Project No. 2487

STANDARD PROJECT

Primary Supervisor

Prof Sumeet Mahajan- University of Southampton

Co-Supervisor(s)

Prof Louise Serpell – University of Sussex

Prof Amrit Mudher – University of Southampton

Summary

Intrinsically disordered proteins (IDPs) are an integral part of many biological systems.

This structural flexibility is used to modulate function, with correct folding, unfolding and misfolding being associated with normal cellular processes such as apoptosis through to abnormal function in cancer and amyloidosis. The mechanisms by which the folded state of IDPs are controlled are not clear, and there is therefore a pressing need to develop and apply technologies to understand and modulate this behaviour. In this project, we will develop a novel method that combines experiment and in silico modelling to explore the conformational dynamics of IDPs.

In previous work, we have demonstrated that vibrational Raman spectroscopy is sensitive to protein conformation and aggregation state. Separately, we have demonstrated that we can calculate the electric fields, and hence the vibrational frequencies in silico, of molecular probes in proteins. Here we will combine these methods to explore the effects of small molecule probes on protein conformation and aggregation by experiment and in silico modelling.

The methodology will be developed and tested on two relevant hexapeptides VQIVYK (PHF6) and VQIINK (PHF6*). Both spontaneously aggregate and form fibrils. Spectra will be obtained with our Raman approach with the aggregation mechanism being explored through the addition of small molecule probes. Advanced polarisable force fields will be used to calculate vibrational spectra of the probes giving molecular-level insights into the protein aggregation process, and hence the structure-function relationship.

To provide additional, experimental insight, the student will carry out X-ray diffraction and negative stain transmission electron microscopy of fibrils in the presence and absence of the small molecule probes. The Serpell lab have extensive experience in this area.