Prof. Elspeth Garman
Helena Taberman —
I obtained my BSc and MSc in Chemistry continuing to PhD in Structural biology at the University of Eastern Finland. With a grant from the Finnish Cultural Foundation to work on ‘overcoming challenges of radiation damage in macromolecular complexes at the atomic level’ I will carry out systematic studies on radiation damage to protein, DNA, protein/DNA and protein/RNA crystals during structure determination by X-ray diffraction at cryo- and room temperatures. The new electron density loss pipeline, RIDL, will be used to calculate per-atom metrics to quantify the sensitivity to specific damage. Secondly, the newly established metric, Bdamage, will be used to search for incorrect metal assignments in the PDB followed by measuring some of these proteins using the microPIXE method to unambiguously identify the metals. The results will be then used to analyse if the re-identification of the metal affects the assumed function of the chosen proteins. The third aim of the project is to further improve RADDOSE-3D, which allows the radiation dose distribution during a diffraction experiment to be calculated with both time and space resolution.
Katharina Jungnickel — Crystallisation of Membrane Transporters
As part of the NanoMem Network (nanomem.eu) funded by the European Commission Framework Seven Programme my work is mainly focussed on membrane protein structural biology using novel tools such as X-ray free electron lasers (XFEL). Together with Molecular Dimensions Ltd. and supervision by Prof. Elspeth Garman and Dr. Simon Newstead I work on crystallisation of membrane transporters. I aim to understand the difficulties of structure determination of this class of protein towards development of crystallisation screens and the usage of new techniques in structure determination gaining high resolution data of membrane proteins.
Charlie Bury — Investigation of X-ray induced radiation damage in proteins, nucleic acids, and their complexes
Significant progress has been made over recent years in understanding how radiation damage mechanisms affect crystalline protein structure determination in macromolecular X-ray crystallography (MX) experiments conducted at 100 K. Despite an active field studying the radiation chemistry of nucleic acids interacting with ionising radiation, few MX investigations exist on ‘specific' damage manifestations (chemical/conformational changes) for crystalline DNA/RNA. Our systematic damage analyses on nucleoprotein case studies have indicated that nucleic acids are intrinsically less radiation-sensitive than protein in both protein -DNA and -RNA systems, at the doses typically accumulated in cryocooled data collection at 3rd generation synchrotrons. In conjunction with these investigations I have additionally been developing an automated tool for objectively detecting and quantifying radiation-induced electron density changes on a per-atom basis, as a function of dose. This approach is widely applicable to the systematic investigation of any single crystal MX damage (or time-resolved) data series.
Part II students
Kathryn Shelley — Advances in specific damage detection using Bdamage metric
The specific radiation damage which accumulates during x-ray diffraction data collection can introduce errors into the structure derived from this data. The Bdamage metric developed by the Garman group is able to detect sites of specific radiation damage within individual macromolecular structures. The aim of my project is to complete the writing of an open source programme to calculate Bdamage values for PDB files.
Elizabeth Hamilton — Investigation into scavengers for use in room temperature MX
I am investigating the specific damage sites on a biologically relevant protein (a GH7 family protein) to identify the effects of local environment on damage rates and also the influence of radiation damage on the active site. I will also be using microPIXE to analyse the heavy atom content of protein samples from other groups.
Katie Nichols — Investigation into scavengers for use in room temperature MX
I am currently investigating the applicability of radical scavengers to mitigate radiation damage in room temperature MX. I will be testing different compounds on their ability to prevent both global and specific damage to test protein systems.
Visiting masters students
Diane Barret — Systematic investigation into specific damage in room temperature MX
The radiation damage to protein crystals remains a significant obstacle to structure determination by MX. It has been widely investigated at 100 K, but systematic investigations into specific radiation damage at RT are lacking to date. Due to recent renewed interest in RT data collection (with advances in detectors, availability of high flux X-ray synchrotron beamlines and FELs), a detailed understanding of RT radiation damage is now required. The aim of this project is to perform a series of systematic and quantitative analyses of radiation damage for macromolecular crystals at RT, which have previously been well characterised at 100 K.
DTP rotation students
Steve Walsh — Implementation of the Compton effect into RADDOSE-3D
I studied my Undergraduate and Masters degree at The University of Liverpool, studying first Biochemistry before moving onto the more computational side of biology for my masters. I am currently in my first year at Oxford as part of the Interdisciplinary Bioscience Doctoral Training Program (DTP), I am completing my first rotation project within the Garman group. For this project I am looking to extend the RADDOSE-3D program so that it accounts for the Compton effect when predicting the damage a crystallized protein may suffer during X-ray crystallography.