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

ReferenceBB/L006383/1
Principal Investigator / Supervisor Professor Kevin Cowtan
Co-Investigators /
Co-Supervisors		 Professor Keith Wilson
Institution University of York
DepartmentChemistry
Funding typeResearch
Value (£) 310,300
StatusCompleted
TypeResearch Grant
Start date 01/04/2015
End date 31/03/2020
Duration60 months

Abstract

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.

Summary

Proteins, DNA and RNA are the active machines of the cells which make up living organisms, and are collectively known as macromolecules. They carry out all of the functions that sustain life, from metabolism through replication to the exchange of information between a cell and its environment. They are coded for by a 'blueprint' in the form of the DNA sequence in the genome, which describes how to make them as linear strings of building blocks. In order to function, however, most macromolecules fold into a precise 3D structure, which in turn depends primarily on the sequence of building blocks from which they are made. Knowledge of the molecule's 3D structure allows us both to understand its function, and to design chemicals to interfere with it. Due to advances in molecular biology, a number of projects, including the Human Genome Project, have led to the determination of the complete DNA sequences of many organisms, from which we can now read the linear blueprints for many macromolecules. As yet, however, the 3D structure cannot be predicted from knowledge of the sequence alone. One way to "see" macromolecules, and so to determine their 3D structure, involves initially crystallising the molecule under investigation, and subsequently imaging it with suitable radiation. Macromolecules are too small to see with normal light, and so a different approach is required. With an optical microscope we cannot see objects which are smaller than the wavelength of light, roughly 1 millionth of a metre: Atoms are about 1000 times smaller than this. However X-rays have a wavelength about the same as the size of the atoms. For this reason, in order to resolve the atomic detail of macromolecular structure, we image them with X-rays rather than with visible light. The process of imaging the structures of macromolecules that have been crystallised is known as X-ray crystallography. X-ray crystallography is like using a microscope to magnify objects that are too small to be seen with visible light. Unfortunately X-ray crystallography is complicated because, unlike a microscope, there is no lens system for X-rays and so additional information and complex computation are required to reconstruct the final image. This information may come from known protein structures using the Molecular Replacement (MR) method, or from other sources including Electron Microscopy (EM). Once the structure is known, it is easier to pinpoint how macromolecules contribute to the living cellular machinery. Pharmaceutical research uses this as the basis for designing drugs to turn the molecules on or off when required. Drugs are designed to interact with the target molecule to either block or promote the chemical processes which they perform within the body. Other applications include protein engineering and carbohydrate engineering. The aim of this project is to improve the key computational tools needed to extract a 3D structure from X-ray crystallography experiments. It will provide continuing support to a Collaborative Computing Project (CCP4 first established in 1979), which has become one of the leading sources of software for this task. The project will help efficient and effective use to be made of the synchrotrons that make the X-rays that are used in most crystallographic experiments. It will provide more powerful tools to allow users to exploit information from known protein structures when the match to the unknown structure is very poor. It will also automate the use of information from electron microscopy, even when the crystal structure has been distorted by the process of growing the protein crystal. Finally, it will allow structures to be solved, even when poor quality and very small crystals are obtained.

Impact Summary

The generic importance of macromolecular crystallography in general and CCP4 in particular is provided in the Pathways to Impacts section. CCP4 users in the pharmaceutical and biotechnology sector are most often involved in the study of protein-ligand (most often drug) complexes. The critical computational step in this process is molecular replacement (MR), in which a known atomic model from a similar structure is used to explain the diffraction pattern of the unknown structure. The MR approach is used in more than 70% of structure solutions. However it is not uncommon for the molecular replacement to yield a poor electron density map due to changes in the conformation of the protein. The software developed in work package 3 aims to significantly reduce the number of cases in which problems occur by introducing an additional flexible fitting step between the molecular replacement and refinement steps. The same approach will be applied to related problems, including the use of cryo-EM data to interpret the X-ray diffraction pattern. Improvement of the protein model also improves the electron density for the unmodeled ligand or drug, since the electron density features of the known and unknown regions of the structure are related through the diffraction pattern. Provision of an additional, highly automated refinement step in this process will therefore increase the coverage of automated methods for high throughput screening, which are widely used in the commercial sector. The impact of these developments will be to reduce the number of cases where structure solutions fails, to reduce the level of manual intervention required in successful studies, and to increase the accuracy of the resulting structures. YSBL has played a significant role in the commercial impact of CCP4, with two YSBL-originated developments (the REFMAC and COOT software) being the most-used tools in their field. The YSBL group engage with commercial customers through through commercial representation on the CCP4 Executive Committee and Working Group 1, through workshops and the CCP4 bulletin board. CCP4 developers including the York group, conduct an annual meeting with structural biologists at GSK to guide future developments, and plans and developments are presented at this meeting. There are occasional visits to other customers. The resulting software will be added to the CCP4 suite. This package is in use world-wide and is available on Windows, Linux and Mac_OS platforms, providing a direct distribution channel to the vast majority of macromolecular crystallographers. CCP4 is updated with major version releases roughly every year, and had recently introduced an automated update mechanism to enable faster access to new developments. As a result, once the software has been added to the package it will within weeks to months be available to both the academic and commercial user community.
Committee Research Committee D (Molecules, cells and industrial biotechnology)
Research TopicsStructural Biology
Research PriorityX – Research Priority information not available
Research Initiative X - not in an Initiative
Funding SchemeX – not Funded via a specific Funding Scheme
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