Structural Plasticity in Antigen Selection

Our bodies have evolved an intricate and powerful system to distinguish "self" from "non-self" called the immune system. This formidable task force allows us fight off foreign invaders such as viruses and bacterial pathogens. Since it can cause devastation and disease when it is going wrong, e.g. by attacking the self, such as in auto immune diseases, it needs to be highly regulated and finely tuned.
The proposed research investigates a key process to regulate to power of the immune system. Almost every cell in an individual constantly presents samples of short protein fragments from the inside of the cell to the immune system. If these samples are recognised as foreign, the cell will be destroyed. Hence, the control over which peptide samples are shown to the immune system constitutes a key control mechanism to direct the immune response. We are investigating the molecular mechanism of how these representative samples are selected at the cellular level and at the molecular level. We propose that the ability of the protein, called MHC, that recognises the peptides to be malleable and change shape is essential to perform the selection task. We hope that by understanding the molecular nature of this recognition process and its relationship to directing the immune response we will in the future develop new ways of fighting diseases such as cancer and auto-immune diseases by directing an individual's capacity to eradicate what it perceives as non-self.

Antigen processing describes the cellular mechanisms that lead to the selection of antigens inside a cell for the presentation to the immune system. This process forms a critical component in eliciting and directing an immune response. Hence, understanding the control of the process at the molecular level potentially offers new avenues of controlling infections, cancer and auto-immune diseases.
We are integrating cellular biochemistry and systems modelling with structural biology - NMR, molecular dynamics simulation and biophysical measurements - to determine the molecular mechanism of antigen processing.
Two key players, MHC class I and tapasin, have been identified as shaping the antigen repertoire. Furthermore, by analysing cellular experiments that monitor the time dependency of the shaping of the peptide repertoire by these players using systems modelling we could identify specific molecular reaction rates and protein states that control the biological outcome. The analysis implies that peptide selection by MHC class I depends critically on the presence of an intermediate conformational state of MHC and that tapasin enhances the rate of exchange between the intermediate and the fully formed MHC:peptide complex.
We are proposing a set of experiments to study the nature of the MHC intermediate and its interaction with tapasin using NMR in conjunction with molecular dynamics simulations and to use kinetic analysis to establish the reaction scheme and associated rates for the MHC peptide binding as well as the role of tapasin in this. We choose mouse derived MHC alleles for technical reasons and because the feasibility of follow-up studies on whole animal physiology using established mouse models for cancer and infection that would not be possible in humans.

We think that being able to link a significant biological function to a transient protein state has wider implications for our understanding of how proteins may govern biological processes.

Academic impact: The academic impact of the current project will be in a number of areas as the project combines cellular biochemistry, systems modelling with NMR, molecular dynamics simulations and biophysical measurements in addition to the broader scientific community whose research focuses on immunology and structural biology. In particular our proposed project will benefit the following academic communities:
1. Molecular Immunologists who will benefit from the results and the methodology of the proposed study.
2. Structural biologists with interests in protein structure and function relationships in particular in protein dynamics.
3. Biophysicists interested in the protein ligand binding and kinetics
4. The systems biologist community will benefit from the models we develop as they can be adapted to other pathways such as MHC class II. In addition systems biologists interested in understanding the molecular events associated with the trafficking of proteins between different intracellular compartments, will also benefit.
5. NMR community will benefit from the development and application of techniques for the analysis of protein dynamics as well as protein/protein interactions.
6. Molecular simulation and modelling community who will benefit from the applications and data generated in this project.
7. Academic researchers working on the molecular basis of viral infections, cancer or auto-immune diseases as novel mechanism in the control of these diseases are discovered.
8. Our association with two doctoral training centres (Complex Systems Simulations and Biology) will of course provide training of researchers in both fields.

Public engagement: Aspects of the current project will be used for outreach activities to local schools. The very visual element of molecular structures and simulations for the generation of 'movies' from simulation trajectories render them ideal for this purpose. In addition, to schools-based outreach, JW and TE will contribute to the award-winning science and engineering day hosted by the University of Southampton and is open to the general public.
We disseminate the aims, and results of our work in terms of biological complexity to the lay audience at various events including the science week the LifeLab project and arts exhibitions in collaboration with Tessa Coe. Lastly, we will create a page on the project website that is targeted towards the general public.

Commercial: We do not anticipate any immediate commercial impact to arise directly from our project. However, the systems and computational as well as biophysical techniques do have the potential for becoming a tool for rational drug-design. The methods developed here inform researchers at Microsoft in formulating languages and tools aimed at the general life science market.