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Understanding Specific Radiation Damage
1
Markus Gerstel, 1Isaac Turner, 2Charlotte Deane, 1Elspeth Garman
1
Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU
2
Department of Statistics, University of Oxford, South Parks Road, Oxford, OX1 3QU
In a diffraction experiment the specific structural damage to the protein in the crystal
occurs in a reproducible order. Disulphide bonds are especially sensitive to radiation damage,
and are not only affected before other bonds, but when there is more than one disulphide bond
present in the molecule, they are damaged in a defined order [1]. Disulphide bonds are highly
susceptible because they are very electro-affinic and act as a ‘sink’ for electrons which are
mobile even at 100K. These electrons are secondary products of the photoelectric effect.
However, exactly why some disulphide bonds are more susceptible than others is, as yet,
unknown.
We aim to identify a causal connection between physico-chemical parameters and
preferential radiation damage. Potential parameters being investigated are amino acid
exposure (Ooi and cx number), pKa, neighbouring residues, bond angles and solvent
accessibility. In the only study on this subject to date, the latter was found not to be a
predominant factor [2].
Based on unpublished work [3] which used known protein structures to estimate
damage rates to disulphide bonds and correlated these rates with the local environment of the
disulphide bonds, a two-pronged approach is being followed. Firstly, data are being mined
computationally from the RCSB Protein Data Bank [4] and Electron-Density Server [5] and
subjected to statistical analysis. Specific damage susceptibility patterns are being identified.
Secondly, alongside the computational investigation, we are carrying out a qualitative,
quantitative and then comparative study of radiation damage and radiation damage
progression on rhoGDI protein derivatives with similar, yet distinct crystal contact surfaces,
obtained by surface-entropy reduction [6]. These mutants have a high sequence identity but
are sufficiently distinct to crystallize in different space groups. We hope to gain enough
information to be able to make statements and predictions about specific radiation damage
progression within crystals.
From the results of these experiments, a predictive radiation damage progression
model will be postulated and then verified.
References
[1] M. Weik, J. Bergès, M. L. Raves, P. Gros, S. McSweeney, I. Silman, J. L. Sussmann, C. HouéeLevin and R: B: G: Ravelli (2002) Evidence for the formation of disulfide radicals in protein crystals
upon X-ray irradiation, J. Synchrotron Rad. 9, 342-346.
[2] E. Fioravanti, F. M. D. Vellieux, P. Amara, D. Madern and M. Weik (2007) Specific radiation
damage to acidic residues and its relation to their chemical and structural environment, J. Synchrotron
Rad. 14, 84-91.
[3] I. Turner, C. Deane and E. Garman (2010) Specific X-ray Radiation Damage to Disulphide Bonds,
Project report, unpublished.
[4] H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov and P.
E. Bourne (2000) The Protein Data Bank, Nucleic Acids Research, 28: 235-242.
[5] G. J. Kleywegt, M. R. Harris, J. Y. Zou, T. C. Taylor, A. Wählby and T. A. Jones (2004) The
Uppsala Electron-Density Server, Acta Cryst. D60, 2240-2249.
[6] Z. S. Derewenda (2011) It's all in the crystals..., Acta Cryst. D67, 243-248.
Email corresponding author: [email protected]
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