Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM): Supporting the software infrastructure for cryoEM techniques.

Understanding how biological molecules function inside cells is vital to combating disease. While experimental techniques such as macromolecular crystallography and nuclear magnetic resonance spectroscopy have for many years given detailed information on important molecules in the cell, attention is now moving to how these molecules interact with each other and how they are affected by their location in the cell. Electron cryo-Microscopy (cryo-EM) provides very useful information here, and bridges the gap between individual molecules and the whole cell. In the most favourable cases, detailed images of assemblies of molecules can be obtained, while at lower resolutions electron tomograms can show internal molecular details from within intact parts of cells or tissues. Advances in instrumentation and data processing have led to a significant increase in the application of cryo-EM in recent years, such that it is now one of the most important experimental techniques available in structural and cellular biology.

To exploit fully cryo-EM requires good software for processing the primary experimental data and for interpretating it in terms of molecular or cellular structure. However, software provision is patchy and fragmented, and individual labs face a steep learning curve when trying to create a suitable software environment for their projects. The macromolecular crystallography community faced such a challenge more than 30 years ago, and the Collaborative Computational Project No. 4 (CCP4) was created to address this challenge. In the years following, CCP4 has grown to be a major international project, and has underpinned many of the advances in our understanding of cells at the molecular level. In the last 10 years, similar collaborative projects for structural biology have been created: CCPN for nuclear magnetic resonance spectroscopy, CCPBioSim for biomolecular simulation, and CCP-SAS for small angle X-ray and neutron scattering. In response to the growing scientific role of cryoEM, we have recently created the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM).

There are at least 25 groups in the UK active in the field of cryo-EM, with a rapidly increasing number of crystallography groups looking to obtain complementary information from cryoEM. CCP-EM is open to all these groups, and will coordinate efforts within the UK community. It will support users through dissemination of information on available software, helpdesk support, and directed training. It will support developers through technical help and by helping to distribute their software to the community. CCP-EM is also developing its own software suite for processing cryoEM data by integrating existing programmes into a robust and user-friendly framework. The creation of CCP-EM was facilitated by the award of a Partnership Grant, and we now seek a follow-on Partnership Grant to support the collaborative project as it matures and expands. While the first grant focussed on single particle techniques, wherein individual molecules or complexes are imaged, we now proposed to expand the scope to electron tomography which provides in situ imaging of complexes and larger structures in the cell.

A continuation of CCP-EM will lead to a better use of software within UK groups. The support of a dedicated group of scientists will greatly speed up the process of establishing new groups or helping established microscopists move into new areas (such as tomography). CCP-EM will directly support the new national EM facility on the Harwell Campus, helping users get the most from a new resource. However, the most important output is the development of a community spirit, that encourages individual scientists to pool their efforts. The creation of scientific communities in the UK leads to the best use of public money, and maximises the return on the UK's investment in microscopy facilities

The aims of CCP-EM will be achieved through two computational scientists based at the Research Complex at Harwell, directed by 10 investigators active in cryoEM. The PDRAs will maintain the necessary infrastructure in terms of community events, software development environment, and collaboration tools. Together with the named investigators, they will consult the whole community on software requirements. Specifically, they will continue to develop the CCP-EM software framework, and integrate existing programs via close collaboration with scientists/developers in the wider community. The framework has been developed in Python/PyQt which is suitable for integration of disparate programmes. A database backend allows recording of compute jobs, and subsequent review or modified re-run. The CCP-EM PDRAs will also organise conferences and workshops, in order to train new students or scientists entering from another field. These events will include training in specific software, and also more general workshops on issues of common interest.

The outputs of the project will include an easy-to-install and easy-to-use software suite, additional tools and resources on the web site, a substantial number of training days delivered, and a range of community events and conferences. Usage of these various resources will be promoted by the investigators and the members of Working Group 1, and monitored via downloads and registrations. The PI and the co-investigators will be responsible for linking CCP-EM activities to other structural biology disciplines, and to the international community. In particular, the PI has a background in the CCP4 project for crystallography, one co-I has responsibility for the Electron Microscopy Data Bank at the EMBL-EBI, and one co-I has led the effort to establish a national EM facility.

In the international research community, there is widespread interest in using cryo-EM to tackle big challenges, such as molecular machines in action and membrane complexes in situ. The field has strong links to atomic structure methods, especially crystallography, while electron tomography has strong connections to cell biology. The spatial dimension is needed to understand biological networks and machines, and complements traditional systems biology approaches. By supporting cryo-EM research groups in the UK and encouraging a collaborative effort, CCP-EM advances the usage of cryoEM, and has an impact on many structural biology projects.

CCP-EM will also have an impact on individual researchers through its training and knowledge exchange aspects. The expansion of cryo-EM as an important component in the toolkit for understanding cellular and sub-cellular biology relies on the availability of researchers competent in the computational techniques required to interpret the data. Existing researchers will of course benefit through improved software tools and environment. However, we specifically wish to lower the barriers to entry into the field of cryo-EM. This applies not only to students and young postdocs, but also to researchers moving from other fields or wishing to use cryo-EM as an additional technique.

The problems being addressed by cryo-EM are of major importance in biomedical science, e.g. dynamic systems involving protein folding/refolding/misfolding, important in neurodegeneration and other misfolding diseases, virus-host interactions, and chromatin structure and modification. Although our primary focus in the Partnership is on the fundamental science, advances here ultimately have an impact on translational and medical research. We are focussing on a technique rather than a particular scientific area, so the impact is likely to be very broad, leading eventually to improved medicine and health for the nation.

The insight that cryoEM provides to disease mechanisms is attracting the attention of a number of pharmaceutical companies. Representatives from at least half-a-dozen companies have either made enquiries or registered for a CCP-EM event. As well as helping to elucidate the underlying mechanisms of disease, cryoEM allows scientists to visualise the effect of drug molecules on proteins and complexes, in a near-native environment. As the technique matures, it is likely to become part of the drug development pipeline. Other industries (biotechnology, agribusiness) will also potentially benefit from the extra insight into biological processes provided by cryo-EM.

By uniting the UK cryo-EM community, the Partnership will have an impact on the strategy for future developments. By acting together, the UK cryo-EM community will have a stronger voice. This will be used to influence software developers, instrument manufacturers and standards development. They will also be able to provide input for national and international policy makers and funders. Finally, CCP-EM will take part in public engagement events to help strengthen the public understanding and appreciation of biomedical research.