both at MS Vision).
WorkPackage 3: Application
The different theoretical methods and instruments are applied to the structural approaches for the study of biological systems. Near-edge X-ray absorption mass spectrometry is used to investigate the properties of proteins related to Alzheimer´s disease, while the structural stability of the protruding domain of the norovirus capsid protein is analysed with a combination of IM-MS, collision-, temperature-, and laser-induced unfolding. The structure and stability of proteins in the gas phase are also addressed by the FTICR mass spectrometer application and the dynamic behaviour of viral systems, specifically on self-assembly and disassembly, and protein–protein interactions is carried out on SARS-CoV-2 non-structural proteins.
The work of WP3 is carried out by DC2 (University of Lübeck), DC3 (Vrije Universiteit Amsterdam), DC4 (Deutsches Elektronen-Synchrotron), DC5 (University Lyon 1 Claude Bernard), DC8 (Institute of Microbiology of the Czech Academy of Sciences).
WorkPackage 4: Training
The SPIDoc's training programme covers the three scientific workpackages including courses on molecular dynamics simulations, instruments' development, sample preparation, as examples. Additionally to the scientific courses, the training programme offers courses on 'green science', diversity and microaggression at the workplace, research integrity and data management, as examples. Participation to conferences is also part of the training programme, as well as the organization of outreach events.
