I recently submitted my Ph.D. thesis, which is entitled "Effects of ligand binding on the rigidity and mobility of proteins: a computational and experimental approach". My Ph.D. project was supervised by Rudolf Römer, Claudia Blindauer and Robert Freedman.
I began my Ph.D. with a theoretical study on the rigidity of HIV-1 protease using the software FIRST (Floppy Inclusions and Rigid Substructure Topography). This work has now been published in the journal Bioinformatics.
Following on from this, I studied the protein cyclophilin A (CypA) computationally and experimentally. I used FIRST to study the rigidity of the protein and FRODA (framework rigidity optimized dynamic algorithm) to study its dynamics through coarse-grained simulations.
Experimentally I worked in the School of Life Sciences and the Department of Chemistry, characterising the interaction between CypA and the ligand cyclosporin A. I used biophyscial techniques including circular dischroism and fluorescence spectroscopy. In addition, under the supervision of Claudia Blindauer, we carried out hydrogen-deuterium exchange NMR experiments on unbound CypA and the CypA-CsA complex.
I compared these experimental results directly with data I obtained from computer simulations. This work is currently in preparation for publication.