CCP4 Grant Renewal 2014-2019: Question-driven crystallographic data collection and advanced structure solution

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This proposal incorporates five related work packages.

In WP1 we will track synchrotron-collected data through computational structure determination, to find whether the most useful data can be recognised a priori using established or novel metrics of data quality and consistency. We will then enable data collection software to communicate with pipelines and graphics programs to assess when sufficient data have been collected for a given scientific question, and so to prioritise further beamtime usage. We will also communicate extra information about diffraction data to structure determination programs, and so support the statistical models and algorithms being developed in WP4.

WP2 will improve the key MR step of model preparation, especially from diverged, NMR, or ab initio models. One development will be to extend the size limit of ab initio search model generation by exploiting sequence covariance algorithms.

In WP3 we will use our description of electron density maps as a field of control points to better use electron density or atomic models positioned by MR. Restrained manipulation of these points provides a low-order parameterisation of refinement decoupled from atomic models, and therefore suitable for highly diverged atomic models or EM-derived maps. We will extend this approach to characterise local protein mobility without the requirement of TLS for predefinition of rigid groups.

In WP4 we will statistically model non-idealities in experimental data, including non isomorphism, spot overlap, and radiation damage. The resulting models, implemented in REFMAC, will be applied to refinement using data that are annotated by WP1 tools and tracked by WP0.

WP0 will provide the tools to integrate the other WPs. For this, it will create a cloud environment where storage- and compute-resources can be utilised optimally, and where rich information can be passed among beamlines, pipelines, and graphics programs.

Noble (Newcastle University) and Brown (University of Kent) are chairman and chairman elect of CCP4, and have responsibility to their grant-funding agencies (currently BBSRC and MRC) and commercial license holders for delivery of CCP4s software development, maintenance, distribution, and outreach programs. The impact of their respective contributions, therefore, relates to the specific proposed program of work from the co-applicant centres (summarised in each of the relevant grant applictions), to the output of CCP4 as a whole, and to the array of basic and applied macromolecular crystallography (MX) that depends upon CCP4.

MX is an essential enabling technology for the cellular and molecular biosciences, and consequently for UK pharmaceutical and biotechnological industries. UK research councils and research charities have recognised the need for infrastructural support of the discipline, most recently by assigning the last available Phase III slot at the Diamond Light Source (DLS) to a state-of-the-art facility for micro-focus and in situ crystallography for the academic and commercial MX community. In turn, the biotechnological and pharmaceutical science base that is fostered by such investments contributes hugely to the UK economy: in 2010 the pharmaceutical sector provided 67,000 jobs, each contributing £195,000 of GVA, with 25,000 of these positions being in high skill R&D activities (source: http://www.abpi.org.uk). In particular the majority of industrial access to DLS is for MX - amounting to almost 20% of the total user activity in MX.

Collaborative Computational Project 4 (CCP4) was established by the Research Councils in 1979 to promote the development and dissemination of software and best-practice in MX. To achieve this end, it uses Research Council funding to leverage a circa 3x larger commercial income, which it invests in MX training and in software development, maintenance, and distribution. As such, grant funding of CCP4 has the additional impact of strengthening an important interface between UK academic and commercial scientific endeavours.

CCP4s dissemination activities include the hosting of an annual methods-development meeting, attended typically by 400-500 graduate students, young researchers and PIs. It also co-sponsors with the British Crystallographic Association annual week-long graduate summer schools, held alternately in Scotland and England, at which a cohort of 40+ students are intensively trained in current methods in protein crystallography. These two elements, supported primarily by CCP4s commercial license income, serve to keep the UK at the forefront of methods development in this central technique, and ensure that a pool of well-trained, increasingly interdisciplinary scientists are available to apply the technique in academic and/or commercial settings.

The program of work described here, for which Noble and Brown will have ultimate oversight, looks forward to the next stage of the development of MX, to address some of the outstanding obstacles that limit the success and/or efficient application of the technique. By allowing structures to be determined from ever more challenging targets, including membrane proteins and proteins for which sample preparation is inherently difficult, this work will impact directly upon areas of biomedical and otherwise commercial interest. For example, WP0, WP1 and WP4 address the challenge of maximising output from challenging samples, while WP2 tackles the potential applicaiton of ab initio modelling to generate molecular replacement models. These packages address known bottle necks in the determination of structures for membrane proteins, a structural class for which structural information is badly needed (since > 50% of drugs target membrane proteins), but notoriously hard to obtain