PhD Studentships in “Computer simulation of peptides and peptide permeation through biological membranes”

Location:  Highfield Campus
Reference:  229613EB

Start Date: TBC

Project description: Applications are invited for two PhD students to work with Professor Jonathan Essex to use classical computer simulations and free energy calculations to model peptide conformations in water and other environments, and to simulate how peptides permeate through biological membranes. Peptides are not only widely used by biological systems as signalling molecules, but there is also increasing interest in using peptides as new drugs to disrupt protein-protein interactions. To understand how peptides bind to proteins and hence to rationally modify them to achieve improved potency, the ability to accurately model their conformations is crucial. In addition, a major limiting factor to the exploitation of peptides as drugs is the extent to which they are able to permeate through cell membranes and hence reach their sites of action. Understanding peptide permeation through computer simulation is therefore essential if peptides are to be rationally modified to improve their bioavailability.

In the first studentship, supported by AstraZeneca, advanced classical computer simulation methodology will be implemented and tested to explore the solution-phase conformations of peptides predicted to disrupt important protein-protein interactions. The simulation predictions will be tested and validated through comparison with the latest experimental data. In addition, dual resolution molecular dynamics simulations will be used to model peptide permeation through biological membranes, as a route to the rational modification of the peptides to improve bioavailability. This work will build on methodology developed in the Essex group which has previously been used to model drug permeation.

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The second studentship, supported by the PeReNe EU Interreg collaboration, involves the simulation of two important cyclic-peptide signalling molecules – Urotensin II (UII) and Urotensin II Related Peptide (URP). These peptides have been implicated in a wide range of cellular processes, and are presumed to act through interactions with G-protein coupled receptors. In this project, the conformations of these peptides in a range of different environments (including the aqueous phase and in micelles) will be simulated, and direct comparison made with experiment. Membrane permeability will also be studied using dual-resolution molecular dynamics computer simulations. This project involves close collaboration with experimental and theoretical partners in the UK and northern France.

Due to funding restrictions, these studentships are only available to EU/UK students

The studentships will be supervised by Prof Jonathan Essex ( at the University of Southampton.

Entry requirements: Applicants should have, or expect to receive shortly, a good degree in Chemistry, Physics, Biochemistry, or a relevant discipline, and a keen interest in molecular modelling. Please contact Prof Jonathan Essex (, 023 8059 2794) for informal enquiries related to this project.

Administrative contact and how to apply:

Please complete the University’s online application form, which you can find at:

You should enter Dr John Essex as your proposed supervisor. Queries on the application procedure should be addressed to

Closing Date:   Saturday 31 August 2013

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