Antreas Kalli

University of Leeds

Antreas is an Associate Professor at the University of Leeds. Before this, he was a post-doctoral researcher in the Sansom group at the University of Oxford. While there, he used computational methodologies to study how membrane proteins function at the molecular level. He holds a DPhil in Structural Biology from the University of Oxford and a BSc in Physics from the University of Cyprus. His research group uses multi-scale molecular dynamics simulations (i.e. coarse-grained and all-atom) and molecular modelling to simulate how proteins in cell membranes work and interact with their environment.

Investigating protein-lipid interactions with molecular simulations and machine learning

Interactions of membrane proteins with lipids in the cell membrane play a key role in regulating their activity. For example, membrane proteins will recognise specific anionic lipids in the membrane, and this interaction is critical for e.g. regulation of signalling pathways in cells. However, the specific interactions between proteins and lipid molecules remain challenging to characterize in molecular detail, especially at a large scale. Our study used Bebe supercomputer to run high throughput coarse-grained molecular dynamics simulations of membrane proteins and study their interactions with lipids. This will create novel information about such interactions, allowing us to develop machine learning models for such interactions.

How has your research benefitted from using Bede?

Bede allowed access to large computational power and GPU acceleration of our calculations, which were very beneficial for our project. We are using the outcomes of this research to apply for further funding.