Bioscience for an integrated understanding of health

Category: Standard Studentships

Unravelling the Molecular Mechanism of Progression in Alzheimer’s Disease: Implications for therapy

Primary Supervisor

Prof Jonathan Essex – University of Southampton


Prof Louise Serpell – University of Sussex

Dr Amrit Mudher – University of Southampton

Prof Sumeet Mahajan – University of Southampton


Alzheimer’s disease (AD) is a neurodegenerative disorder that affects 36 million people worldwide.

Owing to an increased life expectancy and aging populations, by 2050 more 115 million are predicted to have AD. The pathology of AD results from the progressive accumulation of protein aggregates (called amyloid plaques and neurofibrillary tangles) in the brain and no disease modifying therapies exist. Tangles are made up of Tau protein monomers that misfold in disease. In this project, we will develop novel spectroscopic and in silico tools to understand the structure-pathogenicity relationships in Tau protein that determine its disease-related misfolding, subsequent aggregation and spread of disease. In this way we will pave the way for disease-modifying therapies.

In previous work, we have demonstrated that we can acquire the vibrational Raman spectra of tau oligomers, and demonstrated time evolution as fibrils form. Separately, we have demonstrated that we can calculate the electric fields, and hence the vibrational frequencies, of molecular probes in proteins. Here we will combine novel spectroscopic and molecular simulation studies, to study peptide aggregation in general, and tau oligomer structure and evolution into larger fibrils, in particular.

To confirm that simulation and spectroscopy can be combined and to determine the conformation of Tau seeds, the methodology will be developed and tested on two relevant hexapeptides VQIVYK (PHF6) and VQIINK (PHF6*). Both are essential for fibril formation in Tau and spontaneously aggregate. Spectra will be derived using our previously published Raman approach. Markov State Model (MSM) simulation techniques and Hamilitonian replica exchange will be used to characterise the kinetic and thermodynamic parameters of peptide aggregate formation. Advanced polarisable force fields will be used to calculate vibrational spectra. Calibration of simulation force fields will be carried out using experimental Raman spectra acquired from pure crystalline samples of amino acids and salts. Following refinement of computational models using calibration data, Raman spectra of hexapeptides as monomers, oligomers and fibrils will be acquired. Predictions from simulations will be tested against monomer spectra first. This will be followed by optimisation which will allow understanding the Raman spectra of oligomers and fibrils, which are more complex, and can consist of polymorphs. Thus, elucidation of conformational structures in terms of molecular motifs, intra- and inter-molecular bonding will be possible. The insight gained by simulations will help understand interactions and allow the development of  in silico models of compound (drug) interactions with tau aggregates. This in turn will allow the development of an efficient screening method of inhibitors against disease causing misfolded-Tau, oligomers and their aggregates.

To establish and verify ground truth of the structures, and to further correlate the Raman spectra with simulations, the student will visit the University of Sussex, to the Serpell lab, to prepare X-ray fibre diffraction samples of the fibrils formed by PHF6 and PHF6*. This will help gain further insight into the molecular architecture of the mature fibrils.  The Serpell lab have extensively experience of working with tau peptides and other amyloidogenic fragments and investigating the structural organisation of fibrils using X-ray fibre diffraction. Negative stain transmission electron microscopy will be performed at Sussex to verify the morphology of filaments.

This project will link experimental and simulation structural ensembles, allowing the mechanism of oligomer formation to be followed with molecular detail, giving vital insights into potential therapeutic interventions.