Computational Crystallography

Lead Research Organisation: MRC Laboratory of Molecular Biology

Abstract

We aim to develop computational tools to study structures of the molecules, which are responsible for functioning of organisms. The developed tools are used to analyse 3D structures of complex bio-macromolecules.
Knowledge of the 3D structures of molecules is key for understanding how they work. Understanding their mechanisms of action is an important step in fixing them when they go wrong, and therefore in designing drugs to cure a range of illnesses.
X-ray crystallography and single particle Electron Microscopy are powerful experimental tools to study 3D structures of Macromolecules. They can give atomic and electronic details of molecules thus help in analysing intricate details of the molecules’ action.
We have already developed software for automatic structure solution that works in many cases. We have also developed several computational tools for detailed analysis of macromolecules. However many macromolecules structures are not trivial to analyse. The main reason is that experimental data are often noisy and limited. To make matters worse when crystals are put under X-ray they interact and crystals may change.
Our group is developing novel statistical and computational tools to extract biologically relevant information from such noisy and limited data produced by the crystals changing under X-ray radiation.

Technical Summary

Our main aim is to develop state of the art mathematical, computational, statistical, bioinformatics tools for the analysis of Macromolecular Crystallographic (MX) data and Electron Microscopy (EM) maps, and to derive of chemically and structurally consistent atomic models.
Focus of our research is on several interlinked, but independent aspects of the Macromolecular 3D structure analysis:
1) Low-resolution MX (3-7A). Most of the existing tools have been designed for medium and high resolution MX analysis. As a result only less than 2% of all structures deposited to the Protein Data Bank have been analysed at lower than 3.5A. There are two problems related to the analysis of such data: a) smeared and noisy electron density resulting from Fourier series termination, high mobility of the molecules and phase errors, b) low ratio of the number of observations to the number of parameters. We are developing several image processing techniques to improve electron densities and Bayesian techniques to transfer information from all or class of macromolecules to low-resolution structure analysis.
2) Modelling processes in the crystals during X-ray experiments. Most of the MX software assumes that data are collected from static crystals. However radiation damage phenomenon demonstrates that they may change during data collection. We have started application of hidden Markov models to address this problem. Developed tools will help to increase reliability of the derived models
3) Automatic and manual model building and analysis of macromolecular structures. Dr Paul Emsley leads this project. His molecular graphics program – COOT is the leading software in the field.
4) Automatic structure solution pipeline. We have developed an automatic structure solution pipeline for initial phasing using molecular replacement. We plan to develop a pipeline for all stages of MX. Decision at every stage will be made using all available information. An integral part of such systems is custom designed database of accumulated knowledge.
5) Semiautomatic ligand design. One of the applications of MX is to enzymatic reaction mechanism study. For this, many inhibitor/substrate - protein crystals are analysed. Accurate ligand description is essential for such analysis. The problem looks deceptively simple however many mistakes in the PDB are due to inaccurate ligand descriptions. We are using computational chemical techniques to improve their reliability.
6) Interpretation of EM models with atomic models and their optimal fit to maps. To achieve optimal fit we aim to use all available information about macromolecules and properties of EM maps that are different in some aspects from MX derived maps.
We also plan to combine several experimental techniques to derive reliable 3D models. In particular we are developing techniques for joint analysis NMR/MX and EM/MX data.

Publications

10 25 50
 
Description EMBL/BBSRC
Amount £53,766 (GBP)
Funding ID BB/P026893/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 10/2018
 
Description EU Marie Curie Fellowship
Amount € 231,283 (EUR)
Funding ID FP7-PEOPLE-2012-IEF 330033 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 06/2013 
End 06/2015
 
Description STFC CCP4
Amount £423,880 (GBP)
Funding ID STFC CN 3017 
Organisation Science and Technologies Facilities Council (STFC) 
Sector Academic/University
Country United Kingdom
Start 08/2014 
End 07/2016
 
Description Structural data-mining of high-resolution 3DEM maps in EMDB
Amount £150,481 (GBP)
Funding ID BB/P026893/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2018 
End 01/2019
 
Description Wellcome Trust
Amount £134,134 (GBP)
Funding ID 208398/Z/17/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2018 
End 12/2020
 
Description Modulated Crystals 
Organisation University of Nebraska–Lincoln
Department Eppley Institute for Research in Cancer and Allied Diseases
Country United States 
Sector Academic/University 
PI Contribution Design of statistical basis for analyses of macromolecular structures using modulated crystals
Collaborator Contribution Experimental design, carrying out experiments and testing of designed software
Impact This collaboration is multidisplinary and involves computational crystallography, small molecular crystallography and structural biology
Start Year 2014
 
Description NMR and X-ray refinement 
Organisation University of Florence
Country Italy 
Sector Academic/University 
PI Contribution Implementation of statistical tools in the program of refinement for joint analysis of Macromolecular Structures using X-ray crystallographic and nMR data
Collaborator Contribution Design of experiment, carrying out the experiment and testing the software and algorithms
Impact 10.1107/S1399004713034160
Start Year 2011
 
Description PDB_REDO 
Organisation Netherlands Cancer Institute (NKI)
Country Netherlands 
Sector Academic/University 
PI Contribution Retuning of our software and help in designing a webserver for large scale calculation for re-interpretation of the Protein Data Bank
Collaborator Contribution Re-analysis and re-interpretation of the macromolecular structures in the Protein Data Bank
Impact 10.1107/S0907444911054515 10.1107/S2052252514009324
Start Year 2011
 
Title ProSHADE - software for map manupilation 
Description ProSHADE is a software for rapid matching, symmetry detection and simlarity identification between maps as well atomic coordinates. It can also perform reboxing of cryoEM maps to help to increase efficiency othe calculations. The software is based rotational and cartesian space Fast Fourier Transformations. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact It is now being distributed by CCPEM and used by structural biology community. One of the uses is by the EMDB to valdiated claimed symmetry of maps., 
 
Title ProSmart 
Description Conformational independent comparison of macromolecular structures. It can also design information to be transferred from high resolution macromolecular structures to low resolution refinement thus increasing reliability of atomic models derived using limited and noisy data. 
Type Of Technology Software 
Year Produced 2011 
Open Source License? Yes  
Impact Low resolution crystal structure refinement and fitting into cryo-EM maps cannot be imagined without this tool 
URL http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
 
Title acedrg 
Description Design of chemical and topological information about ligands using open source small crystallography open database - COD 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact Too early to judge 
 
Title balbes 
Description Automatic crystal structure solution using re-designed macromolecular structures of existing atomic models. 
Type Of Technology Software 
Impact More that 500 hundred crystal structures have been analysed using this software 
URL http://www.ccp4.ac.uk/ccp4online
 
Title ccp-em refmac interface 
Description A pipeline designed for refinement of enormously large cryoEM structures consisting of hundreds of chains. It writes out every chain plus its surroundings, prepares maps covering that regions and run all REFMAC5 refinements in parallel either on cluster or locally on multiple CPUs. The pipeline is included in CCPEM package and is in active development right now. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This software is just to be released. It is expected that it will make fitting of atomic models to cryo-EM maps easy and will have impact on model quality. 
 
Title coot 
Description A software for manual and automatic model building and validation of macromolecular structures. It can fit against crystallographic data as well as cryo-EM reconstructions 
Type Of Technology Software 
Open Source License? Yes  
Impact One paper describing this software has been cited more than 10000 times. Most macromolecular structures now are analysed using coot 
URL http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
 
Title libg 
Description Generate structural prior information for RNA/DNA molecules to be used in refinement and model building 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact Accurate fitting of ribosome molecules in cryo-EM reconstructions 
 
Title lorester 
Description A new software for automatic refinement of low resolution crystal structures have been designed. The software using the sequence of the target protein identifies most similar structures from the PDB and then runs the number of protocols using jelly body as well as ProSmart derived reference structure restraints and gives the best refined model as well as corresponding protocol. The software is included in new ccp4 release. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact According to reports several crystal structures have been analysed using this software although it is too early to judge its impact. r 
 
Title refmac5 
Description refinement of macromolecular structures using X-ray crystallographic dat and cryo-EM reconstruction 
Type Of Technology Software 
Impact More than 40000 of the PDB has been analysed using this software 
URL http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
 
Title sigHalves 
Description A tool for cryoEM that takes two half maps and calculates Fourier shell correlation as well as signal and noise levels in resolution shells in reciprocal space. It is supposed to work with REFMAC5 and improves refinement against cryoEM data 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This software is due to be released. It is too early to assess its impact. 
 
Description APS workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I am one of the organisers, speakers and tutor in this annual workshop. Every talk is followed by stimulating discussions.

After the workshop many PhD students and young scientists solve the problem they are facing as well as gain skills to solve similar problems in future.
Year(s) Of Engagement Activity 2008,2009,2010,2011,2012
URL http://www.ccp4.ac.uk/schools/APS-school/
 
Description BGU/CCP4 workshop on C 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This is one of the international workshop we organise. The aim of these workshops is to teach PhD students and young scientists the best practice in the field of macromolecular crystallography.
Year(s) Of Engagement Activity 2018
 
Description CCP4 School in Chandigarh 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This is one of the international workshop we organise. The aim of these workshops is to teach PhD students and young scientists the best practice in the field of macromolecular crystallography.
Year(s) Of Engagement Activity 2018
 
Description CCP4/APS School in Argonne 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The aim of these workshops is to teach PhD students and young scientists the best practices in structural biology.
Year(s) Of Engagement Activity 2018
 
Description Crystallography Workshop: Japan 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I was an organiser, lecturer and tutor in this workshop. This type of workshops are very popular and they stimulate discussions and helps to spread out knowledge and skills gained in my group as well as worldwide.

This workshop helps young PhD students and Postgraduate scientists to gain skills while solving particular problems they are facing.
Year(s) Of Engagement Activity 2006,2008,2010,2011,2012
URL http://www.ccp4.ac.uk/schools/Japan-2014/index.php
 
Description Diamond workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact It is one of the one week workshops series aimed to teach PhD students and young researchers the latest methods in the field of MAcromolecular Crystallpgraphy. There were around 30 participants, 20 of which were students and 10 of them lecturers/tutors.
Year(s) Of Engagement Activity 2015,2016
 
Description EM workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact It was a workshop designed for international PhD students and young scientists who want to apply cryo-EM technique in their research. The workshop was very lively with many questions after the lectures.
Year(s) Of Engagement Activity 2016,2017
 
Description EM/Diamond workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The aim of this workshop is to teach fitting of atomic models into cryo-EM maps. Workshop consists of lectures followed by tutorials. This type of workshops are usually very lively.
Year(s) Of Engagement Activity 2015,2016,2017
 
Description EMBO workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The aim of this workshop is to teach cryo-EM techniques to young researchers and PhD students.
Year(s) Of Engagement Activity 2016,2017
URL https://www.embl.de/training/events/2016/CRY16-01/
 
Description MAX4ESSFUN School in Aarhus 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The aim of these workshops is to teach PhD students and young scientists state-of-the-art structural biology tools.
Year(s) Of Engagement Activity 2018
 
Description SEA-COAST workshop on MX 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The aim of these workshops is to teach PhD students and young scientists the best practices in structural biology.
Year(s) Of Engagement Activity 2019
 
Description SPRING8/CCP4 worksop on MX 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The aim of these workshops is to teach PhD students and young scientists the best practices in structural biology.
Year(s) Of Engagement Activity 2018
 
Description Science festival 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact There was demonstration of some of the research carried out in our group for school children - winners in the nationwide crystal growing competition. Demonstration was done by Andrea Thorn.

School children asked some questions about activities in LMB
Year(s) Of Engagement Activity 2014
 
Description SouthAmerican Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This workshop helps to spread out skills and helps PhD students to gain knowledge from experts in the field. It has impact in all Latin American region. For example as a result of this workshop one of the attendees of the workshop organised a crystallographic group in Peru.

Talks and tutorials in this workshop help to solve problems PhD students are facing.
Year(s) Of Engagement Activity 2013,2014,2015,2016,2017
 
Description school visit (Exeter) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact It was a visit to The Maynard School for Girls in Exeter, Devon, UK by group member - Andrea Thorn. There were discussions afterwards

One of the schoolgirls later visited LMB
Year(s) Of Engagement Activity 2014