Towards a Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) and bridging the gaps between structure determination methods

Understanding how cells work 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 slices through 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, the sister project CCPN has performed a similar role for the nuclear magnetic resonance spectroscopy community. The field of cryo-EM needs a similar initiative, and this proposal is a first step in that direction.

There are at least 25 groups in the UK active in the field of cryo-EM. We are proposing a Partnership open to all UK groups with the aim of establishing a Collaborative Computational Project (CCP-EM). The CCP-EM 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. Gaps in software provision will be identified, and where feasible new software written.

The Partnership will lead to a better use of software within UK groups. It will relieve some of the burden connected with understanding and installing a wide range of incompatible software. 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). 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 Partnership will address three broad areas: It will provide a forum for planning a Collaborative Computational Project (CCP) in cryoEM, and for developing a roadmap for future software developments. It will support the users of software for cryoEM through dissemination of information on available software, directed training and improvements to the useability of software. Finally, it will provide support for software developers, including porting, optimisation and distribution of software.
These aims will be achieved through two computational scientists based at the Research Complex at Harwell, directed by 7 investigators from a range of relevant disciplines. The PDRAs will establish the necessary infrastructure in terms of web site, software development environment, and collaboration tools. Together with the named investigators, they will consult with the whole community on software requirements. Some software is available from the applicants, and some from other UK groups. The PDRAs will write additional programs, scripts and workflows as necessary, although we stress the aim is not to replicate existing programs but rather ensure their optimum use. The areas to be covered include single particle reconstruction, helical reconstruction, tomography, and electron crystallography.
In addition, there will be strong links to the macromolecular crystallography community through the involvement of CCP4, and the NMR community through CCPN. These established collaborations provide useful experience for the development of a CCP in cryo-EM. In addition, we will look specifically at bridging the gap between these techniques in order to support multi-disciplinary studies, for example by facilitating data transfer. We will also liaise with the Electron Microscopy Data Bank in the areas of validation, deposition and annotation.

In the international research community, there is widespread interest in using 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 EM research groups in the UK and encouraging a collaborative effort, the proposed Partnership will have an impact in all these fields. We will improve the technological platform upon which scientific advances depend by (i) making existing computational tools more robust and useable, (ii) creating new computational tools and workflows where there are gaps identified, and (iii) promoting best practice through dissemination of information within the community.

The Partnership will also have an impact on individual researchers through its training and knowledge exchange aspects. 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 expansion of EM as an important component in the toolkit for understanding cellular and sub-cellular biology relies on the availability of researchers competant in the computational techniques required to interpret the data. The Partnership will help by rationalising the computations required and by providing training.

The problems being addressed by 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.

By uniting the UK cryo-EM community, the Partnership will also have an impact on the strategy for future development. 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. As a specific example, the CCP-EM will be well-placed to be an important contributor to the European INSTRUCT infrastructure project in structural biology.

An initiative on EM software for the UK community is totally new, will focus work from the entire UK and will also attract considerable international interest. The Partnership proposal is a modest start but long overdue, and will lead to the establishment of a CCP-EM. This will have a huge impact on the UK and international EM community and will greatly facilitate new work and entry of new labs into this expanding field.