Our research. Research in the Yaliraki group is concerned with developing theory to study the structure and dynamics of mesoscopic systems in complex environments. Of particular interest is understanding the properties of biomolecules and molecular-based materials when in strong interaction with their environment - such as when assembled in nanostructures. The motivation is to elucidate the microscopic driving interactions for assembly, to follow the evolution of the ensuing properties from single species to the mesoscale and to unravel the dependence of quantum properties on topology and geometry of the components of the composite system.

Our approach. While accurate methods exist both for isolated small molecules and bulk materials, new theoretical methods are needed to choose the relevant variables (rather than to completely enumerate them) that span time and length scales so that mesoscopic systems at the interface of modern chemistry, materials science and chemical biology can be addressed. Our approach relies on a combination of analytical and computational tools from quantum and statistical mechanics as well as applied mathematics. We collaborate with several experimental groups in the United States, Israel and Europe.

Our work. We have recently shown that we can represent biomolecular structures through energy-weighted, atomistic graphs [04,05] and have developed a series of methods that by exploring stochastic processes on these graphs can very efficiently reveal functional properties of interest across different scales.

Our methods. Two of these methods, Markov transients and Bond-to-bond propensity, have been shown to accurately identify hotspots on a protein surface [01,02]. These hotspots have been correlated with sites of interaction with another ligand, or with another protein. We present here an interactive interface for curious scientists to upload their own protein structure, in the hope of yielding novel biological insights.

The ProteinLens team


Funding bodies. We thank Imperial College London, EPSRC, the Institute of Chemical Biology, the Wellcome Trust and the Grantham Institute for funding. Specifically, Florian and Francesca are funded by EPSRC grant number EP/L015498/1. Léonie is funded by a Wellcome Trust PhD grant number 215360/Z/19/Z. Sophia M, Sophia Y and Mauricio acknowledge funding from the EPSRC award EP/N014529/1 supporting the EPSRC Centre for Mathematics of Precision Healthcare.

Personal Acknowledgments. We thank Benjamin Amor and Antoine Delmotte for the invaluable theoretical work which underpins this web based application.

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Contact information

For any ProteinLens query, or just to say hello, please do contact us at proteinlens@imperial.ac.uk.

The Yaliraki group is located in the Department of Chemistry at Imperial College London:
Lab 109, Molecular Science Research Hub, Wood Lane Campus, W12 0BZ, London UK

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Amor, B. R. C., Yaliraki, S. N., Woscholski, R., & Barahona, M. (2014). Uncovering allosteric pathways in caspase-1 with Markov transient analysis and multiscale community detection. Molecular BioSystems, 10, 2247-2258. https://doi.org/10.1039/C4MB00088A
Amor, B. R. C., Schaub, M. T., Yaliraki, S. N., & Barahona, M. (2016). Prediction of allosteric sites and mediating interactions through bond-to-bond propensities. Nature Communications, 7, 1-30. https://doi.org/10.1038/ncomms12477
Meliga, S. (2009). Graph Clustering of Atomic Networks for Protein Dynamics. Imperial College London.
Delmotte, A., Tate, E. W., Yaliraki, S. N., & Barahona, M. (2011). Protein Multi-Scale Organization through Graph Partitioning and Robustness Analysis: Application to the Myosin-Myosin Light Chain Interaction. Physical Biology, 8, 55010-55022. https://doi.org/10.1088/1478-3975/8/5/055010