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Computational chemistry assisted simulation of the EPR spectra of protein radicals

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  • Full or part time
    Dr Svistunenko
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

A PhD studentship will be available at the Biomedical EPR Facility to develop a new method of simulation of Electron Paramagnetic Resonance (EPR) spectra of protein radicals. Free radicals are often formed on proteins and enzymes during many biologically important reactions. To understand the mechanism of such reactions, it is important to know where exactly on the protein the free radical is located [1]. Computer simulation of experimentally detected free radical EPR spectra provides information about the radical structure and its micro-environment. This information can be related to the protein structure, if known, and the radical location can be found. This approach, however, suffers from ambiguity: there are too many variables in a protein radical EPR spectrum simulation which can yield many local minima in a search for an optimal simulated spectrum. The PhD studentship programme will be focused on using computational chemistry methods applied to model tyrosine and tryptophan radicals [2] in a search for ‘trends’ – functional dependences between several spectra simulation parameters, so that the total number of the parameters, or degrees of freedom of the overall EPR spectra simulation procedure can be significantly reduced. Once such functional dependences are found and incorporated into EPR spectra simulation algorithms, the credibility of the simulation and, consequently, the accuracy of finding the radical location, will be significantly increased. The candidates are expected to have computer programming skills, for example, but not exclusively, in Matlab, and be at least vaguely familiar with Unix/Linux systems. Experience in using computational chemistry methods will be considered advantageous. Successful candidate will benefit from integrating their theoretical computational research with diverse experimental studies conducted in the friendly research environment of the School. The candidates are expected to speak fluent English.

Funding Notes

Entry requirements and application procedures
Applications should be submitted electronically by Tuesday 29 March 2016 see here for details https://www.essex.ac.uk/pgapply/enter.aspx

Additional questions and queries about the studentship can be addressed to Dr Dima Svistunenko at svist (@essex.ac.uk)
The target start date for this 3-year, fully-funded PhD studentship is 6th October 2016. This scholarship will be to the value of £12,500 per annum plus UK tuition fees.

References

1. Svistunenko, D. A. and Jones, G. A. (2009) Tyrosyl radicals in proteins: a comparison of empirical and density functional calculated EPR parameters. Phys Chem Chem Phys. 11, 6600-6613
2. Svistunenko, D. A., Adelusi, M., Dawson, M., Robinson, P., Bernini, C., Sinicropi, A. and Basosi, R. (2011) Computation informed selection of parameters for protein radical EPR spectra simulation. Stud U Babes-Bol Chem. 56, 135-146

How good is research at University of Essex in Biological Sciences?

FTE Category A staff submitted: 23.00

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